JSON output schemas

How to read this page

With --json, every command prints one envelope: ok, schema_version and either data or error (envelope). The sections below describe data for each command and view. They are generated from the JSON Schemas in docs/schema/, which cargo xtask schema gen writes from the Rust types, so they cannot drift from the program. Keys are stable: fields are added freely, and renaming or removing one needs a schema_version bump. Reading the JSON output explains provenance, units and how to decide how far to trust a value.

envelope info info-format info-full info-explain info-structure check check-planes check-against check-report export export-attachment preview stats stats-wells trace table spectra spectrum chromatogram peaks assay qpcr nmr-peaks ephys-features spikes gate batch-table batch-summary link sidecar sidecar file index search search-health search-export watch formats doctor

envelope

Success or failure wrapper.

Field	Type	Meaning
`ok`	boolean	True on success (`data` present), false on failure (`error` present).
`schema_version`	string	[`SCHEMA_VERSION`] at the time of writing.
`tool`	ToolId	The producing tool.
`path` optional	string \| null	The input this envelope answers for, in batch mode (`--jsonl`, JSON arrays, MCP `openreadout_batch`); absent for single-file commands.
`data` optional	any	The command's output, on success.
`error` optional	ErrorBody \| null	What went wrong, on failure.

Types used (2)

ErrorBody Structured error body. hint is meant to be actionable by an agent.

Field	Type	Meaning
`code`	string	Stable code: `unknown_format`, `unsupported_feature`, `corrupt_file`, `usage`, `io`, `error`, `internal_panic` (a bug: the tool panicked; please report it).
`message`	string	Human-readable description of the failure.
`hint` optional	string \| null	What to try next, when the tool knows.
`exit_code`	integer (int32)	The process exit code for this error (see the crate docs).

ToolId Identifies the producing tool so consumers can reason about compatibility.

Field	Type	Meaning
`name`	string	Always `openreadout`.
`version`	string	The tool's version (`CARGO_PKG_VERSION`).

envelope.schema.json · Envelope

info

What info prints: the normalized [FileInfo] plus the derived [Experiment] under the additive experiment key. Dereferences to the FileInfo.

Field	Type	Meaning
`path`	string	The path as given by the caller.
`size_bytes`	integer (uint64)	Size in bytes (for directory formats such as Bruker `.d`, the files that were read).
`format`	FormatDescriptor	The format that read the file.
`format_version` optional	string \| null	Version of the container format as written in the file, if any.
`images`	array of ImageInfo	Images in the file (empty for tables, spectra and traces).
`tables` optional	array of TableInfo	Tabular datasets (flow cytometry events, ...). Empty for image formats.
`spectra` optional	array of SpectraInfo	Mass-spectrometry runs. Empty for other formats.
`traces` optional	array of TraceInfo	Sampled-signal blocks (electrophysiology, chromatography, NMR). Empty for other formats.
`plane_count`	integer (uint64)	Total planes across all images.
`notes` optional	array of string	Notes the reader wants the caller to see (e.g. "pyramid levels skipped").
`experiment` optional	Experiment \| null	Sample, instrument, method, acquisition and measurements, each value with its origin (`book/src/guides/metadata.md`). Absent when nothing is known.
`acquisition` optional	Acquisition2 \| null	Present when the file is not finished: still being written (`in_progress`, with the number of complete planes) or stopped before the end (`interrupted`). See `book/src/guides/lab-shares.md`.
`plate` optional	PlateSummary \| null	Multi-well plates (high-content screening): the plate id and type, rows and columns, the imaged wells with the images (fields) of each, and how many planes the copy on disk is missing (`docs/formats/hcs.md`). Absent for other files.
`images_total` optional	integer (uint64) \| null	Set when `images` lists only the first few images ([`InfoOutput::cap_images`]: screening plates by default, whose field images are all alike, or `--max-images N`): how many images the file holds. `plate.wells[].images` still indexes every field, the image commands take any index, and `--max-images 0` (MCP `max_images: 0`) lists them all.
`assurance` optional	Assurance \| null	Whether this file lies inside what its reader has been validated on: the variant fingerprint with the corpus evidence for each feature, structures not decoded, values assumed, vendor calibrations, and the outputs `--strict` refuses (`docs/assurance.md`).

Types used (43)

Acquisition When and by whom.

Field	Type	Meaning
`started_at` optional	string \| null	ISO-8601 start (same zone rules as the rest of the model).
`ended_at` optional	string \| null	ISO-8601 end, when recorded.
`operator` optional	string \| null	Operator or user name as recorded.
`duration_s` optional	number (double) \| null	Length of the acquisition (run length, recording length, time-lapse span) in seconds.
`comment` optional	string \| null	Free-text comment saved with the acquisition (ABF file comment, FCS `$COM`, Thermo sequence comment, ANDI sample comments), as recorded.
`saved_at` optional	string \| null	ISO-8601 time the file was last saved or exported, when that is the only time it records (a SoftMax Pro text export's `Date Last Saved`). It follows the measurement and is not its start: `started_at` stays empty.

Acquisition2 acquisition in info, info --view structure, check and check --planes: present only for

acquisition in info, info --view structure, check and check --planes: present only for files that are not finished. See book/src/guides/lab-shares.md.

Field	Type	Meaning
`state`	AcquisitionState	`in_progress` or `interrupted`.
`complete_planes`	integer (uint64)	Planes whose data is entirely on disk.
`expected_planes` optional	integer (uint64) \| null	Planes the finished file will hold, when the metadata written so far says so.
`modified_ago_s`	number (double)	Seconds since the file (or the newest member of a directory store) was modified.
`window_s`	number (double)	The live window used for the decision, in seconds.
`missing`	array of string	Structures written at the end of an acquisition that are absent.
`tail_bytes`	integer (uint64)	Bytes after the last complete unit (a unit still being written).
`evidence`	array of string	The observations behind the decision.

AcquisitionState Whether an incomplete file is still being written.

One of: "in_progress" | "interrupted"

Assumed A value the reader assumed (a default, a guess from context) instead of reading it.

Field	Type	Meaning
`field`	string	JSON path of the value in `info` (e.g. `traces[0].channels[1].unit`).
`detail`	string	Why it was assumed and from what.

Assurance The per-file assurance block of info (every view) and check.

Field	Type	Meaning
`level`	AssuranceLevel	`validated`, `partially_validated` or `unvalidated`.
`summary`	string	One line for people and agents.
`fingerprint`	string	The variant fingerprint: `format_id` then `kind=value` for each feature, sorted.
`variant`	array of VariantFeature	Each feature with its corpus evidence.
`reasons` optional	array of string	Why the level is not `validated`, one reason per line.
`undecoded` optional	array of Undecoded	Structures met but not decoded.
`assumed` optional	array of Assumed	Values assumed instead of read.
`calibrations` optional	array of Calibration	Vendor calibrations and corrections the file carries, and whether they were applied.
`inferred_fields` optional	InferredFields	Normalized fields whose meaning is inferred rather than specified.
`inferred` optional	array of InferredValue	Values derived by a rule instead of read, with the evidence for each rule.
`strict_refuses` optional	array of Scope	Outputs `--strict` (MCP `strict: true`) refuses to return for this file.
`strict_withholds` optional	array of Withheld	Fields `--strict` withholds (returned as null; asking for one with `--only` exits 6) while the rest of the output is returned.
`reader_confidence`	Confidence	The reader's overall confidence (evidence rubric), for context.

AssuranceLevel How far a file lies inside what its reader has been validated on.

One of: "validated" | "partially_validated" | "unvalidated"

Calibration A vendor calibration or correction the file carries.

Field	Type	Meaning
`name`	string	What it calibrates (`m/z (MzCalibration)`, `ADC to µV`, `spillover compensation`).
`status`	CalibrationStatus	Applied, not applied, or available on request.
`scope` optional	array of Scope	Outputs it applies to.
`detail`	string	How it is (or is not) applied and how to get calibrated values.

CalibrationStatus Whether a vendor calibration or correction stored in the file was applied.

One of: "applied" | "not_applied" | "available"

ChannelInfo One acquisition channel.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based channel index (the `c` of a plane).
`name` optional	string \| null	Channel name as the acquisition software shows it.
`fluorophore` optional	string \| null	Fluorescent dye or protein imaged in this channel (e.g. `DAPI`, `GFP`), if recorded.
`excitation_nm` optional	number (double) \| null	Excitation wavelength in nanometres: the light used to make the sample fluoresce.
`emission_nm` optional	number (double) \| null	Emission wavelength in nanometres: the light collected from the sample. What the file records varies by format (a dye's emission peak, a filter's centre, the start of a spectral detection window for Leica λ scans); `docs/formats/<fmt>.md` says which. When a detection band is known, `emission_band_*_nm` give it explicitly.
`emission_range_nm` optional	array of number (double) \| null	Detection band `[start_nm, end_nm]` when the instrument records a range instead of a single emission wavelength.
`emission_band_start_nm` optional	number (double) \| null	Short-wavelength edge of the detection band in nanometres (spectral detector window or emission filter), when the file records the band.
`emission_band_end_nm` optional	number (double) \| null	Long-wavelength edge of the detection band in nanometres.
`emission_band_center_nm` optional	number (double) \| null	Centre of the detection band in nanometres: (start + end) / 2.
`color` optional	string \| null	Display colour as `#RRGGBB` if the file records one.
`acquisition_mode` optional	string \| null	Acquisition mode as a readable label, `<technique>[ <contrast>]` (e.g. `Laser Scanning Confocal`, `Widefield Fluorescence`, `Brightfield`, `Phase Contrast`); OME enumeration tokens (`WideField`) are turned into these labels, other vendor wording is kept.
`exposure_ms` optional	number (double) \| null	Exposure (integration) time of the detector in milliseconds.

ColumnInfo A column of a tabular dataset (e.g. an FCS parameter).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based column index.
`name`	string	Short name (FCS `$PnN`).
`label` optional	string \| null	Descriptive label (FCS `$PnS`), if any.
`dtype`	string	NumPy-style dtype of the values as returned by `read_table` (`float32`, `float64`, `uint32`, ...).
`unit` optional	string \| null	Physical unit of the values, if the format records one.
`range` optional	array of number (double) \| null	Nominal `[min, max]` range when the format declares one.
`extra` optional	object	Format-specific column metadata in the reader's documented vocabulary.

Confidence Per-format confidence summary shown by info and self formats.

One of: "high" | "medium" | "low"

Experiment The experiment a file records: sample, instrument, method, acquisition and measurements.

Field	Type	Meaning
`sample` optional	Sample \| null	What was measured on.
`instrument` optional	ExperimentInstrument \| null	What it was measured with.
`method` optional	Method \| null	How.
`acquisition` optional	Acquisition \| null	When and by whom.
`measurements` optional	array of Measurement	What was measured, one entry per kind of data block.
`notes` optional	array of string	Things to know when reading the fields above (several samples in one file, ...).
`provenance` optional	map of Origin	Origin of every value, keyed by its path in this object (`sample.id`, `method.parameters.nucleus`, `measurements[0]`).

ExperimentInstrument The instrument that made the measurement.

Field	Type	Meaning
`vendor` optional	string \| null	Manufacturer.
`model` optional	string \| null	Model (microscope stand, mass spectrometer, cytometer, plate reader, detector module).
`serial` optional	string \| null	Serial number.
`software` optional	string \| null	Acquisition software.
`software_version` optional	string \| null	Version of the acquisition software.
`kind` optional	Term \| null	Kind of instrument (OBI term: `microscope`, `mass spectrometer`, `flow cytometer`, ...).

FeatureKind What a variant feature describes.

FeatureStatus How the corpus covers one feature value.

One of: "validated" | "seen" | "unseen"

FormatDescriptor Static description of a format as the tool understands it.

Field	Type	Meaning
`id`	string	Short id used on the command line, e.g. `czi`.
`name`	string	Human name, e.g. `Zeiss CZI`.
`vendor`	string	Vendor (nominative use only).
`extensions`	array of string	File extensions, lowercase, without the dot.
`family`	string	Family: `microscopy`, `mass-spectrometry`, `flow-cytometry`, ...
`can_read`	boolean	True when the tool can read this format.
`can_write`	boolean	True when `export` can also write this format (e.g. mzML, OME-Zarr).
`confidence`	Confidence	Overall confidence in this reader.
`known_gaps`	array of string	Things this reader knowingly does not handle yet.

ImageInfo One image (a scene, series, or position) inside the file.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based index used by `--image`.
`name` optional	string \| null	Image (scene, series or position) name, if recorded.
`size_x`	integer (uint32)	Width in pixels.
`size_y`	integer (uint32)	Height in pixels.
`size_z`	integer (uint32)	Number of Z planes (focal slices).
`size_c`	integer (uint32)	Number of channels.
`size_t`	integer (uint32)	Number of time points.
`dimension_order`	string	Storage order of planes, e.g. `XYCZT` (X and Y always first).
`pixel_type`	PixelType	Sample type of every plane.
`samples_per_pixel`	integer (uint32)	1 for grayscale channels, 3 for interleaved RGB.
`physical_size`	PhysicalSize	Physical size of one pixel (and the Z step).
`time_increment_s` optional	number (double) \| null	Interval between time points in seconds.
`channels`	array of ChannelInfo	One entry per channel, in channel order.
`objective` optional	ObjectiveInfo \| null	The objective lens, if recorded.
`instrument` optional	InstrumentInfo \| null	Instrument and software, if recorded.
`acquired_at` optional	string \| null	ISO-8601 acquisition start, if recorded.
`mosaic` optional	MosaicInfo \| null	Tile layout when the image was acquired as a mosaic.
`pyramid_levels`	integer (uint32)	Number of resolution levels stored (1 = no pyramid).
`resolution_levels` optional	array of ResolutionLevel	Size, downsampling and stored tile size of every resolution level, level 0 first. Filled by readers of pyramidal or tiled images (read a level with `--level N`, a rectangle with `--region X,Y,W,H`); empty otherwise.
`plane_count`	integer (uint64)	`size_z * size_c * size_t`.
`extra` optional	object	Format-specific extras that have no OME equivalent, in our own vocabulary.

InferredFields Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a

Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a specification: the inferred entries of the reader's provenance map.

Field	Type	Meaning
`count`	integer (uint32)	How many normalized fields have inferred meaning.
`of`	integer (uint32)	How many normalized fields carry provenance at all.
`examples` optional	array of string	Up to 12 of their JSON paths (`info --view full` → `provenance` has all).

InferredValue A value derived by a rule, with the corpus evidence for the rule.

Field	Type	Meaning
`field`	string	JSON path of the value in `info`.
`rule`	string	The rule that derived it.
`status`	FeatureStatus	`validated` when development files' oracles confirmed values derived by this rule.
`detail`	string	What was derived from what.

InstrumentInfo The instrument and software that produced the file.

Field	Type	Meaning
`manufacturer` optional	string \| null	Instrument manufacturer.
`model` optional	string \| null	Instrument model (e.g. microscope stand or mass spectrometer).
`software` optional	string \| null	Acquisition software.
`software_version` optional	string \| null	Version of the acquisition software.
`detector` optional	string \| null	Detector (camera or photomultiplier) name.

Measurement One thing that was measured, in scientific words.

Field	Type	Meaning
`kind`	MeasurementKind	Which array of the file it describes.
`indices`	array of integer (uint32)	Indices into that array (images, tables, traces or runs) this entry covers.
`what`	string	What was measured, e.g. `fluorescence, 3 channels (DAPI, GFP, mCherry), 21 z-slices` or `LC-MS, negative mode, 2,031 scans, MS1`.
`technique` optional	Term \| null	The technique (CHMO, FBbi, OBI or PSI-MS term).
`terms` optional	array of Term	Further terms: polarity, spectrum types, detectors, acquisition modes.
`parameters` optional	map of Quantity	Counts and settings with units (`scans`, `wells`, `wavelength`, `z_slices`).

MeasurementKind Which part of the file a measurement describes.

One of: "image" | "table" | "trace" | "spectra"

Method How the measurement was made.

Field	Type	Meaning
`name` optional	string \| null	Name of the acquisition method, protocol or experiment as the software saved it.
`technique` optional	Term \| null	The technique (CHMO, FBbi or OBI term: `liquid chromatography-mass spectrometry`, ...).
`assay` optional	Term \| null	The kind of assay (OBI term).
`parameters` optional	map of Quantity	Method settings, keyed by our own snake_case names (`nucleus`, `polarity`, `z_step`).

MosaicInfo Mosaic (tiled/stitched) acquisition summary.

Field	Type	Meaning
`tile_count`	integer (uint32)	Number of tiles (fields of view) in the mosaic.
`tile_width` optional	integer (uint32) \| null	Width of one tile in pixels, when all tiles share it.
`tile_height` optional	integer (uint32) \| null	Height of one tile in pixels, when all tiles share it.
`stitched_on_read`	boolean	Whether the reader stitches tiles into a single plane on read.

ObjectiveInfo The objective lens.

Field	Type	Meaning
`model` optional	string \| null	Objective model name as the vendor records it.
`nominal_magnification` optional	number (double) \| null	Nominal magnification (e.g. `63` for a 63× lens).
`lens_na` optional	number (double) \| null	Numerical aperture.
`immersion` optional	string \| null	Immersion medium between lens and sample (`Oil`, `Water`, `Air`, ...).

Origin Where one experiment value came from.

Field	Type	Meaning
`source`	Source	How the meaning of the source field is known (the reader's provenance for that field; `inferred` for our own mapping and derived text).
`from`	string	The field it was taken from: a path into the `info` JSON (`spectra[0].extra.vial`), or a vendor file inside the dataset (`pdata/1/title`).

PhysicalSize Physical pixel size in micrometres (the OME default unit). Every present value is > 0.

Field	Type	Meaning
`x` optional	number (double) \| null	Pixel width in µm (the distance between neighbouring columns).
`y` optional	number (double) \| null	Pixel height in µm (the distance between neighbouring rows).
`z` optional	number (double) \| null	Spacing between Z planes (focal slices) in µm.
`unit`	string	Always `µm` in this schema version.

PixelType Sample type of one channel value. Names follow OME-XML PixelType values.

PlateSummary Layout of a multi-well plate (high-content screening): info → plate.

Field	Type	Meaning
`id` optional	string \| null	Plate identifier or barcode as the acquisition software recorded it.
`name` optional	string \| null	Plate name, when recorded besides the id.
`plate_type` optional	string \| null	Plate type (product) as recorded, e.g. `384 PerkinElmer CellCarrier Ultra`.
`rows`	integer (uint32)	Number of rows of the plate (8 for a 96-well plate).
`columns`	integer (uint32)	Number of columns of the plate (12 for a 96-well plate).
`wells`	array of PlateWell	The imaged wells, row by row.
`field_count`	integer (uint32)	Most fields of view in one well.
`planes_expected`	integer (uint64)	Planes the plate's index lists (every image's `plane_count`).
`planes_absent` optional	integer (uint64)	Planes the instrument never acquired or recorded (they read as blank and are left out of statistics; `images[].extra.absent_planes`).
`planes_missing` optional	integer (uint64)	Planes whose files the index names but that are not on disk (`check` lists them).
`complete`	boolean	True when every plane the index names is on disk.
`extra` optional	object	Format-specific plate facts in the reader's documented vocabulary.

PlateWell One imaged well of a plate.

Field	Type	Meaning
`well`	string	Well name, e.g. `C05` (row letters, column zero-padded to two digits).
`row`	string	Row letters (`C`).
`column`	integer (uint32)	Column number, 1-based (`5`).
`row_index`	integer (uint32)	Zero-based row index (`C` = 2).
`column_index`	integer (uint32)	Zero-based column index.
`images`	array of integer (uint32)	Indices of the images (fields of view) of this well, in field order.
`planes_missing` optional	integer (uint64)	Planes of this well whose files are not on disk (0 when the well is complete).

Quantity A value with an optional unit: {"value": 19, "unit": "min", "ucum": "min"}.

Field	Type	Meaning
`value`	any	A number, a string, or a list of them.
`unit` optional	string \| null	Unit as written for people (`µm`, `°C`), when the value has one.
`ucum` optional	string \| null	UCUM code of `unit` (`um`, `Cel`).

ResolutionLevel Geometry of one resolution level of an image.

Field	Type	Meaning
`level`	integer (uint32)	Level index: 0 is full resolution, larger is more downsampled (`--level`).
`size_x`	integer (uint32)	Width in pixels.
`size_y`	integer (uint32)	Height in pixels.
`downsample_x`	number (double)	Level-0 width over this level's width (1 for level 0; 2, 4, ... for a halving pyramid).
`downsample_y`	number (double)	Level-0 height over this level's height.
`tile_width` optional	integer (uint32) \| null	Width of the tiles (subblocks, chunks) the level is stored in, when it is tiled: region reads aligned to this grid decode each tile once.
`tile_height` optional	integer (uint32) \| null	Height of the stored tiles.
`size_z` optional	integer (uint32) \| null	Number of z planes at this level, when it differs from the image's `size_z` (Imaris downsamples z as well).

Sample What was measured: the sample's identity as the file records it.

Field	Type	Meaning
`id` optional	string \| null	The sample's identifier, from the field named in `source_field`.
`name` optional	string \| null	A descriptive sample name when the file records one besides the id.
`well` optional	string \| null	Plate well (`B2`, `A01`).
`barcode` optional	string \| null	Plate or tube barcode.
`sequence_position` optional	string \| null	Position in the autosampler sequence or tray (vial `D:35`, `2:A,8`).
`source_field` optional	string \| null	Path of the field `id` came from (`spectra[0].extra.sample_name`, `tables[0].extra.specimen`, `pdata/1/title`).

Scope Which outputs of a file a feature, a structure or a calibration affects.

One of: "metadata" | "pixels" | "spectra" | "traces" | "tables"

SignalChannelInfo One channel of a sampled-signal dataset.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based channel index.
`name`	string	Channel name as recorded.
`unit` optional	string \| null	Physical unit of the scaled values (`pA`, `mV`, `AU`, ...).
`dtype`	string	NumPy-style dtype of the raw stored samples.
`scale`	number (double)	`value = raw * scale + offset` when the file stores integers.
`offset`	number (double)	Added after scaling; see `scale`.
`extra` optional	object	Format-specific channel metadata in the reader's documented vocabulary.

Source How we learned what a field means. Ordered from most to least authoritative.

One of: "spec" | "vendor-impl" | "prior-art" | "inferred"

SpectraInfo A collection of mass spectra (one acquisition run).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based run index.
`name` optional	string \| null	Run name, if the file records one.
`scan_count`	integer (uint64)	Number of spectra (scans) in the run.
`ms_levels`	array of integer (uint32)	MS levels present (1 = full scans, 2 = MS/MS, ...).
`rt_range_s` optional	array of number (double) \| null	Retention-time range in seconds.
`instrument` optional	InstrumentInfo \| null	Instrument and software, if recorded.
`extra` optional	object	Format-specific run metadata in the reader's documented vocabulary.

TableInfo A tabular dataset inside the file (rows × columns), e.g. FCS events.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based table index.
`name` optional	string \| null	Table name, if the format has one.
`row_count`	integer (uint64)	Number of rows (e.g. recorded events).
`columns`	array of ColumnInfo	One entry per column.
`extra` optional	object	Format-specific table metadata in the reader's documented vocabulary.

Term An ontology term: its id (CURIE, e.g. CHMO:0000524) and label.

Field	Type	Meaning
`id`	string	Compact id, `PREFIX:local` (`MS:1000130`, `CHMO:0000591`, `FBbi:00000246`, `OBI:0000916`).
`label`	string	The term's label in its ontology (`positive scan`).

TraceInfo A block of uniformly sampled signals (a sweep, a chromatogram run, an FID).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based trace index.
`name` optional	string \| null	Trace name, if the format has one.
`sample_rate_hz`	number (double)	Samples per second.
`sample_count`	integer (uint64)	Samples per sweep (the longest sweep when sweeps differ; see `extra.sweep_sample_counts`).
`sweep_count`	integer (uint32)	Number of sweeps/episodes stored back to back (1 for continuous recordings).
`channels`	array of SignalChannelInfo	One entry per channel.
`start_s` optional	number (double) \| null	Time of the first sample relative to the recording start, seconds.
`extra` optional	object	Format-specific trace metadata in the reader's documented vocabulary.

Undecoded A structure the reader met in the file but did not decode.

Field	Type	Meaning
`structure`	string	What the structure is, in the format notes' vocabulary.
`scope` optional	array of Scope	Outputs that may be incomplete or wrong because of it. Empty: it is left out and the values returned do not depend on it.
`detail`	string	What is known about it and what the reader does instead.

VariantFeature One feature of the file's fingerprint, with the corpus evidence for it.

Field	Type	Meaning
`kind`	FeatureKind	What the feature describes.
`value`	string	Its value.
`scope` optional	array of Scope	Outputs whose decoding depends on it (empty: descriptive only).
`status`	FeatureStatus	`validated`, `seen` or `unseen`.
`corpus_files`	integer (uint32)	Development-corpus files with this value confirmed by an independent reader.
`sources`	integer (uint32)	Distinct depositors among them.

Withheld A field --strict withholds: it is present, but its value was assumed, derived by a rule no

A field --strict withholds: it is present, but its value was assumed, derived by a rule no independent reader confirmed, or never compared with an independent reader.

Field	Type	Meaning
`field`	string	JSON path pattern in `info` (`[]` matches any index).
`reason`	string	Why it is not validated.

info.schema.json · InfoOutput

info-format

Output of info --view format.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id, e.g. `czi`.
`name`	string	Human name of the format, e.g. `Zeiss CZI`.
`confidence`	DetectConfidence	How the format was recognised.
`note` optional	string \| null	Why detection is less than definite, if it is.

Types used (1)

DetectConfidence How sure detection is.

One of: "definite" | "likely" | "extension-only"

info-format.schema.json · DetectOutput

info-full

Output of info --view full.

Field	Type	Meaning
`file`	InfoOutput	What `info` reports, including the derived `experiment`.
`vendor` optional	any	The vendor's own metadata tree, converted to JSON without renaming anything.
`provenance`	map of Source	Where each normalized field came from. Keys are JSON paths into `file`.

Types used (44)

Acquisition When and by whom.

Field	Type	Meaning
`started_at` optional	string \| null	ISO-8601 start (same zone rules as the rest of the model).
`ended_at` optional	string \| null	ISO-8601 end, when recorded.
`operator` optional	string \| null	Operator or user name as recorded.
`duration_s` optional	number (double) \| null	Length of the acquisition (run length, recording length, time-lapse span) in seconds.
`comment` optional	string \| null	Free-text comment saved with the acquisition (ABF file comment, FCS `$COM`, Thermo sequence comment, ANDI sample comments), as recorded.
`saved_at` optional	string \| null	ISO-8601 time the file was last saved or exported, when that is the only time it records (a SoftMax Pro text export's `Date Last Saved`). It follows the measurement and is not its start: `started_at` stays empty.

Acquisition2 acquisition in info, info --view structure, check and check --planes: present only for

acquisition in info, info --view structure, check and check --planes: present only for files that are not finished. See book/src/guides/lab-shares.md.

Field	Type	Meaning
`state`	AcquisitionState	`in_progress` or `interrupted`.
`complete_planes`	integer (uint64)	Planes whose data is entirely on disk.
`expected_planes` optional	integer (uint64) \| null	Planes the finished file will hold, when the metadata written so far says so.
`modified_ago_s`	number (double)	Seconds since the file (or the newest member of a directory store) was modified.
`window_s`	number (double)	The live window used for the decision, in seconds.
`missing`	array of string	Structures written at the end of an acquisition that are absent.
`tail_bytes`	integer (uint64)	Bytes after the last complete unit (a unit still being written).
`evidence`	array of string	The observations behind the decision.

AcquisitionState Whether an incomplete file is still being written.

One of: "in_progress" | "interrupted"

Assumed A value the reader assumed (a default, a guess from context) instead of reading it.

Field	Type	Meaning
`field`	string	JSON path of the value in `info` (e.g. `traces[0].channels[1].unit`).
`detail`	string	Why it was assumed and from what.

Assurance The per-file assurance block of info (every view) and check.

Field	Type	Meaning
`level`	AssuranceLevel	`validated`, `partially_validated` or `unvalidated`.
`summary`	string	One line for people and agents.
`fingerprint`	string	The variant fingerprint: `format_id` then `kind=value` for each feature, sorted.
`variant`	array of VariantFeature	Each feature with its corpus evidence.
`reasons` optional	array of string	Why the level is not `validated`, one reason per line.
`undecoded` optional	array of Undecoded	Structures met but not decoded.
`assumed` optional	array of Assumed	Values assumed instead of read.
`calibrations` optional	array of Calibration	Vendor calibrations and corrections the file carries, and whether they were applied.
`inferred_fields` optional	InferredFields	Normalized fields whose meaning is inferred rather than specified.
`inferred` optional	array of InferredValue	Values derived by a rule instead of read, with the evidence for each rule.
`strict_refuses` optional	array of Scope	Outputs `--strict` (MCP `strict: true`) refuses to return for this file.
`strict_withholds` optional	array of Withheld	Fields `--strict` withholds (returned as null; asking for one with `--only` exits 6) while the rest of the output is returned.
`reader_confidence`	Confidence	The reader's overall confidence (evidence rubric), for context.

AssuranceLevel How far a file lies inside what its reader has been validated on.

One of: "validated" | "partially_validated" | "unvalidated"

Calibration A vendor calibration or correction the file carries.

Field	Type	Meaning
`name`	string	What it calibrates (`m/z (MzCalibration)`, `ADC to µV`, `spillover compensation`).
`status`	CalibrationStatus	Applied, not applied, or available on request.
`scope` optional	array of Scope	Outputs it applies to.
`detail`	string	How it is (or is not) applied and how to get calibrated values.

CalibrationStatus Whether a vendor calibration or correction stored in the file was applied.

One of: "applied" | "not_applied" | "available"

ChannelInfo One acquisition channel.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based channel index (the `c` of a plane).
`name` optional	string \| null	Channel name as the acquisition software shows it.
`fluorophore` optional	string \| null	Fluorescent dye or protein imaged in this channel (e.g. `DAPI`, `GFP`), if recorded.
`excitation_nm` optional	number (double) \| null	Excitation wavelength in nanometres: the light used to make the sample fluoresce.
`emission_nm` optional	number (double) \| null	Emission wavelength in nanometres: the light collected from the sample. What the file records varies by format (a dye's emission peak, a filter's centre, the start of a spectral detection window for Leica λ scans); `docs/formats/<fmt>.md` says which. When a detection band is known, `emission_band_*_nm` give it explicitly.
`emission_range_nm` optional	array of number (double) \| null	Detection band `[start_nm, end_nm]` when the instrument records a range instead of a single emission wavelength.
`emission_band_start_nm` optional	number (double) \| null	Short-wavelength edge of the detection band in nanometres (spectral detector window or emission filter), when the file records the band.
`emission_band_end_nm` optional	number (double) \| null	Long-wavelength edge of the detection band in nanometres.
`emission_band_center_nm` optional	number (double) \| null	Centre of the detection band in nanometres: (start + end) / 2.
`color` optional	string \| null	Display colour as `#RRGGBB` if the file records one.
`acquisition_mode` optional	string \| null	Acquisition mode as a readable label, `<technique>[ <contrast>]` (e.g. `Laser Scanning Confocal`, `Widefield Fluorescence`, `Brightfield`, `Phase Contrast`); OME enumeration tokens (`WideField`) are turned into these labels, other vendor wording is kept.
`exposure_ms` optional	number (double) \| null	Exposure (integration) time of the detector in milliseconds.

ColumnInfo A column of a tabular dataset (e.g. an FCS parameter).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based column index.
`name`	string	Short name (FCS `$PnN`).
`label` optional	string \| null	Descriptive label (FCS `$PnS`), if any.
`dtype`	string	NumPy-style dtype of the values as returned by `read_table` (`float32`, `float64`, `uint32`, ...).
`unit` optional	string \| null	Physical unit of the values, if the format records one.
`range` optional	array of number (double) \| null	Nominal `[min, max]` range when the format declares one.
`extra` optional	object	Format-specific column metadata in the reader's documented vocabulary.

Confidence Per-format confidence summary shown by info and self formats.

One of: "high" | "medium" | "low"

Experiment The experiment a file records: sample, instrument, method, acquisition and measurements.

Field	Type	Meaning
`sample` optional	Sample \| null	What was measured on.
`instrument` optional	ExperimentInstrument \| null	What it was measured with.
`method` optional	Method \| null	How.
`acquisition` optional	Acquisition \| null	When and by whom.
`measurements` optional	array of Measurement	What was measured, one entry per kind of data block.
`notes` optional	array of string	Things to know when reading the fields above (several samples in one file, ...).
`provenance` optional	map of Origin	Origin of every value, keyed by its path in this object (`sample.id`, `method.parameters.nucleus`, `measurements[0]`).

ExperimentInstrument The instrument that made the measurement.

Field	Type	Meaning
`vendor` optional	string \| null	Manufacturer.
`model` optional	string \| null	Model (microscope stand, mass spectrometer, cytometer, plate reader, detector module).
`serial` optional	string \| null	Serial number.
`software` optional	string \| null	Acquisition software.
`software_version` optional	string \| null	Version of the acquisition software.
`kind` optional	Term \| null	Kind of instrument (OBI term: `microscope`, `mass spectrometer`, `flow cytometer`, ...).

FeatureKind What a variant feature describes.

FeatureStatus How the corpus covers one feature value.

One of: "validated" | "seen" | "unseen"

FormatDescriptor Static description of a format as the tool understands it.

Field	Type	Meaning
`id`	string	Short id used on the command line, e.g. `czi`.
`name`	string	Human name, e.g. `Zeiss CZI`.
`vendor`	string	Vendor (nominative use only).
`extensions`	array of string	File extensions, lowercase, without the dot.
`family`	string	Family: `microscopy`, `mass-spectrometry`, `flow-cytometry`, ...
`can_read`	boolean	True when the tool can read this format.
`can_write`	boolean	True when `export` can also write this format (e.g. mzML, OME-Zarr).
`confidence`	Confidence	Overall confidence in this reader.
`known_gaps`	array of string	Things this reader knowingly does not handle yet.

ImageInfo One image (a scene, series, or position) inside the file.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based index used by `--image`.
`name` optional	string \| null	Image (scene, series or position) name, if recorded.
`size_x`	integer (uint32)	Width in pixels.
`size_y`	integer (uint32)	Height in pixels.
`size_z`	integer (uint32)	Number of Z planes (focal slices).
`size_c`	integer (uint32)	Number of channels.
`size_t`	integer (uint32)	Number of time points.
`dimension_order`	string	Storage order of planes, e.g. `XYCZT` (X and Y always first).
`pixel_type`	PixelType	Sample type of every plane.
`samples_per_pixel`	integer (uint32)	1 for grayscale channels, 3 for interleaved RGB.
`physical_size`	PhysicalSize	Physical size of one pixel (and the Z step).
`time_increment_s` optional	number (double) \| null	Interval between time points in seconds.
`channels`	array of ChannelInfo	One entry per channel, in channel order.
`objective` optional	ObjectiveInfo \| null	The objective lens, if recorded.
`instrument` optional	InstrumentInfo \| null	Instrument and software, if recorded.
`acquired_at` optional	string \| null	ISO-8601 acquisition start, if recorded.
`mosaic` optional	MosaicInfo \| null	Tile layout when the image was acquired as a mosaic.
`pyramid_levels`	integer (uint32)	Number of resolution levels stored (1 = no pyramid).
`resolution_levels` optional	array of ResolutionLevel	Size, downsampling and stored tile size of every resolution level, level 0 first. Filled by readers of pyramidal or tiled images (read a level with `--level N`, a rectangle with `--region X,Y,W,H`); empty otherwise.
`plane_count`	integer (uint64)	`size_z * size_c * size_t`.
`extra` optional	object	Format-specific extras that have no OME equivalent, in our own vocabulary.

InferredFields Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a

Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a specification: the inferred entries of the reader's provenance map.

Field	Type	Meaning
`count`	integer (uint32)	How many normalized fields have inferred meaning.
`of`	integer (uint32)	How many normalized fields carry provenance at all.
`examples` optional	array of string	Up to 12 of their JSON paths (`info --view full` → `provenance` has all).

InferredValue A value derived by a rule, with the corpus evidence for the rule.

Field	Type	Meaning
`field`	string	JSON path of the value in `info`.
`rule`	string	The rule that derived it.
`status`	FeatureStatus	`validated` when development files' oracles confirmed values derived by this rule.
`detail`	string	What was derived from what.

InfoOutput What info prints: the normalized [FileInfo] plus the derived [Experiment] under the

What info prints: the normalized [FileInfo] plus the derived [Experiment] under the additive experiment key. Dereferences to the FileInfo.

Field	Type	Meaning
`path`	string	The path as given by the caller.
`size_bytes`	integer (uint64)	Size in bytes (for directory formats such as Bruker `.d`, the files that were read).
`format`	FormatDescriptor	The format that read the file.
`format_version` optional	string \| null	Version of the container format as written in the file, if any.
`images`	array of ImageInfo	Images in the file (empty for tables, spectra and traces).
`tables` optional	array of TableInfo	Tabular datasets (flow cytometry events, ...). Empty for image formats.
`spectra` optional	array of SpectraInfo	Mass-spectrometry runs. Empty for other formats.
`traces` optional	array of TraceInfo	Sampled-signal blocks (electrophysiology, chromatography, NMR). Empty for other formats.
`plane_count`	integer (uint64)	Total planes across all images.
`notes` optional	array of string	Notes the reader wants the caller to see (e.g. "pyramid levels skipped").
`experiment` optional	Experiment \| null	Sample, instrument, method, acquisition and measurements, each value with its origin (`book/src/guides/metadata.md`). Absent when nothing is known.
`acquisition` optional	Acquisition2 \| null	Present when the file is not finished: still being written (`in_progress`, with the number of complete planes) or stopped before the end (`interrupted`). See `book/src/guides/lab-shares.md`.
`plate` optional	PlateSummary \| null	Multi-well plates (high-content screening): the plate id and type, rows and columns, the imaged wells with the images (fields) of each, and how many planes the copy on disk is missing (`docs/formats/hcs.md`). Absent for other files.
`images_total` optional	integer (uint64) \| null	Set when `images` lists only the first few images ([`InfoOutput::cap_images`]: screening plates by default, whose field images are all alike, or `--max-images N`): how many images the file holds. `plate.wells[].images` still indexes every field, the image commands take any index, and `--max-images 0` (MCP `max_images: 0`) lists them all.
`assurance` optional	Assurance \| null	Whether this file lies inside what its reader has been validated on: the variant fingerprint with the corpus evidence for each feature, structures not decoded, values assumed, vendor calibrations, and the outputs `--strict` refuses (`docs/assurance.md`).

InstrumentInfo The instrument and software that produced the file.

Field	Type	Meaning
`manufacturer` optional	string \| null	Instrument manufacturer.
`model` optional	string \| null	Instrument model (e.g. microscope stand or mass spectrometer).
`software` optional	string \| null	Acquisition software.
`software_version` optional	string \| null	Version of the acquisition software.
`detector` optional	string \| null	Detector (camera or photomultiplier) name.

Measurement One thing that was measured, in scientific words.

Field	Type	Meaning
`kind`	MeasurementKind	Which array of the file it describes.
`indices`	array of integer (uint32)	Indices into that array (images, tables, traces or runs) this entry covers.
`what`	string	What was measured, e.g. `fluorescence, 3 channels (DAPI, GFP, mCherry), 21 z-slices` or `LC-MS, negative mode, 2,031 scans, MS1`.
`technique` optional	Term \| null	The technique (CHMO, FBbi, OBI or PSI-MS term).
`terms` optional	array of Term	Further terms: polarity, spectrum types, detectors, acquisition modes.
`parameters` optional	map of Quantity	Counts and settings with units (`scans`, `wells`, `wavelength`, `z_slices`).

MeasurementKind Which part of the file a measurement describes.

One of: "image" | "table" | "trace" | "spectra"

Method How the measurement was made.

Field	Type	Meaning
`name` optional	string \| null	Name of the acquisition method, protocol or experiment as the software saved it.
`technique` optional	Term \| null	The technique (CHMO, FBbi or OBI term: `liquid chromatography-mass spectrometry`, ...).
`assay` optional	Term \| null	The kind of assay (OBI term).
`parameters` optional	map of Quantity	Method settings, keyed by our own snake_case names (`nucleus`, `polarity`, `z_step`).

MosaicInfo Mosaic (tiled/stitched) acquisition summary.

Field	Type	Meaning
`tile_count`	integer (uint32)	Number of tiles (fields of view) in the mosaic.
`tile_width` optional	integer (uint32) \| null	Width of one tile in pixels, when all tiles share it.
`tile_height` optional	integer (uint32) \| null	Height of one tile in pixels, when all tiles share it.
`stitched_on_read`	boolean	Whether the reader stitches tiles into a single plane on read.

ObjectiveInfo The objective lens.

Field	Type	Meaning
`model` optional	string \| null	Objective model name as the vendor records it.
`nominal_magnification` optional	number (double) \| null	Nominal magnification (e.g. `63` for a 63× lens).
`lens_na` optional	number (double) \| null	Numerical aperture.
`immersion` optional	string \| null	Immersion medium between lens and sample (`Oil`, `Water`, `Air`, ...).

Origin Where one experiment value came from.

Field	Type	Meaning
`source`	Source	How the meaning of the source field is known (the reader's provenance for that field; `inferred` for our own mapping and derived text).
`from`	string	The field it was taken from: a path into the `info` JSON (`spectra[0].extra.vial`), or a vendor file inside the dataset (`pdata/1/title`).

PhysicalSize Physical pixel size in micrometres (the OME default unit). Every present value is > 0.

Field	Type	Meaning
`x` optional	number (double) \| null	Pixel width in µm (the distance between neighbouring columns).
`y` optional	number (double) \| null	Pixel height in µm (the distance between neighbouring rows).
`z` optional	number (double) \| null	Spacing between Z planes (focal slices) in µm.
`unit`	string	Always `µm` in this schema version.

PixelType Sample type of one channel value. Names follow OME-XML PixelType values.

PlateSummary Layout of a multi-well plate (high-content screening): info → plate.

Field	Type	Meaning
`id` optional	string \| null	Plate identifier or barcode as the acquisition software recorded it.
`name` optional	string \| null	Plate name, when recorded besides the id.
`plate_type` optional	string \| null	Plate type (product) as recorded, e.g. `384 PerkinElmer CellCarrier Ultra`.
`rows`	integer (uint32)	Number of rows of the plate (8 for a 96-well plate).
`columns`	integer (uint32)	Number of columns of the plate (12 for a 96-well plate).
`wells`	array of PlateWell	The imaged wells, row by row.
`field_count`	integer (uint32)	Most fields of view in one well.
`planes_expected`	integer (uint64)	Planes the plate's index lists (every image's `plane_count`).
`planes_absent` optional	integer (uint64)	Planes the instrument never acquired or recorded (they read as blank and are left out of statistics; `images[].extra.absent_planes`).
`planes_missing` optional	integer (uint64)	Planes whose files the index names but that are not on disk (`check` lists them).
`complete`	boolean	True when every plane the index names is on disk.
`extra` optional	object	Format-specific plate facts in the reader's documented vocabulary.

PlateWell One imaged well of a plate.

Field	Type	Meaning
`well`	string	Well name, e.g. `C05` (row letters, column zero-padded to two digits).
`row`	string	Row letters (`C`).
`column`	integer (uint32)	Column number, 1-based (`5`).
`row_index`	integer (uint32)	Zero-based row index (`C` = 2).
`column_index`	integer (uint32)	Zero-based column index.
`images`	array of integer (uint32)	Indices of the images (fields of view) of this well, in field order.
`planes_missing` optional	integer (uint64)	Planes of this well whose files are not on disk (0 when the well is complete).

Quantity A value with an optional unit: {"value": 19, "unit": "min", "ucum": "min"}.

Field	Type	Meaning
`value`	any	A number, a string, or a list of them.
`unit` optional	string \| null	Unit as written for people (`µm`, `°C`), when the value has one.
`ucum` optional	string \| null	UCUM code of `unit` (`um`, `Cel`).

ResolutionLevel Geometry of one resolution level of an image.

Field	Type	Meaning
`level`	integer (uint32)	Level index: 0 is full resolution, larger is more downsampled (`--level`).
`size_x`	integer (uint32)	Width in pixels.
`size_y`	integer (uint32)	Height in pixels.
`downsample_x`	number (double)	Level-0 width over this level's width (1 for level 0; 2, 4, ... for a halving pyramid).
`downsample_y`	number (double)	Level-0 height over this level's height.
`tile_width` optional	integer (uint32) \| null	Width of the tiles (subblocks, chunks) the level is stored in, when it is tiled: region reads aligned to this grid decode each tile once.
`tile_height` optional	integer (uint32) \| null	Height of the stored tiles.
`size_z` optional	integer (uint32) \| null	Number of z planes at this level, when it differs from the image's `size_z` (Imaris downsamples z as well).

Sample What was measured: the sample's identity as the file records it.

Field	Type	Meaning
`id` optional	string \| null	The sample's identifier, from the field named in `source_field`.
`name` optional	string \| null	A descriptive sample name when the file records one besides the id.
`well` optional	string \| null	Plate well (`B2`, `A01`).
`barcode` optional	string \| null	Plate or tube barcode.
`sequence_position` optional	string \| null	Position in the autosampler sequence or tray (vial `D:35`, `2:A,8`).
`source_field` optional	string \| null	Path of the field `id` came from (`spectra[0].extra.sample_name`, `tables[0].extra.specimen`, `pdata/1/title`).

Scope Which outputs of a file a feature, a structure or a calibration affects.

One of: "metadata" | "pixels" | "spectra" | "traces" | "tables"

SignalChannelInfo One channel of a sampled-signal dataset.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based channel index.
`name`	string	Channel name as recorded.
`unit` optional	string \| null	Physical unit of the scaled values (`pA`, `mV`, `AU`, ...).
`dtype`	string	NumPy-style dtype of the raw stored samples.
`scale`	number (double)	`value = raw * scale + offset` when the file stores integers.
`offset`	number (double)	Added after scaling; see `scale`.
`extra` optional	object	Format-specific channel metadata in the reader's documented vocabulary.

Source How we learned what a field means. Ordered from most to least authoritative.

One of: "spec" | "vendor-impl" | "prior-art" | "inferred"

SpectraInfo A collection of mass spectra (one acquisition run).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based run index.
`name` optional	string \| null	Run name, if the file records one.
`scan_count`	integer (uint64)	Number of spectra (scans) in the run.
`ms_levels`	array of integer (uint32)	MS levels present (1 = full scans, 2 = MS/MS, ...).
`rt_range_s` optional	array of number (double) \| null	Retention-time range in seconds.
`instrument` optional	InstrumentInfo \| null	Instrument and software, if recorded.
`extra` optional	object	Format-specific run metadata in the reader's documented vocabulary.

TableInfo A tabular dataset inside the file (rows × columns), e.g. FCS events.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based table index.
`name` optional	string \| null	Table name, if the format has one.
`row_count`	integer (uint64)	Number of rows (e.g. recorded events).
`columns`	array of ColumnInfo	One entry per column.
`extra` optional	object	Format-specific table metadata in the reader's documented vocabulary.

Term An ontology term: its id (CURIE, e.g. CHMO:0000524) and label.

Field	Type	Meaning
`id`	string	Compact id, `PREFIX:local` (`MS:1000130`, `CHMO:0000591`, `FBbi:00000246`, `OBI:0000916`).
`label`	string	The term's label in its ontology (`positive scan`).

TraceInfo A block of uniformly sampled signals (a sweep, a chromatogram run, an FID).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based trace index.
`name` optional	string \| null	Trace name, if the format has one.
`sample_rate_hz`	number (double)	Samples per second.
`sample_count`	integer (uint64)	Samples per sweep (the longest sweep when sweeps differ; see `extra.sweep_sample_counts`).
`sweep_count`	integer (uint32)	Number of sweeps/episodes stored back to back (1 for continuous recordings).
`channels`	array of SignalChannelInfo	One entry per channel.
`start_s` optional	number (double) \| null	Time of the first sample relative to the recording start, seconds.
`extra` optional	object	Format-specific trace metadata in the reader's documented vocabulary.

Undecoded A structure the reader met in the file but did not decode.

Field	Type	Meaning
`structure`	string	What the structure is, in the format notes' vocabulary.
`scope` optional	array of Scope	Outputs that may be incomplete or wrong because of it. Empty: it is left out and the values returned do not depend on it.
`detail`	string	What is known about it and what the reader does instead.

VariantFeature One feature of the file's fingerprint, with the corpus evidence for it.

Field	Type	Meaning
`kind`	FeatureKind	What the feature describes.
`value`	string	Its value.
`scope` optional	array of Scope	Outputs whose decoding depends on it (empty: descriptive only).
`status`	FeatureStatus	`validated`, `seen` or `unseen`.
`corpus_files`	integer (uint32)	Development-corpus files with this value confirmed by an independent reader.
`sources`	integer (uint32)	Distinct depositors among them.

Withheld A field --strict withholds: it is present, but its value was assumed, derived by a rule no

A field --strict withholds: it is present, but its value was assumed, derived by a rule no independent reader confirmed, or never compared with an independent reader.

Field	Type	Meaning
`field`	string	JSON path pattern in `info` (`[]` matches any index).
`reason`	string	Why it is not validated.

info-full.schema.json · Dump

info-explain

Output of info --view explain.

Field	Type	Meaning
`summary`	string	One or two sentences: what the file is and what it holds.
`paragraphs`	array of string	The narrative, one topic per paragraph (contents, channels, optics, timing, what is unusual).
`suggested_commands`	array of string	Shell commands tailored to this file, most useful first.
`caveats`	array of string	Things the reader should not take for granted (reader notes, missing calibration, ...).
`answers` optional	array of Answer	Answers to the question asked with `--ask`, one per topic it touches; empty without one.
`assurance` optional	Assurance \| null	Whether the file lies inside what its reader has been validated on (as `info` → `assurance`); its summary is also the first caveat when the file is not validated.

Types used (15)

Answer One answer to an --ask question, from the experiment model.

Field	Type	Meaning
`topic`	string	The topic the question matched: `sample`, `channels`, `method`, `run_length`, `polarity`, `ms_levels`, `instrument`, `operator`, `acquired`, `technique`.
`answer`	string	The answer in one or two sentences; says so when the file does not record it.
`fields` optional	array of string	Paths of the fields the answer came from (into the `info` JSON, or `experiment.*`).

Assumed A value the reader assumed (a default, a guess from context) instead of reading it.

Field	Type	Meaning
`field`	string	JSON path of the value in `info` (e.g. `traces[0].channels[1].unit`).
`detail`	string	Why it was assumed and from what.

Assurance The per-file assurance block of info (every view) and check.

Field	Type	Meaning
`level`	AssuranceLevel	`validated`, `partially_validated` or `unvalidated`.
`summary`	string	One line for people and agents.
`fingerprint`	string	The variant fingerprint: `format_id` then `kind=value` for each feature, sorted.
`variant`	array of VariantFeature	Each feature with its corpus evidence.
`reasons` optional	array of string	Why the level is not `validated`, one reason per line.
`undecoded` optional	array of Undecoded	Structures met but not decoded.
`assumed` optional	array of Assumed	Values assumed instead of read.
`calibrations` optional	array of Calibration	Vendor calibrations and corrections the file carries, and whether they were applied.
`inferred_fields` optional	InferredFields	Normalized fields whose meaning is inferred rather than specified.
`inferred` optional	array of InferredValue	Values derived by a rule instead of read, with the evidence for each rule.
`strict_refuses` optional	array of Scope	Outputs `--strict` (MCP `strict: true`) refuses to return for this file.
`strict_withholds` optional	array of Withheld	Fields `--strict` withholds (returned as null; asking for one with `--only` exits 6) while the rest of the output is returned.
`reader_confidence`	Confidence	The reader's overall confidence (evidence rubric), for context.

AssuranceLevel How far a file lies inside what its reader has been validated on.

One of: "validated" | "partially_validated" | "unvalidated"

Calibration A vendor calibration or correction the file carries.

Field	Type	Meaning
`name`	string	What it calibrates (`m/z (MzCalibration)`, `ADC to µV`, `spillover compensation`).
`status`	CalibrationStatus	Applied, not applied, or available on request.
`scope` optional	array of Scope	Outputs it applies to.
`detail`	string	How it is (or is not) applied and how to get calibrated values.

CalibrationStatus Whether a vendor calibration or correction stored in the file was applied.

One of: "applied" | "not_applied" | "available"

Confidence Per-format confidence summary shown by info and self formats.

One of: "high" | "medium" | "low"

FeatureKind What a variant feature describes.

FeatureStatus How the corpus covers one feature value.

One of: "validated" | "seen" | "unseen"

InferredFields Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a

Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a specification: the inferred entries of the reader's provenance map.

Field	Type	Meaning
`count`	integer (uint32)	How many normalized fields have inferred meaning.
`of`	integer (uint32)	How many normalized fields carry provenance at all.
`examples` optional	array of string	Up to 12 of their JSON paths (`info --view full` → `provenance` has all).

InferredValue A value derived by a rule, with the corpus evidence for the rule.

Field	Type	Meaning
`field`	string	JSON path of the value in `info`.
`rule`	string	The rule that derived it.
`status`	FeatureStatus	`validated` when development files' oracles confirmed values derived by this rule.
`detail`	string	What was derived from what.

Scope Which outputs of a file a feature, a structure or a calibration affects.

One of: "metadata" | "pixels" | "spectra" | "traces" | "tables"

Undecoded A structure the reader met in the file but did not decode.

Field	Type	Meaning
`structure`	string	What the structure is, in the format notes' vocabulary.
`scope` optional	array of Scope	Outputs that may be incomplete or wrong because of it. Empty: it is left out and the values returned do not depend on it.
`detail`	string	What is known about it and what the reader does instead.

VariantFeature One feature of the file's fingerprint, with the corpus evidence for it.

Field	Type	Meaning
`kind`	FeatureKind	What the feature describes.
`value`	string	Its value.
`scope` optional	array of Scope	Outputs whose decoding depends on it (empty: descriptive only).
`status`	FeatureStatus	`validated`, `seen` or `unseen`.
`corpus_files`	integer (uint32)	Development-corpus files with this value confirmed by an independent reader.
`sources`	integer (uint32)	Distinct depositors among them.

Withheld A field --strict withholds: it is present, but its value was assumed, derived by a rule no

A field --strict withholds: it is present, but its value was assumed, derived by a rule no independent reader confirmed, or never compared with an independent reader.

Field	Type	Meaning
`field`	string	JSON path pattern in `info` (`[]` matches any index).
`reason`	string	Why it is not validated.

info-explain.schema.json · Explanation

info-structure

Output of info --view structure.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`entries`	array of LsEntry	Container elements in file order.
`acquisition` optional	Acquisition \| null	Present when the file is not finished: still being written (`in_progress`) or stopped before the end (`interrupted`). See `book/src/guides/lab-shares.md`.

Types used (3)

Acquisition acquisition in info, info --view structure, check and check --planes: present only for

acquisition in info, info --view structure, check and check --planes: present only for files that are not finished. See book/src/guides/lab-shares.md.

Field	Type	Meaning
`state`	AcquisitionState	`in_progress` or `interrupted`.
`complete_planes`	integer (uint64)	Planes whose data is entirely on disk.
`expected_planes` optional	integer (uint64) \| null	Planes the finished file will hold, when the metadata written so far says so.
`modified_ago_s`	number (double)	Seconds since the file (or the newest member of a directory store) was modified.
`window_s`	number (double)	The live window used for the decision, in seconds.
`missing`	array of string	Structures written at the end of an acquisition that are absent.
`tail_bytes`	integer (uint64)	Bytes after the last complete unit (a unit still being written).
`evidence`	array of string	The observations behind the decision.

AcquisitionState Whether an incomplete file is still being written.

One of: "in_progress" | "interrupted"

LsEntry One row of info --view structure: a structural element of the container.

Field	Type	Meaning
`kind`	string	`image`, `plane`, `segment`, `chunk`, `block`, `attachment`, `metadata`, `pyramid-level`, ...
`name`	string	Element name (an id, a chunk name or a path inside the container).
`offset` optional	integer (uint64) \| null	Byte offset of the element in the file, when it has one.
`size` optional	integer (uint64) \| null	Size of the element in bytes, when known.
`image` optional	integer (uint32) \| null	Which image this element belongs to, if any.
`details` optional	any	Format-specific details (JSON), omitted when empty.

info-structure.schema.json · Listing

check

Output of check.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`ok`	boolean	True when no finding has severity `error`.
`checks_performed`	array of string	What was verified, in plain words, so the caller knows what "ok" covers.
`findings`	array of Finding	Everything found, in the order checked.
`acquisition` optional	Acquisition \| null	Present when the file is not finished: still being written (`in_progress`: findings about the unfinished tail are warnings and `ok` covers the complete part) or stopped before the end (`interrupted`). See `book/src/guides/lab-shares.md`.
`assurance` optional	Assurance \| null	Whether the file lies inside what its reader has been validated on (the same block as `info` → `assurance`). `ok` says the file is intact; `assurance` says whether its values can be trusted. Filled by the `check` command when the header can be read.

Types used (18)

Acquisition acquisition in info, info --view structure, check and check --planes: present only for

acquisition in info, info --view structure, check and check --planes: present only for files that are not finished. See book/src/guides/lab-shares.md.

Field	Type	Meaning
`state`	AcquisitionState	`in_progress` or `interrupted`.
`complete_planes`	integer (uint64)	Planes whose data is entirely on disk.
`expected_planes` optional	integer (uint64) \| null	Planes the finished file will hold, when the metadata written so far says so.
`modified_ago_s`	number (double)	Seconds since the file (or the newest member of a directory store) was modified.
`window_s`	number (double)	The live window used for the decision, in seconds.
`missing`	array of string	Structures written at the end of an acquisition that are absent.
`tail_bytes`	integer (uint64)	Bytes after the last complete unit (a unit still being written).
`evidence`	array of string	The observations behind the decision.

AcquisitionState Whether an incomplete file is still being written.

One of: "in_progress" | "interrupted"

Assumed A value the reader assumed (a default, a guess from context) instead of reading it.

Field	Type	Meaning
`field`	string	JSON path of the value in `info` (e.g. `traces[0].channels[1].unit`).
`detail`	string	Why it was assumed and from what.

Assurance The per-file assurance block of info (every view) and check.

Field	Type	Meaning
`level`	AssuranceLevel	`validated`, `partially_validated` or `unvalidated`.
`summary`	string	One line for people and agents.
`fingerprint`	string	The variant fingerprint: `format_id` then `kind=value` for each feature, sorted.
`variant`	array of VariantFeature	Each feature with its corpus evidence.
`reasons` optional	array of string	Why the level is not `validated`, one reason per line.
`undecoded` optional	array of Undecoded	Structures met but not decoded.
`assumed` optional	array of Assumed	Values assumed instead of read.
`calibrations` optional	array of Calibration	Vendor calibrations and corrections the file carries, and whether they were applied.
`inferred_fields` optional	InferredFields	Normalized fields whose meaning is inferred rather than specified.
`inferred` optional	array of InferredValue	Values derived by a rule instead of read, with the evidence for each rule.
`strict_refuses` optional	array of Scope	Outputs `--strict` (MCP `strict: true`) refuses to return for this file.
`strict_withholds` optional	array of Withheld	Fields `--strict` withholds (returned as null; asking for one with `--only` exits 6) while the rest of the output is returned.
`reader_confidence`	Confidence	The reader's overall confidence (evidence rubric), for context.

AssuranceLevel How far a file lies inside what its reader has been validated on.

One of: "validated" | "partially_validated" | "unvalidated"

Calibration A vendor calibration or correction the file carries.

Field	Type	Meaning
`name`	string	What it calibrates (`m/z (MzCalibration)`, `ADC to µV`, `spillover compensation`).
`status`	CalibrationStatus	Applied, not applied, or available on request.
`scope` optional	array of Scope	Outputs it applies to.
`detail`	string	How it is (or is not) applied and how to get calibrated values.

CalibrationStatus Whether a vendor calibration or correction stored in the file was applied.

One of: "applied" | "not_applied" | "available"

Confidence Per-format confidence summary shown by info and self formats.

One of: "high" | "medium" | "low"

FeatureKind What a variant feature describes.

FeatureStatus How the corpus covers one feature value.

One of: "validated" | "seen" | "unseen"

Finding One check finding.

Field	Type	Meaning
`severity`	Severity	How serious the finding is.
`code`	string	Stable code, e.g. `truncated`, `bad_offset`, `missing_planes`, `directory_mismatch`.
`message`	string	Plain-English description.
`offset` optional	integer (uint64) \| null	Byte offset the finding refers to, if any.

InferredFields Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a

Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a specification: the inferred entries of the reader's provenance map.

Field	Type	Meaning
`count`	integer (uint32)	How many normalized fields have inferred meaning.
`of`	integer (uint32)	How many normalized fields carry provenance at all.
`examples` optional	array of string	Up to 12 of their JSON paths (`info --view full` → `provenance` has all).

InferredValue A value derived by a rule, with the corpus evidence for the rule.

Field	Type	Meaning
`field`	string	JSON path of the value in `info`.
`rule`	string	The rule that derived it.
`status`	FeatureStatus	`validated` when development files' oracles confirmed values derived by this rule.
`detail`	string	What was derived from what.

Scope Which outputs of a file a feature, a structure or a calibration affects.

One of: "metadata" | "pixels" | "spectra" | "traces" | "tables"

Severity Severity of a check finding.

One of: "info" | "warning" | "error"

Undecoded A structure the reader met in the file but did not decode.

Field	Type	Meaning
`structure`	string	What the structure is, in the format notes' vocabulary.
`scope` optional	array of Scope	Outputs that may be incomplete or wrong because of it. Empty: it is left out and the values returned do not depend on it.
`detail`	string	What is known about it and what the reader does instead.

VariantFeature One feature of the file's fingerprint, with the corpus evidence for it.

Field	Type	Meaning
`kind`	FeatureKind	What the feature describes.
`value`	string	Its value.
`scope` optional	array of Scope	Outputs whose decoding depends on it (empty: descriptive only).
`status`	FeatureStatus	`validated`, `seen` or `unseen`.
`corpus_files`	integer (uint32)	Development-corpus files with this value confirmed by an independent reader.
`sources`	integer (uint32)	Distinct depositors among them.

Withheld A field --strict withholds: it is present, but its value was assumed, derived by a rule no

A field --strict withholds: it is present, but its value was assumed, derived by a rule no independent reader confirmed, or never compared with an independent reader.

Field	Type	Meaning
`field`	string	JSON path pattern in `info` (`[]` matches any index).
`reason`	string	Why it is not validated.

check.schema.json · CheckReport

check-planes

Output of check --planes.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`planes`	array of PlaneHash	One row per plane, in the order read.
`acquisition` optional	Acquisition \| null	Present when the file is not finished; while it is `in_progress` only complete planes are read. See `book/src/guides/lab-shares.md`.

Types used (5)

Acquisition acquisition in info, info --view structure, check and check --planes: present only for

acquisition in info, info --view structure, check and check --planes: present only for files that are not finished. See book/src/guides/lab-shares.md.

Field	Type	Meaning
`state`	AcquisitionState	`in_progress` or `interrupted`.
`complete_planes`	integer (uint64)	Planes whose data is entirely on disk.
`expected_planes` optional	integer (uint64) \| null	Planes the finished file will hold, when the metadata written so far says so.
`modified_ago_s`	number (double)	Seconds since the file (or the newest member of a directory store) was modified.
`window_s`	number (double)	The live window used for the decision, in seconds.
`missing`	array of string	Structures written at the end of an acquisition that are absent.
`tail_bytes`	integer (uint64)	Bytes after the last complete unit (a unit still being written).
`evidence`	array of string	The observations behind the decision.

AcquisitionState Whether an incomplete file is still being written.

One of: "in_progress" | "interrupted"

PixelType Sample type of one channel value. Names follow OME-XML PixelType values.

PlaneHash One row of check --planes.

Field	Type	Meaning
`image`	integer (uint32)	Image index.
`level` optional	integer (uint32)	Pyramid level (0 = full resolution); omitted when 0.
`region` optional	Region \| null	The rectangle read (level pixel coordinates) when `--region` was given; the hash and `width`/`height` are then those of the region. Absent = the whole plane.
`c`	integer (uint32)	Channel index.
`z`	integer (uint32)	Z index (focal plane).
`t`	integer (uint32)	Time index.
`width`	integer (uint32)	Plane width in pixels.
`height`	integer (uint32)	Plane height in pixels.
`pixel_type`	PixelType	Sample type.
`samples_per_pixel`	integer (uint32)	1 for grayscale, 3 for interleaved RGB.
`xxh3`	string	xxh3-128 of the raw little-endian sample bytes, 32 hex chars.

Region A rectangle of a plane, in the pixel coordinates of the resolution level it is read at.

Field	Type	Meaning
`x`	integer (uint32)	Left edge (column of the first pixel).
`y`	integer (uint32)	Top edge (row of the first pixel).
`width`	integer (uint32)	Width in pixels (at least 1).
`height`	integer (uint32)	Height in pixels (at least 1).

check-planes.schema.json · PlanesOutput

check-against

Output of check --against.

Field	Type	Meaning
`identical`	boolean	Nothing compared differs: metadata (unless skipped), geometry, channel names, physical sizes and planes (within the tolerance). The exit code is 0 when true, 1 when false.
`ours`	CompareSide	The first file.
`theirs`	CompareSide	The second file.
`metadata`	MetadataComparison	The normalized-metadata diff.
`images`	array of ImageComparison	Geometry, channel-name and physical-size comparison per image index.
`planes`	PlaneComparison	The plane-by-plane comparison.
`notes`	array of string	Caveats (e.g. formats that store different metadata for the same acquisition).

Types used (9)

CompareSide One file of the pair.

Field	Type	Meaning
`path`	string	The file as given.
`format`	string	Its format id.
`images`	integer (uint32)	Number of images.
`tables`	integer (uint32)	Number of tables.
`traces`	integer (uint32)	Number of traces.

Difference A value that differs, at an RFC 6901 JSON pointer into info --json data.

Field	Type	Meaning
`pointer`	string	RFC 6901 JSON pointer to the value, e.g. `/images/0/physical_size/x`.
`ours` optional	any	Value in the first file; absent when the first file lacks the field.
`theirs` optional	any	Value in the second file; absent when the second file lacks the field.

Geometry Geometry of one image.

Field	Type	Meaning
`size_x`	integer (uint32)	Width in pixels.
`size_y`	integer (uint32)	Height in pixels.
`size_z`	integer (uint32)	Number of Z planes.
`size_c`	integer (uint32)	Number of channels.
`size_t`	integer (uint32)	Number of time points.
`pixel_type`	PixelType	Sample type.
`samples_per_pixel`	integer (uint32)	1 for grayscale, 3 for interleaved RGB.

ImageComparison One image index present in either file.

Field	Type	Meaning
`image`	integer (uint32)	Image index.
`ours` optional	Geometry \| null	Absent when the first file has no image with this index.
`theirs` optional	Geometry \| null	Absent when the second file has no image with this index.
`geometry_equal`	boolean	Both files have the image and their geometries agree (with `selected`, after the selection).
`selected` optional	boolean	The second file holds only the selected planes of this image (an export made with the same selection): planes, channels and the metadata diff were matched in selection order, and `ours` is the geometry after the selection.
`channel_names_equal`	boolean	Channel names agree.
`ours_channels`	array of string \| null	Channel names of the first file (listed only when they differ).
`theirs_channels`	array of string \| null	Channel names of the second file (listed only when they differ).
`physical_size_equal`	boolean	Physical sizes agree to a relative 1e-6 (both absent counts as equal).
`ours_physical_size` optional	PhysicalSize \| null	Physical pixel size in the first file (listed only when the sizes differ).
`theirs_physical_size` optional	PhysicalSize \| null	Physical pixel size in the second file (listed only when the sizes differ).

MetadataComparison The normalized-metadata diff.

Field	Type	Meaning
`compared`	boolean	False with `--no-metadata`.
`equal`	boolean	True when no difference was found.
`ignored`	array of string	Pointers left out (defaults plus `--ignore`); `extra` objects are also left out unless `include_extra`.
`include_extra`	boolean	Whether `extra` objects were compared.
`difference_count`	integer (uint64)	Total number of differences (the list holds at most 1000).
`differences`	array of Difference	The differences, at most 1000.

PhysicalSize Physical pixel size in micrometres (the OME default unit). Every present value is > 0.

Field	Type	Meaning
`x` optional	number (double) \| null	Pixel width in µm (the distance between neighbouring columns).
`y` optional	number (double) \| null	Pixel height in µm (the distance between neighbouring rows).
`z` optional	number (double) \| null	Spacing between Z planes (focal slices) in µm.
`unit`	string	Always `µm` in this schema version.

PixelType Sample type of one channel value. Names follow OME-XML PixelType values.

PlaneComparison Plane-by-plane comparison.

Field	Type	Meaning
`compared`	boolean	False with `--no-pixels`.
`tolerance` optional	number (double) \| null	The `--tolerance` used, if any.
`planes`	integer (uint64)	Planes read from both files.
`identical`	integer (uint64)	Planes with identical xxh3-128.
`within_tolerance`	integer (uint64)	Planes that differ but within the tolerance.
`mismatched`	integer (uint64)	Planes that differ beyond the tolerance (or at all, without one).
`skipped_images`	array of integer (uint32)	Image indices not compared plane by plane (missing on one side or geometry differs).
`mismatches`	array of PlaneMismatch	At most 1000 entries, in plane order.

PlaneMismatch A plane that differs.

Field	Type	Meaning
`image`	integer (uint32)	Image index.
`c`	integer (uint32)	Channel index.
`z`	integer (uint32)	Z index.
`t`	integer (uint32)	Time index.
`ours_xxh3`	string	xxh3-128 of the plane in the first file.
`theirs_xxh3`	string	xxh3-128 of the plane in the second file.
`differing_samples` optional	integer (uint64) \| null	Samples that differ (absent when the planes' shapes differ).
`max_abs_diff` optional	number (double) \| null	Largest absolute difference between corresponding samples.
`within_tolerance`	boolean	With a tolerance: whether `max_abs_diff` is within it (then the plane counts as equal).
`note` optional	string \| null	Why the samples could not be compared (e.g. the plane shapes differ).

check-against.schema.json · CompareOutput

check-report

What openreadout check FILE --report prints under --json.

Field	Type	Meaning
`output` optional	string \| null	Where the bundle was written; `None` with `--dry-run` (or from MCP without `output`).
`bytes` optional	integer (uint64) \| null	Size of the written bundle.
`issue_url`	string	Where to file it (never contacted by the program).
`report`	Report	The bundle, exactly as written.

Types used (28)

Assumed A value the reader assumed (a default, a guess from context) instead of reading it.

Field	Type	Meaning
`field`	string	JSON path of the value in `info` (e.g. `traces[0].channels[1].unit`).
`detail`	string	Why it was assumed and from what.

Assurance The per-file assurance block of info (every view) and check.

Field	Type	Meaning
`level`	AssuranceLevel	`validated`, `partially_validated` or `unvalidated`.
`summary`	string	One line for people and agents.
`fingerprint`	string	The variant fingerprint: `format_id` then `kind=value` for each feature, sorted.
`variant`	array of VariantFeature	Each feature with its corpus evidence.
`reasons` optional	array of string	Why the level is not `validated`, one reason per line.
`undecoded` optional	array of Undecoded	Structures met but not decoded.
`assumed` optional	array of Assumed	Values assumed instead of read.
`calibrations` optional	array of Calibration	Vendor calibrations and corrections the file carries, and whether they were applied.
`inferred_fields` optional	InferredFields	Normalized fields whose meaning is inferred rather than specified.
`inferred` optional	array of InferredValue	Values derived by a rule instead of read, with the evidence for each rule.
`strict_refuses` optional	array of Scope	Outputs `--strict` (MCP `strict: true`) refuses to return for this file.
`strict_withholds` optional	array of Withheld	Fields `--strict` withholds (returned as null; asking for one with `--only` exits 6) while the rest of the output is returned.
`reader_confidence`	Confidence	The reader's overall confidence (evidence rubric), for context.

AssuranceLevel How far a file lies inside what its reader has been validated on.

One of: "validated" | "partially_validated" | "unvalidated"

Calibration A vendor calibration or correction the file carries.

Field	Type	Meaning
`name`	string	What it calibrates (`m/z (MzCalibration)`, `ADC to µV`, `spillover compensation`).
`status`	CalibrationStatus	Applied, not applied, or available on request.
`scope` optional	array of Scope	Outputs it applies to.
`detail`	string	How it is (or is not) applied and how to get calibrated values.

CalibrationStatus Whether a vendor calibration or correction stored in the file was applied.

One of: "applied" | "not_applied" | "available"

Confidence Per-format confidence summary shown by info and self formats.

One of: "high" | "medium" | "low"

DetectionSummary The reader that claimed the input.

Field	Type	Meaning
`format`	string	Format id.
`confidence`	string	`definite`, `likely` or `extension_only`.
`note` optional	string \| null	Why the match is less than definite.
`reader_confidence`	string	The reader's confidence level (`high`, `medium`, `low`).

FeatureKind What a variant feature describes.

FeatureStatus How the corpus covers one feature value.

One of: "validated" | "seen" | "unseen"

Generator Program name and version.

Field	Type	Meaning
`name`	string	`openreadout`.
`version`	string	Its version.

HexSample A hex excerpt.

Field	Type	Meaning
`at`	string	`head` or the structure entry (`kind name`).
`offset`	integer (uint64)	Byte offset.
`hex`	string	Space-separated bytes; masked text bytes are `__`.

InferredFields Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a

Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a specification: the inferred entries of the reader's provenance map.

Field	Type	Meaning
`count`	integer (uint32)	How many normalized fields have inferred meaning.
`of`	integer (uint32)	How many normalized fields carry provenance at all.
`examples` optional	array of string	Up to 12 of their JSON paths (`info --view full` → `provenance` has all).

InferredValue A value derived by a rule, with the corpus evidence for the rule.

Field	Type	Meaning
`field`	string	JSON path of the value in `info`.
`rule`	string	The rule that derived it.
`status`	FeatureStatus	`validated` when development files' oracles confirmed values derived by this rule.
`detail`	string	What was derived from what.

InputSummary The input without its name.

Field	Type	Meaning
`kind`	string	`file` or `directory`.
`size_bytes`	integer (uint64)	Bytes (a directory: the sum over its members).
`extension` optional	string \| null	Lower-case extension without the dot (`nd2`, `raw`, `d`), when there is one.
`sha256` optional	string \| null	SHA-256 of the whole file (files up to 1 GiB).
`sha256_first_64mib` optional	string \| null	SHA-256 of the first 64 MiB (larger files).
`signature_hex` optional	string \| null	The first 16 bytes in hex; printable runs that are not a plain token are masked (`__`).
`signature_text` optional	string \| null	The same bytes as text where they are a plain token (`ZISRAWFILE`, `ABF2`).
`text_like` optional	boolean	The file looks like text (a delimited export, XML, JSON).
`members` optional	array of Member	A directory's members: relative paths with names that are not plain tokens replaced.
`members_omitted` optional	integer (uint64)	Members not listed (more than 2000).
`member_extensions` optional	map of integer (uint64)	Member counts per extension.

Integrity Integrity findings.

Field	Type	Meaning
`mode`	string	`headers` (`check --headers-only`) or `full`.
`ok`	boolean	No finding of severity error.
`checks_performed`	array of string	What was verified.
`findings`	array of any	Findings: severity, code, message (scrubbed), offset.

KindCount Count and bytes of one entry kind.

Field	Type	Meaning
`kind`	string	Entry kind.
`count`	integer (uint64)	How many.
`bytes`	integer (uint64)	Their total size, where sizes are known.

Member One member of a directory data set.

Field	Type	Meaning
`path`	string	Path relative to the data set, `/`-separated.
`size`	integer (uint64)	Bytes.

Privacy The privacy statement of a bundle.

Field	Type	Meaning
`mode`	string	`structure_only` (default) or `with_text` (`--include-text`).
`included`	array of string	What the bundle contains, in plain words.
`excluded`	array of string	What it leaves out.
`redacted_strings`	integer (uint32)	Distinct strings from the file replaced by `<redacted-N>` or `<text:LEN>` placeholders.
`personal_data` optional	array of string	Personal-data flags (kind and rule, never the value) found in the metadata.

Report The diagnostic bundle.

Field	Type	Meaning
`report_version`	string	Bundle layout version ([`REPORT_VERSION`]).
`generator`	Generator	The program that wrote it.
`privacy`	Privacy	What the bundle contains and leaves out; read before sharing.
`input`	InputSummary	The input, without its name or path.
`detection` optional	DetectionSummary \| null	The reader that claimed the input, when one did.
`candidates` optional	array of string	Readers registered for the input's extension (what the user probably expected).
`stages`	array of Stage	The decode path: each stage in order with its result.
`assurance` optional	Assurance \| null	The assurance block (`info` → `assurance`), text scrubbed.
`metadata` optional	any	The normalized metadata (`info`) with numbers kept and free text replaced.
`structure` optional	StructureMap \| null	The container's structure (`info --view structure`).
`integrity` optional	Integrity \| null	Integrity findings (`check`).
`vendor_keys` optional	VendorKeys \| null	Key skeleton of the vendor metadata tree (`info --view full` → `vendor`): paths and value types.
`samples` optional	array of HexSample	Hex excerpts (only with `hex_bytes`).

Scope Which outputs of a file a feature, a structure or a calibration affects.

One of: "metadata" | "pixels" | "spectra" | "traces" | "tables"

Stage One stage of the decode path.

Field	Type	Meaning
`stage`	string	`detect`, `open`, `info`, `assurance`, `ls`, `check`, `vendor`, `first_read`.
`status`	string	`ok`, `error`, `skipped` or `panic` (a bug: the reader crashed in this stage).
`detail` optional	string \| null	What the stage found, in a few words (`12 entries`, `plane 512x512 uint16`).
`error` optional	StageError \| null	The error, when the stage failed.
`elapsed_ms` optional	integer (uint64) \| null	Milliseconds the stage took.

StageError An error as the CLI would report it, text scrubbed.

Field	Type	Meaning
`code`	string	Stable code (`corrupt_file`, `unsupported_feature`, ...).
`exit_code`	integer (int32)	Process exit code the CLI would return.
`message`	string	The message.
`hint` optional	string \| null	The hint.
`offset` optional	integer (uint64) \| null	Byte offset of the problem, when the reader knows it.

StructureMap The container's structure.

Field	Type	Meaning
`entries_total`	integer (uint64)	Entries `info --view structure` lists.
`by_kind`	array of KindCount	Count and bytes per entry kind.
`entries`	array of any	The first 400 entries in file order.

Undecoded A structure the reader met in the file but did not decode.

Field	Type	Meaning
`structure`	string	What the structure is, in the format notes' vocabulary.
`scope` optional	array of Scope	Outputs that may be incomplete or wrong because of it. Empty: it is left out and the values returned do not depend on it.
`detail`	string	What is known about it and what the reader does instead.

VariantFeature One feature of the file's fingerprint, with the corpus evidence for it.

Field	Type	Meaning
`kind`	FeatureKind	What the feature describes.
`value`	string	Its value.
`scope` optional	array of Scope	Outputs whose decoding depends on it (empty: descriptive only).
`status`	FeatureStatus	`validated`, `seen` or `unseen`.
`corpus_files`	integer (uint32)	Development-corpus files with this value confirmed by an independent reader.
`sources`	integer (uint32)	Distinct depositors among them.

VendorKeys Key skeleton of the vendor tree.

Field	Type	Meaning
`total_paths`	integer (uint64)	Distinct key paths (array indices folded to `[]`).
`omitted` optional	integer (uint64)	Paths not listed (beyond 3000).
`paths`	array of VendorPath	`path`, value `type` (`string`, `number`, `bool`, `null`, `object`, `array`), `count`.

VendorPath One vendor key path.

Field	Type	Meaning
`path`	string	Dotted key path, arrays as `[]`.
`type`	string	JSON type of the values (several joined by `\|`).
`count`	integer (uint64)	Occurrences.

Withheld A field --strict withholds: it is present, but its value was assumed, derived by a rule no

A field --strict withholds: it is present, but its value was assumed, derived by a rule no independent reader confirmed, or never compared with an independent reader.

Field	Type	Meaning
`field`	string	JSON path pattern in `info` (`[]` matches any index).
`reason`	string	Why it is not validated.

check-report.schema.json · ReportOutput

export

Output of export: an image export report (OME-TIFF, OME-Zarr), a CSV report for tables or traces, or an mzML report for mass spectra.

Types used (16)

AsmExportReport Output of export --to asm.

Field	Type	Meaning
`input`	string	The plate-reader export that was converted.
`output`	string	Where the ASM JSON document was written.
`format`	string	Always `asm`.
`manifest`	string	The ASM manifest IRI the document declares.
`documents`	integer (uint64)	`plate reader document` entries (one per plate and well).
`measurements`	integer (uint64)	Measurement documents (one per well and measured read).
`values`	integer (uint64)	Numeric values carried by the measurement documents (cube points counted singly).
`errors`	integer (uint64)	Non-numeric cells written as error documents.
`calculated`	integer (uint64)	Values of reads calculated by the vendor software, written as calculated-data documents.
`bytes_written`	integer (uint64)	Size of the written document in bytes.
`verified`	boolean	True when the written file was parsed back and its measured values matched the source.
`notes` optional	array of string	Caveats of the conversion (e.g. a time zone assumed because the export records none).

Codec Compression codec for the TIFF strips.

One of: "none" | "deflate" | "lzw"

ColumnarExportReport Output of a Parquet or Arrow IPC export.

Field	Type	Meaning
`input`	string	The input file.
`output`	string	The file written.
`format`	string	`parquet` or `arrow`.
`kind`	string	What was exported: `table`, `trace` or `spectra`.
`index`	integer (uint32)	Table, trace or spectra-run index.
`rows_written`	integer (uint64)	Rows written (table rows, trace samples over all sweeps, or spectrum points).
`columns`	array of string	Column names, in order.
`compression`	string	`none`, `snappy` or `lz4`.
`bytes_written`	integer (uint64)	Size of the written file in bytes.
`verified`	boolean	True when the file was read back and its schema, metadata and every value matched.
`sweeps` optional	array of integer (uint32) \| null	Traces: the sweeps written.
`first_row` optional	integer (uint64) \| null	Tables and traces: the first row (sample of each sweep) written, zero-based.
`spectra_written` optional	integer (uint64) \| null	Spectra: spectra (scans) written.
`summary_output` optional	string \| null	Spectra: the per-scan summary file (`<name>.scans.parquet`).
`summary_bytes` optional	integer (uint64) \| null	Spectra: size of the summary file in bytes.

ExportReport What export reports.

Field	Type	Meaning
`input`	string	The file that was read.
`output`	string	The OME-TIFF (or OME-Zarr) written.
`format`	string	`ome-tiff` or `ome-zarr`.
`images_written`	integer (uint32)	Images written.
`planes_written`	integer (uint64)	Planes written, over all images.
`bytes_written`	integer (uint64)	Size of the output in bytes.
`verified`	boolean	True when every written plane was read back and hashed equal to the source plane.
`codec`	Codec	Compression used.
`ome_xml_bytes`	integer (uint64)	Size of the embedded OME-XML in bytes.
`resolutions` optional	array of WrittenLevels	Per image, the resolution levels written (tiled exports: pyramids, regions, levels); absent for single-resolution exports of whole planes.
`layout` optional	string \| null	OME-Zarr: `plate` when the store is an OME-NGFF high-content screening plate (row, column and field groups); absent for single images and collections.
`images_skipped` optional	array of integer (uint32)	Images left out because plane files they need are missing (`--skip-incomplete`).

JcampExportReport Output of export --to jcamp.

Field	Type	Meaning
`input`	string	The input file.
`output`	string	The JCAMP-DX file written.
`format`	string	Always `jcamp-dx`.
`jcamp_version`	string	`##JCAMP-DX=` version written (`5.01`).
`data_type`	string	`##DATA TYPE=` written (`NMR FID`, `NMR SPECTRUM`, or the source's data type).
`data_class`	string	`XYDATA` or `NTUPLES`.
`trace`	integer (uint32)	Trace index written.
`sweeps`	array of integer (uint32)	Sweeps written.
`pages`	integer (uint32)	Data tables (NTUPLES pages; 1 for XYDATA).
`first_sample`	integer (uint64)	First sample of each sweep written (zero-based).
`samples_written`	integer (uint64)	Points per sweep written.
`channels_written`	integer (uint32)	Channels written (one table per channel and sweep).
`encoding`	string	`difdup` or `affn`.
`factors`	array of number (double)	The ordinate factor of each channel (value = integer × factor).
`exact`	boolean	True when every value round-trips bit-exactly.
`max_abs_error`	number (double)	Largest \|written − source\| over all values (0 when `exact`; at most half the factor).
`bytes_written`	integer (uint64)	Size of the written file in bytes.
`verified`	boolean	True when the file was re-read and every ordinate matched.

MzmlExportReport Result of an mzML export.

Field	Type	Meaning
`input`	string	The file that was read.
`output`	string	The mzML file written.
`format`	string	Always `mzml`.
`spectra_written`	integer (uint64)	Spectra written.
`points_written`	integer (uint64)	Data points (m/z-intensity pairs) written, over all spectra.
`bytes_written`	integer (uint64)	Size of the written file in bytes.
`verified`	boolean	True when the file was read back and every array, the index and the checksum agreed.
`view`	string	`primary` or `centroid`.
`sha1`	string	SHA-1 of the file up to the checksum element, as recorded in it.

NwbExportReport Output of export --to nwb.

Field	Type	Meaning
`input`	string	The input file.
`output`	string	The NWB file written.
`format`	string	Always `nwb`.
`nwb_version`	string	NWB schema version written (`nwb_version`).
`identifier`	string	`identifier` written (a UUID derived from the source and the time of writing).
`session_start_time`	string	`session_start_time` written.
`series`	array of NwbSeriesReport	One entry per `TimeSeries`, in the order written.
`samples_written`	integer (uint64)	Samples written over all series and channels.
`bytes_written`	integer (uint64)	Size of the written file in bytes.
`verified`	boolean	True when the file was re-opened and every series and sample matched.
`notes` optional	array of string	What the export assumed (e.g. a session start taken from the file's modification time).

NwbSeriesReport One TimeSeries written.

Field	Type	Meaning
`name`	string	Name under `/acquisition/`.
`trace`	integer (uint32)	Source trace index.
`sweep`	integer (uint32)	Source sweep index.
`samples`	integer (uint64)	Samples (rows of `data`).
`channels`	integer (uint32)	Channels (columns of `data`).
`channel_indices`	array of integer (uint32)	Source channel indices, in column order.
`unit` optional	string \| null	`data` unit, when the channels record one.
`rate_hz`	number (double)	`starting_time` `rate` in Hz.
`starting_time_s`	number (double)	`starting_time` in seconds.

PerImageExport Output of export --to ome-tiff --per-image.

Field	Type	Meaning
`input`	string	The file that was read.
`output`	string	The directory the files were written into.
`format`	string	Always `ome-tiff`.
`files`	array of PerImageFile	One entry per image written.
`images_skipped` optional	array of integer (uint32)	Images left out because plane files they need are missing (`--skip-incomplete`).
`verified`	boolean	True when every file was verified.

PerImageFile One file of a --per-image export.

Field	Type	Meaning
`image`	integer (uint32)	Image index in the input.
`well` optional	string \| null	Well of the image (plates only).
`field` optional	integer (uint64) \| null	Field number of the image (plates only).
`output`	string	The OME-TIFF written.
`planes_written`	integer (uint64)	Planes written.
`bytes_written`	integer (uint64)	Size of the file in bytes.
`verified`	boolean	True when every plane was read back and hashed equal to the source plane.

PyramidMode Where the lower resolutions of an export come from.

One of: "auto" | "none" | "source" | "mean"

RdmlExportReport What export --to rdml wrote.

Field	Type	Meaning
`input`	string	The input file.
`output`	string	The RDML file written.
`format`	string	Always `rdml`.
`rdml_version`	string	RDML schema version written (`1.3`).
`runs`	integer (uint32)	Runs (plates) written.
`reactions`	integer (uint64)	Reactions (`react` elements).
`data_elements`	integer (uint64)	Data elements (one per reaction × target).
`cq_values`	integer (uint64)	Cq values written.
`amplification_points`	integer (uint64)	Amplification data points (`adp`).
`melt_points`	integer (uint64)	Melt data points (`mdp`).
`samples`	integer (uint32)	Samples, targets, dyes defined.
`targets`	integer (uint32)	Targets defined.
`dyes`	integer (uint32)	Dyes defined.
`bytes_written`	integer (uint64)	Size of the file.
`verified`	boolean	The file was read back and every reaction, Cq and data point matched.
`notes`	array of string	What could not be carried over and why.

Region A rectangle of a plane, in the pixel coordinates of the resolution level it is read at.

Field	Type	Meaning
`x`	integer (uint32)	Left edge (column of the first pixel).
`y`	integer (uint32)	Top edge (row of the first pixel).
`width`	integer (uint32)	Width in pixels (at least 1).
`height`	integer (uint32)	Height in pixels (at least 1).

TableExportReport Output of export --to csv.

Field	Type	Meaning
`input`	string	The input file.
`output`	string	The CSV file written.
`format`	string	Always `csv` in this schema version.
`table`	integer (uint32)	Table index written.
`first_row`	integer (uint64)	First row written (zero-based).
`rows_written`	integer (uint64)	Data rows written.
`columns_written`	integer (uint32)	Columns written.
`header_lines`	integer (uint32)	Header lines before the data (1, or 2 with `--labels`).
`bytes_written`	integer (uint64)	Size of the written file in bytes.
`verified`	boolean	True when the written file was read back and every value parsed equal to the source.

TraceExportReport Output of export --to csv for a trace (one sweep: a time column plus one column per channel).

Field	Type	Meaning
`input`	string	The input file.
`output`	string	The CSV file written.
`format`	string	Always `csv` in this schema version.
`trace`	integer (uint32)	Trace index written.
`sweep`	integer (uint32)	Sweep index written.
`first_sample`	integer (uint64)	First sample of the sweep written (zero-based).
`samples_written`	integer (uint64)	Samples (rows) written.
`channels_written`	integer (uint32)	Signal channels written (the time column is not counted).
`bytes_written`	integer (uint64)	Size of the written file in bytes.
`verified`	boolean	True when the written file was read back and every value parsed equal to the source.

WrittenLevels Resolution levels written for one image by a tiled export.

Field	Type	Meaning
`image`	integer (uint32)	Source image index.
`source_level`	integer (uint32)	Source pyramid level the exported full resolution was read from.
`region` optional	Region \| null	Rectangle of that level that was exported (absent: all of it).
`pyramid`	PyramidMode	Where the lower levels came from: `source` (copied), `mean` (2 x 2 means) or `none`.
`sizes`	array of array of integer (uint32)	`[width, height]` of every level written, full resolution first.
`factors`	array of number (double)	Downsampling factor of every level relative to the exported full resolution (x).

export.schema.json · ExportOutput

export-attachment

Output of export --attachment.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`attachment`	AttachmentInfo	The attachment that was extracted.
`output`	string	Where the bytes were written.
`bytes_written`	integer (uint64)	Number of bytes written.
`xxh3`	string	xxh3-128 of the written bytes, 32 hex chars.
`verified`	boolean	True once the output was read back and matched.

Types used (1)

AttachmentInfo A file embedded in the container (thumbnail, label image, time stamps, ...).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based index, usable with `export --attachment #<index>`.
`name`	string	Name as stored in the container (e.g. `Thumbnail`, `Label`).
`content_type`	string	Content type as the file declares it (e.g. `JPG`, `CZI`, `CZTIMS`).
`extension`	string	Suggested file extension for the extracted bytes, without the dot.
`offset` optional	integer (uint64) \| null	Byte offset of the attachment payload in its file.
`size`	integer (uint64)	Payload size in bytes.
`extra` optional	object	Format-specific details in the reader's documented vocabulary.

export-attachment.schema.json · ExtractOutput

preview

Output of preview: what was rendered, and where it went.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`kind`	string	`image`, `trace`, `spectrum` or `plate`.
`output` optional	string \| null	The written file (CLI); absent when the preview is returned inline (MCP image content).
`encoding`	string	`png` or `jpeg`.
`width`	integer (uint32)	Image width in pixels.
`height`	integer (uint32)	Image height in pixels.
`bytes`	integer (uint64)	Size of the encoded image.
`xxh3`	string	xxh3-128 of the encoded bytes, 32 hex chars (identical across runs for the same request).
`verified`	boolean	True once a written file was read back and matched.
`image` optional	ImagePreview \| null	Present for image previews.
`trace` optional	TracePreview \| null	Present for trace previews.
`spectrum` optional	SpectrumPreview \| null	Present for spectrum previews.
`plate` optional	PlatePreview \| null	Present for plate previews.
`notes` optional	array of string	Anything the caller should know (fallbacks, caps, implied options).
`hint` optional	string \| null	What to do next with the picture (look at it; zoom with a region read off the rulers).

Types used (10)

ImagePreview Details of an image preview.

Details of an image preview.

PNG pixel (px, py) inside plot_area shows full-resolution source pixel x = source_origin.x + (px - plot_area.x) * source_per_pixel, y = source_origin.y + (py - plot_area.y) * source_per_pixel_y (left/top edges of the PNG pixel), whatever pyramid level, downsample or region was drawn; the ruler labels use the same numbers, so a region read off them can be passed straight back.

Field	Type	Meaning
`image`	integer (uint32)	Image index.
`level`	integer (uint32)	Pyramid level read (0 = full resolution).
`source_width`	integer (uint32)	Plane size at that level.
`source_height`	integer (uint32)	Plane height at that level.
`region` optional	Region \| null	The rectangle drawn, in the pixel coordinates of `level`, when a region was asked for.
`downsample`	integer (uint32)	Block size of the averaging downsample (1 = none).
`c`	array of integer (uint32)	Channels, z-planes and time points used.
`z`	array of integer (uint32)	Z indices used.
`t`	array of integer (uint32)	Time indices used.
`projection` optional	string \| null	`max-z` or `max-t` for a maximum-intensity projection.
`composite`	boolean	True when channels were blended into one colour image.
`rgb`	boolean	True when the planes are RGB (samples_per_pixel 3).
`contrast`	string	Contrast rule applied (`auto` resolved to what it did, e.g. `percentile:0.1,99.9`).
`lut`	string	`gray`, `channel-color` or `rgb`.
`channels`	array of PreviewChannel	One entry per channel drawn.
`axes` optional	boolean	True when the picture is framed by coordinate rulers (labelled in full-resolution pixels), with a scale bar when the pixel size is known.
`grid` optional	boolean	True when grid lines were drawn over the data at the ruler ticks.
`plot_area` optional	Region	The data's rectangle inside the PNG, in PNG pixels (the whole PNG without rulers).
`source_origin` optional	SourcePoint	Full-resolution source coordinate of the plot area's top-left corner.
`source_per_pixel` optional	number (double)	Full-resolution source pixels per PNG pixel, horizontally (pyramid level scale × `downsample`).
`source_per_pixel_y` optional	number (double)	Full-resolution source pixels per PNG pixel, vertically (equal to `source_per_pixel` up to the rounding of pyramid level sizes).
`full_res_region` optional	Region	The full-resolution (level 0) rectangle the plot area shows: pass it, or a part of it, back as `region` to zoom.
`scale_bar` optional	ScaleBar \| null	The scale bar drawn, when the physical pixel size is known.

PlatePreview Details of a plate heat map.

Field	Type	Meaning
`table`	integer (uint32)	Table index.
`layout`	string	`wide` (one column per well) or `long` (`well` or `row` + `column` columns).
`rows`	integer (uint32)	Plate geometry, e.g. 8 × 12.
`columns`	integer (uint32)	Plate columns (e.g. 12 for a 96-well plate).
`wells`	integer (uint32)	Wells with a finite value.
`value`	string	What each cell shows (a column name, or `mean of N rows`).
`min` optional	number (double) \| null	Colour-scale ends (dark = min, yellow = max).
`max` optional	number (double) \| null	Value shown at the yellow end of the scale.

PreviewChannel One channel of an image preview.

Field	Type	Meaning
`index`	integer (uint32)	C index.
`name` optional	string \| null	Channel name, if recorded.
`color`	string	Display colour `#RRGGBB` (`#FFFFFF` with the gray LUT).
`color_source`	string	Where the colour came from: `file` (`channels[].color`), `wavelength`, `palette` or `lut`.
`display_min`	number (double)	Sample value shown as black.
`display_max`	number (double)	Sample value shown at full brightness.

Region A rectangle of a plane, in the pixel coordinates of the resolution level it is read at.

Field	Type	Meaning
`x`	integer (uint32)	Left edge (column of the first pixel).
`y`	integer (uint32)	Top edge (row of the first pixel).
`width`	integer (uint32)	Width in pixels (at least 1).
`height`	integer (uint32)	Height in pixels (at least 1).

ScaleBar The scale bar drawn under an image preview.

Field	Type	Meaning
`length`	number (double)	Length as labelled (e.g. `50`).
`unit`	string	Unit of the label: `nm`, `µm` or `mm`.
`length_um`	number (double)	Length in µm.
`pixels`	integer (uint32)	Length in PNG pixels.

SourcePoint A point in full-resolution (level 0) source pixel coordinates.

Field	Type	Meaning
`x`	number (double)	Column (may be fractional on a downsampled pyramid level).
`y`	number (double)	Row.

SpectrumPreview Details of a mass-spectrum preview.

Field	Type	Meaning
`run`	integer (uint32)	Run index.
`index`	integer (uint64)	Zero-based spectrum index.
`scan_number`	integer (uint64)	Scan number as the instrument counts it.
`ms_level`	integer (uint32)	MS level (1 = full scan, 2 = fragment scan, ...).
`rt_s` optional	number (double) \| null	Retention time in seconds; null when the file states none.
`style`	string	`sticks` (centroided) or `profile` (a line through the points).
`point_count`	integer (uint64)	Points in the spectrum.
`x_axis`	XAxis	m/z range of the x axis.
`max_intensity` optional	number (double) \| null	Largest intensity (the top of the plot).
`precursor_mz` optional	number (double) \| null	Precursor m/z of a fragment (MS2+) scan.

TracePreview Details of a trace preview.

Field	Type	Meaning
`trace`	integer (uint32)	Trace index.
`sweep`	integer (uint32)	Sweep index.
`sample_rate_hz`	number (double)	Samples per second.
`sweep_sample_count`	integer (uint64)	Samples in the sweep.
`sample_count`	integer (uint64)	Samples drawn (from the start of the sweep).
`truncated`	boolean	True when the sweep is longer than the samples drawn.
`x_axis` optional	XAxis \| null	Label of the horizontal axis, when known.
`channels`	array of TracePreviewChannel	One panel per channel, top to bottom.

TracePreviewChannel One channel of a trace preview.

Field	Type	Meaning
`index`	integer (uint32)	Channel index.
`name`	string	Channel name.
`unit` optional	string \| null	Physical unit of the samples.
`color`	string	Line colour `#RRGGBB`.
`min` optional	number (double) \| null	Bottom and top of the panel's y axis (the channel's finite range, padded by 5 %).
`max` optional	number (double) \| null	Top of the panel's y axis.

XAxis The horizontal axis of a trace or spectrum preview (the labels at its two ends).

Field	Type	Meaning
`quantity`	string	`time`, `chemical_shift`, `mz`, `sample`, … (the reader's `extra.axis.quantity` when set).
`unit`	string	`s`, `min`, `ppm`, `m/z`, … (empty for sample indices).
`first`	number (double)	Value at the left edge.
`last`	number (double)	Value at the right edge (smaller than `first` for NMR chemical shift, which runs right to left).

preview.schema.json · PreviewOutput

stats

Output of stats.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`level` optional	integer (uint32)	Pyramid level the planes were read at (0 = full resolution); omitted when 0.
`region` optional	Region \| null	The rectangle of each plane the statistics cover (level pixel coordinates), when a region was asked for; absent = whole planes.
`select`	array of string	The selection as given (`c=0`, …); empty = every plane.
`bins`	integer (uint32)	Requested histogram bins (0 = none). Integer data with fewer distinct values in its range uses fewer, one per value.
`planes` optional	array of PlaneStats	Per-plane statistics (omitted with `--no-planes`).
`channels`	array of ChannelStats	One aggregate per image and channel.
`images`	array of ImageStats	One aggregate per image over all its selected planes.
`mip` optional	Projection \| null	Set with `--mip`: the statistics are of maximum-intensity projections along this axis (per pixel, the largest value over the selected planes); `planes[]` entries are the projections, with the projected axis's index reported as 0.

Types used (11)

ChannelStats Statistics of every selected plane of one channel.

Field	Type	Meaning
`image`	integer (uint32)	Image index.
`c`	integer (uint32)	Channel index.
`name` optional	string \| null	Channel name, if recorded.
`image_name` optional	string \| null	Name of the image (scene, series, position) the channel belongs to, if recorded.
`planes`	integer (uint64)	Number of planes aggregated.
`stats`	SampleStats	Statistics over those planes (RGB: every colour sample pooled).
`components` optional	array of ComponentStats	Multi-sample (RGB) pixels: the statistics of each colour component on its own (`components[0]` = red, `[1]` = green, `[2]` = blue).

ComponentStats Statistics of one colour component of interleaved multi-sample (RGB) pixels.

Field	Type	Meaning
`sample`	integer (uint32)	Sample index within a pixel: for RGB 0 = red, 1 = green, 2 = blue (every reader returns R, G, B order; CZI's stored B, G, R is swapped on read).
`name` optional	string \| null	`red`, `green`, `blue` (and `alpha`) for 3- and 4-sample pixels.
`stats`	SampleStats	Statistics of that component's samples only.

Histogram A histogram of the finite samples.

Field	Type	Meaning
`scale`	HistogramScale	Linear or logarithmic bin spacing.
`edges`	array of number (double)	`bins + 1` bin edges; bin `i` is `[edges[i], edges[i+1])`, the last bin includes its upper edge.
`counts`	array of integer (uint64)	Samples per bin (`bins` entries).
`nonpositive` optional	integer (uint64) \| null	Log scale only: samples ≤ 0, which have no place on a log axis.

HistogramScale Spacing of histogram bin edges.

One of: "linear" | "log"

ImageStats Statistics of every selected plane of one image (the selection aggregate).

Field	Type	Meaning
`image`	integer (uint32)	Image index.
`name` optional	string \| null	Image (scene, series, position) name, if recorded (`info` → `images[].name`).
`pixel_type`	PixelType	Sample type.
`planes`	integer (uint64)	Number of planes aggregated.
`stats`	SampleStats	Statistics over those planes.
`components` optional	array of ComponentStats	Multi-sample (RGB) pixels: the statistics of each colour component over those planes (`components[0]` = red, `[1]` = green, `[2]` = blue).

Percentiles NumPy-style percentiles of the finite samples.

Field	Type	Meaning
`p1`	number (double)	1st percentile.
`p5`	number (double)	5th percentile.
`p50`	number (double)	Median.
`p95`	number (double)	95th percentile.
`p99`	number (double)	99th percentile.

PixelType Sample type of one channel value. Names follow OME-XML PixelType values.

PlaneStats Statistics of one plane.

Field	Type	Meaning
`image`	integer (uint32)	Image index.
`level` optional	integer (uint32)	Pyramid level (0 = full resolution); omitted when 0.
`c`	integer (uint32)	Channel index.
`z`	integer (uint32)	Z index.
`t`	integer (uint32)	Time index.
`width`	integer (uint32)	Plane width in pixels.
`height`	integer (uint32)	Plane height in pixels.
`pixel_type`	PixelType	Sample type.
`stats`	SampleStats	Statistics of the plane's samples.
`components` optional	array of ComponentStats	Multi-sample (RGB) pixels: the statistics of each colour component on its own.

Projection The axis of a maximum-intensity projection (stats --mip z).

One of: "z" | "t"

Region A rectangle of a plane, in the pixel coordinates of the resolution level it is read at.

Field	Type	Meaning
`x`	integer (uint32)	Left edge (column of the first pixel).
`y`	integer (uint32)	Top edge (row of the first pixel).
`width`	integer (uint32)	Width in pixels (at least 1).
`height`	integer (uint32)	Height in pixels (at least 1).

SampleStats Summary statistics of a set of samples.

Field	Type	Meaning
`count`	integer (uint64)	Finite samples.
`non_finite`	integer (uint64)	NaN and infinite samples (excluded from everything else).
`min` optional	number (double) \| null	Absent when there are no finite samples (as are mean, std, percentiles).
`max` optional	number (double) \| null	Largest finite sample.
`mean` optional	number (double) \| null	Mean of the finite samples.
`std` optional	number (double) \| null	Population standard deviation.
`percentiles` optional	Percentiles \| null	1st, 5th, 50th, 95th and 99th percentiles.
`exact`	boolean	True when the percentiles and histogram are exact (see the module documentation).
`zero_fraction`	number (double)	Fraction of finite samples equal to 0.
`saturated_fraction` optional	number (double) \| null	Integer pixel types: fraction of samples at the saturation level (`saturation_level`): the detector's ceiling 2^bits − 1 when the file records its significant bits (16383 for 14-bit data stored as uint16), else the type's maximum (255 for uint8, 65535 for uint16, …), i.e. clipped by the detector or the digitizer.
`saturated_count` optional	integer (uint64) \| null	Integer pixel types: the number of samples at `saturation_level` (exact; use it for "how many pixels are saturated").
`saturation_level` optional	number (double) \| null	The value a sample must equal to count as saturated (integer pixel types).
`saturation_basis` optional	string \| null	Why that level: `significant_bits` (2^bits − 1 from the bit depth the file records; `saturation_source` names the field) or `pixel_type` (the type's maximum: no bit depth recorded, channels of different depths merged, or values above the recorded depth).
`saturation_source` optional	string \| null	For `significant_bits`: the `info` field the bit depth came from, e.g. `images[].extra.component_bit_count` (CZI) or `images[].extra.bits_significant`.
`histogram` optional	Histogram \| null	Present when histograms were requested (`bins` > 0).

stats.schema.json · StatsOutput

stats-wells

Output of stats --per well and MCP openreadout_stats with per: "well".

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`plate` optional	string \| null	Plate id or barcode, when recorded.
`level` optional	integer (uint32)	Pyramid level read (0 = full resolution); omitted when 0.
`select`	array of string	The selection as given; empty = every plane.
`per_field`	boolean	True when rows are per field of view.
`columns`	array of string	Column names of `rows`, in order (for tables and CSV).
`rows`	array of WellStatsRow	One row per (well, channel), or per (well, field, channel) with `per_field`, in plate order (row by row, then field, then channel).
`wells_without_data` optional	array of string	Selected wells without a single readable plane (every file missing).
`notes` optional	array of string	Things to know when reading the rows (absent planes left out, missing files skipped).

Types used (1)

WellStatsRow One tidy row of [WellStatsOutput]: the statistics of one channel over the selected planes

One tidy row of [WellStatsOutput]: the statistics of one channel over the selected planes of one well (or one field of it).

Field	Type	Meaning
`plate` optional	string \| null	Plate id or barcode, when recorded (the same on every row).
`well`	string	Well name (`C05`).
`row`	string	Row letters.
`column`	integer (uint32)	Column number, 1-based.
`image` optional	integer (uint32) \| null	Per-field rows only: the image index of the field.
`field` optional	integer (uint32) \| null	Per-field rows only: the field number as the acquisition software counts it.
`c`	integer (uint32)	Channel index.
`channel` optional	string \| null	Channel name, if recorded.
`fields`	integer (uint32)	Fields of view whose planes were read into this row.
`planes`	integer (uint64)	Planes aggregated.
`planes_missing`	integer (uint64)	Selected planes whose files are missing (skipped).
`count`	integer (uint64)	Finite samples.
`mean` optional	number (double) \| null	Mean intensity (absent when no plane was read).
`std` optional	number (double) \| null	Population standard deviation.
`min` optional	number (double) \| null	Smallest sample.
`max` optional	number (double) \| null	Largest sample.
`p1` optional	number (double) \| null	1st percentile (NumPy `linear` interpolation).
`median` optional	number (double) \| null	Median.
`p99` optional	number (double) \| null	99th percentile.
`zero_fraction` optional	number (double) \| null	Fraction of samples equal to 0.
`saturated_fraction` optional	number (double) \| null	Integer data: fraction of samples at the type's maximum (detector saturation).

stats-wells.schema.json · WellStatsOutput

trace

Output of trace: a window of one sweep of one trace.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`trace`	integer (uint32)	Trace index (see `info` → `traces[]`).
`sweep`	integer (uint32)	Sweep index.
`sweep_count`	integer (uint32)	Sweeps in the trace.
`sample_rate_hz`	number (double)	Samples per second.
`sweep_sample_count`	integer (uint64)	Samples in this sweep.
`first_sample`	integer (uint64)	First sample of the window (zero-based, within the sweep).
`sample_count`	integer (uint64)	Samples in the window (statistics cover all of them).
`start_s`	number (double)	Time of the first window sample in seconds. Single-sweep traces use the trace's own clock: `info.traces[].start_s + first_sample / sample_rate_hz` (a chromatogram's retention time, negative when acquisition began before injection; an electrophysiology recording's clock). Multi-sweep traces are timed from the start of the sweep (`first_sample / sample_rate_hz`; `sweep_start_s` places the sweep in the recording). Irregularly sampled traces (`sample_rate_hz` 0 with a `time` channel) report that channel's first window value; traces without a time base (spectra) report 0.
`sweep_start_s` optional	number (double) \| null	Time of the sweep's first sample on the recording clock, seconds, when the file records it (`info.traces[].start_s` for a single sweep, `extra.sweep_starts_s[sweep]` for multi-sweep traces).
`channels`	array of TraceChannelSlice	One entry per requested channel.
`truncated`	boolean	True when fewer samples are returned than the window holds.
`axis` optional	any	The trace's abscissa (`info` → `traces[].extra.axis`: `{quantity, unit, first, step, …}`), e.g. the ppm axis of an NMR spectrum or a chromatogram's retention time in minutes; sample `i` of the sweep is at `first + i * step`. For a time axis this agrees with `start_s` and `sample_rate_hz` (`first` = `start_s` at `first_sample` 0, `step` = 1 / `sample_rate_hz`, in `unit`). Irregular axes (`irregular: true`) name the channel holding each sample's abscissa instead.
`x_range` optional	array of number (double) \| null	The axis window asked for (`x_range`, low to high): axis units, or seconds for signals without an axis. `first_sample`/`sample_count` are the samples inside it.

Types used (2)

TraceChannelSlice One channel of a TraceSlice.

Field	Type	Meaning
`index`	integer (uint32)	Channel index.
`name`	string	Channel name.
`unit` optional	string \| null	Physical unit of the samples.
`stats`	TraceStats	Statistics over the whole window.
`samples`	array of number (double)	The first `max_samples` samples of the window, scaled to `unit`.

TraceStats Summary statistics of one channel over the requested window.

Field	Type	Meaning
`count`	integer (uint64)	Samples in the window.
`finite`	integer (uint64)	Finite samples (NaN/inf are skipped by min/max/mean/std).
`min` optional	number (double) \| null	Smallest finite sample.
`max` optional	number (double) \| null	Largest finite sample.
`mean` optional	number (double) \| null	Mean of the finite samples.
`std` optional	number (double) \| null	Population standard deviation.
`argmin` optional	integer (uint64) \| null	Sample index of the minimum, counted from the start of the sweep (not of the window: the index within `samples` is `argmin - first_sample`).
`argmax` optional	integer (uint64) \| null	Sample index of the maximum, counted from the start of the sweep (not of the window: the index within `samples` is `argmax - first_sample`).
`argmin_time_s` optional	number (double) \| null	Time of the minimum in seconds, on the same clock as the slice's `start_s`. Absent when the trace has no time base (a spectrum; see `argmin_axis_value`).
`argmax_time_s` optional	number (double) \| null	Time of the maximum in seconds, on the same clock as the slice's `start_s` (for a chromatogram: the retention time of the tallest point, in seconds).
`argmin_axis_value` optional	number (double) \| null	Position of the minimum on the slice's `axis`, in `axis.unit` (retention time in minutes, chemical shift in ppm, wavenumber, …). Present only when the slice has an `axis`.
`argmax_axis_value` optional	number (double) \| null	Position of the maximum on the slice's `axis`, in `axis.unit`: `axis.first + argmax * axis.step`, or the abscissa channel's value for an irregular axis.

trace.schema.json · TraceSlice

table

A slice of a table as rows, for JSON consumers (openreadout_table).

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`table`	integer (uint32)	Table index (see `info` → `tables[]`).
`first_row`	integer (uint64)	Zero-based index of the first row returned.
`total_rows`	integer (uint64)	Rows in the whole table.
`columns`	array of string	Column names (FCS `$PnN`).
`labels`	array of string \| null	Column labels (FCS `$PnS`), `null` where absent.
`rows`	array of array of number (double)	Row-major values; `rows[r][c]`. Non-finite values serialize as `null`.
`truncated`	boolean	True when more rows follow the returned slice.
`processing` optional	TableProcessing \| null	Present when the values were processed (FCS scale values, compensation, transforms, population membership columns); absent for raw values.
`filter` optional	TableFilterSummary \| null	Present with `--where`/`--count`: the row conditions and how many rows of the whole table meet them. `rows`, `first_row` and `truncated` then page through the matching rows.

Types used (5)

AppliedTransform A transform applied to one table column.

Field	Type	Meaning
`parameter`	string	Column (`$PnN`).
`kind`	string	Transform kind.
`parameters`	map of number (double)	Its parameters.

CompensationSummary A compensation or unmixing matrix.

Field	Type	Meaning
`name`	string	Matrix name or id; `$SPILLOVER`/`$SPILL`/`SPILL` for the FCS file's own.
`source`	string	Where it comes from: `workspace`, `gating-ml`, `fcs` or `command-line`.
`detectors`	array of string	Detectors (columns), `$PnN`.
`fluorochromes`	array of string	Rows: fluorochromes, or the detectors that receive the unmixed values.
`matrix`	array of array of number (double)	Row-major coefficients (spillover fractions).
`spectral`	boolean	More detectors than rows: unmixed by ordinary least squares.
`used`	boolean	Whether a gate (or the table) used it.

GateColumn A population membership column.

Field	Type	Meaning
`column`	string	Column name in the table (`gate:<path>`).
`population`	string	Population path.
`gating_file`	string	Path of the workspace or Gating-ML file that defines the population.
`count_in_rows`	integer (uint64)	Members among the returned rows.

TableFilterSummary Rows of a whole table that meet every condition (table --where, --count).

Field	Type	Meaning
`conditions`	array of string	The conditions as parsed (`FITC-A > 1000`), all of which a row must meet. Empty with `--count` alone (every row counts).
`matched_rows`	integer (uint64)	Rows of the whole table that meet every condition (not only the returned page).
`total_rows`	integer (uint64)	Rows in the whole table.
`percent`	number (double)	`matched_rows / total_rows × 100` (0 for an empty table).
`values`	string	The values the conditions were tested on: `raw` (as stored) or `processed` (FCS scale values after compensation/transforms; see `processing`).

TableProcessing What table did to the raw values before returning them.

Field	Type	Meaning
`scale`	array of string	Channel-to-scale conversions applied (`$PnE`, `$PnG`, `$TIMESTEP`); every processed table starts from scale values.
`compensation` optional	CompensationSummary \| null	The compensation applied, if any.
`transforms`	array of AppliedTransform	Transforms applied, by parameter.
`gates`	array of GateColumn	Membership columns appended (1 = in the population, 0 = not).

table.schema.json · TableSlice

spectra

Output of spectra (scan list): the matching scans of one run, one page of them listed.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`run`	integer (uint32)	Run index.
`scan_count`	integer (uint64)	Spectra in the run.
`source`	string	`headers` when the reader listed scan headers without decoding peaks, `spectra` when every spectrum had to be decoded to list it.
`filter` optional	ScanFilter	The conditions applied (omitted when every scan is listed).
`matched`	integer (uint64)	Scans matching the conditions (all of them are counted, not only the page listed).
`offset`	integer (uint64)	Position of the first listed scan among the matching ones (0-based; `--offset`).
`returned`	integer (uint64)	Number of scans listed.
`truncated`	boolean	True when more matching scans follow the page (`offset + returned < matched`).
`ms_level_counts`	map of integer (uint64)	Counts of the matching scans per MS level (`"1"`, `"2"`, ...).
`rt_range_s` optional	array of number (double) \| null	Retention-time range of the matching scans in seconds.
`scans`	array of ScanHeader	The listed scans, in spectrum-index order.

Types used (2)

ScanFilter Which scans to list. Every condition that is set must hold.

Field	Type	Meaning
`ms_level` optional	integer (uint32) \| null	Only this MS level (1 = full scans, 2 = MS/MS).
`polarity` optional	string \| null	Only `positive` or `negative` scans.
`rt_min_s` optional	number (double) \| null	Retention time at least this many seconds.
`rt_max_s` optional	number (double) \| null	Retention time at most this many seconds.
`precursor_mz` optional	number (double) \| null	Precursor m/z near this value (within `precursor_tol_mz`, or `precursor_tol_ppm`).
`precursor_tol_mz` optional	number (double) \| null	Absolute precursor tolerance in m/z (default 0.01 when neither tolerance is given).
`precursor_tol_ppm` optional	number (double) \| null	Relative precursor tolerance in ppm.
`charge` optional	integer (int32) \| null	Only precursors of this charge state.
`activation` optional	string \| null	Only this activation (`HCD`, `CID`, ...; case-insensitive).
`filter_contains` optional	string \| null	Only scans whose filter string contains this text (case-insensitive).

ScanHeader Everything about one spectrum except its peaks.

Field	Type	Meaning
`index`	integer (uint64)	Zero-based spectrum index within its run (`spectra --index`).
`scan_number`	integer (uint64)	Scan number as the instrument counts it (`spectra --scan`).
`native_id` optional	string \| null	The spectrum's identifier in its file (mzML `id`), when it has one.
`ms_level`	integer (uint32)	MS level: 1 for a full scan, 2 for a fragment (MS/MS) scan, and so on.
`rt_s` optional	number (double) \| null	Retention time in seconds; null when the file states none for this scan (such a scan never matches a retention-time filter).
`polarity`	string	`positive`, `negative` or `unknown`.
`centroided`	boolean	True when the stored peaks are centroids.
`precursor_mz` optional	number (double) \| null	m/z of the isolated precursor ion (MS2 and above).
`precursor_charge` optional	integer (int32) \| null	Charge state of the precursor, when the instrument determined it.
`precursor_intensity` optional	number (double) \| null	Intensity of the selected precursor ion, when recorded.
`isolation_window_mz` optional	array of number (double) \| null	Precursor isolation window `[lower, upper]` in m/z.
`activation` optional	string \| null	Dissociation method (`CID`, `HCD`, `ETD`, ...), upper case.
`collision_energy` optional	number (double) \| null	Collision energy as recorded.
`inverse_reduced_mobility` optional	number (double) \| null	Ion mobility 1/K0 in V·s/cm², when the scan or precursor has one.
`scan_filter` optional	string \| null	Instrument scan filter or scan description (e.g. Thermo `FTMS + p ESI d Full ms2 …`).
`scan_window_mz` optional	array of number (double) \| null	Scan (acquisition) window `[lower, upper]` in m/z.
`total_ion_current` optional	number (double) \| null	Total ion current as the file records it for the scan (an index or header value; not recomputed from the peaks). Absent when the file keeps none.
`base_peak_mz` optional	number (double) \| null	Base-peak m/z as the file records it for the scan.
`base_peak_intensity` optional	number (double) \| null	Base-peak intensity as the file records it for the scan.
`point_count` optional	integer (uint64) \| null	Number of stored points (peaks or profile samples), when the header records it.
`extra` optional	object	Format-specific scan metadata in the reader's documented vocabulary.

spectra.schema.json · ScanList

spectrum

Output of spectra --scan/--index: one spectrum with its arrays.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`run`	integer (uint32)	Run index the spectrum belongs to.
`view`	string	`primary` (profile when recorded) or `centroid` (the instrument's centroid list).
`point_count`	integer (uint64)	Number of points in the full spectrum (the arrays may be shortened by `max_points`).
`truncated`	boolean	True when `mz`/`intensity` were shortened to `max_points`.
`spectrum`	Spectrum	The spectrum, with its arrays.

Types used (1)

Spectrum One mass spectrum.

Field	Type	Meaning
`index`	integer (uint64)	Zero-based spectrum index within its run.
`scan_number`	integer (uint64)	Scan number as the instrument counts it (1-based in most formats).
`ms_level`	integer (uint32)	MS level: 1 for a full scan, 2 for a fragment (MS/MS) scan, and so on.
`rt_s` optional	number (double) \| null	Retention time in seconds; null when the file states none for this spectrum (never an invented 0).
`polarity`	string	`positive`, `negative` or `unknown`.
`centroided`	boolean	True when the peaks are centroids (one point per peak) rather than a sampled profile.
`precursor_mz` optional	number (double) \| null	m/z of the precursor ion that was isolated and fragmented (MS2 and above).
`precursor_charge` optional	integer (int32) \| null	Charge state of the precursor, when the instrument determined it.
`scan_filter` optional	string \| null	Instrument scan filter or scan description string (e.g. Thermo `FTMS + p ESI Full ms`).
`total_ion_current` optional	number (double) \| null	Sum of all intensities in the spectrum (TIC).
`native_id` optional	string \| null	The spectrum's identifier in its file (mzML `id`, e.g. `controllerType=0 controllerNumber=1 scan=17`).
`base_peak_mz` optional	number (double) \| null	m/z of the most intense peak.
`base_peak_intensity` optional	number (double) \| null	Intensity of the most intense peak.
`precursor_intensity` optional	number (double) \| null	Intensity of the selected precursor ion, when recorded.
`isolation_window_mz` optional	array of number (double) \| null	Precursor isolation window `[lower, upper]` in m/z.
`activation` optional	string \| null	Dissociation method: `CID`, `HCD`, `ETD`, `ECD`, `ETHCD`, `UVPD`, ... (upper case).
`collision_energy` optional	number (double) \| null	Collision energy as recorded (usually eV, or % normalized for Thermo `@hcd35.00`).
`inverse_reduced_mobility` optional	number (double) \| null	Ion mobility of the precursor or scan, as inverse reduced mobility 1/K0 in V·s/cm².
`scan_window_mz` optional	array of number (double) \| null	Scan (acquisition) window `[lower, upper]` in m/z.
`extra` optional	object	Format-specific scan metadata in the reader's documented vocabulary.
`mz`	array of number (double)	Mass-to-charge ratios of the points, ascending.
`intensity`	array of number (float)	Intensity of each point (same length as `mz`).

spectrum.schema.json · SpectrumOutput

chromatogram

Output of analyze chromatogram.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`run` optional	integer (uint32) \| null	Spectra run used, when any chromatogram was computed from spectra.
`spectra_read`	integer (uint64)	Spectra decoded.
`chromatograms`	array of Chromatogram	One entry per requested chromatogram.
`output` optional	string \| null	File written (`-o`), when any.
`notes` optional	array of string	Anything the caller should know.

Types used (1)

Chromatogram One chromatogram: retention times (minutes) and intensities, with how they were obtained

One chromatogram: retention times (minutes) and intensities, with how they were obtained and a summary.

Field	Type	Meaning
`label`	string	Short label, e.g. `TIC`, `XIC 301.1410 ±10 ppm`, `SRM 279.2 > 179.2`, `DAD1 A`.
`kind`	string	`tic`, `bpc`, `xic`, `srm` or `trace`.
`source`	string	Where the points come from: `spectra` (computed from the mass spectra), `trace N` (a stored chromatogram or detector signal) or `table N` (an MRM table column).
`mz` optional	number (double) \| null	XIC target m/z.
`mz_window` optional	array of number (double) \| null	XIC window `[low, high]` m/z.
`mz_range` optional	array of number (double) \| null	TIC/BPC m/z range.
`precursor_mz` optional	number (double) \| null	SRM: the precursor (Q1) m/z matched in the file.
`product_mz` optional	number (double) \| null	SRM: the product (Q3) m/z matched in the file.
`ms_level` optional	integer (uint32) \| null	MS level of the scans used.
`polarity` optional	string \| null	Polarity filter applied.
`scan_filter` optional	string \| null	Scan-filter text required.
`aggregation` optional	string \| null	`sum` or `max` (XIC).
`centroid_scans` optional	integer (uint64) \| null	Scans read as centroids.
`profile_scans` optional	integer (uint64) \| null	Scans read as profiles (their points inside the window are summed).
`intensity_source` optional	string \| null	TIC/BPC: points from the scan's recorded value (`recorded`), from its points (`computed`), or both (`mixed`).
`intensity_unit` optional	string \| null	Unit of `intensity` (`counts` for mass spectra, the detector's unit for traces).
`points`	integer (uint64)	Points in the chromatogram.
`apex_rt_min` optional	number (double) \| null	Retention time of the most intense point, minutes.
`apex_intensity` optional	number (double) \| null	Intensity of the most intense point.
`integral` optional	number (double) \| null	Trapezoidal integral of the whole chromatogram (no baseline), intensity × minutes.
`rt_min`	array of number (double)	Retention times, minutes (ascending).
`intensity`	array of number (double)	Intensities.
`decimated` optional	boolean	True when `rt_min`/`intensity` were thinned to `max_points` (the most intense point of each of `max_points` equal slices is kept); the summary covers every point.
`notes` optional	array of string	Anything the caller should know.

chromatogram.schema.json · ChromatogramOutput

peaks

Output of analyze peaks.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input file.
`chromatograms`	array of ChromatogramPeaks	One entry per analysed chromatogram.
`compounds` optional	array of CompoundResult	One row per compound of the compound list.
`spectra` optional	array of SpectrumBands	Spectra (traces whose axis is not time: wavenumber, wavelength, ppm, …): bands and integrated regions, one entry per analysed spectrum.
`outputs` optional	array of string	Files written (`-o`, `--plot`).
`notes` optional	array of string	Anything the caller should know.

Types used (9)

Band One detected band.

Field	Type	Meaning
`number`	integer (uint32)	1-based band number in order of increasing x.
`x`	number (double)	Apex position (vertex of the parabola through the three highest smoothed points), axis units.
`start`	number (double)	Band start, axis units.
`end`	number (double)	Band end, axis units.
`height`	number (double)	Height above the baseline (depth below it when bands are minima), signal units.
`area`	number (double)	Area above the baseline (below it when bands are minima), signal units × axis units.
`area_percent`	number (double)	Share of the summed area of all bands of the spectrum, %.
`centroid` optional	number (double) \| null	(signal − baseline)-weighted mean position.
`width_half` optional	number (double) \| null	Full width at half height, axis units.
`snr` optional	number (double) \| null	Height / noise σ.
`points`	integer (uint32)	Samples from start to end.
`baseline_code`	string	How each end meets the baseline (as `analyze peaks`: `B`, `V`, `T`).
`baseline_start`	number (double)	Baseline at the start, signal units.
`baseline_end`	number (double)	Baseline at the end, signal units.
`baseline_reason` optional	string \| null	`auto` baseline: why the baseline was drawn this way (as `analyze peaks`).

BandMethod How the bands were found.

Field	Type	Meaning
`smoothing`	string	`savitzky_golay_quadratic` or `none`.
`smooth_window_points`	integer (uint32)	Smoothing window, points (1 = none).
`noise`	number (double)	Noise σ, signal units.
`noise_method`	string	How the noise was estimated.
`min_snr`	number (double)	Detection threshold, S/N.
`min_height` optional	number (double) \| null	Detection threshold, signal units.
`min_width` optional	number (double) \| null	Smallest width at half height, axis units.
`baseline`	string	Baseline under detected bands: `auto`, `drop`, `valley` or `tangent`.
`region_baseline`	string	Baseline under regions: `linear` or `none`.
`integration`	string	`trapezoid`.

ChromatogramPeaks Peaks of one chromatogram.

Field	Type	Meaning
`label`	string	Chromatogram label (see `analyze chromatogram`).
`kind`	string	`tic`, `bpc`, `xic`, `srm` or `trace`.
`source`	string	`spectra`, `trace N` or `table N`.
`mz` optional	number (double) \| null	XIC m/z.
`mz_window` optional	array of number (double) \| null	XIC window.
`precursor_mz` optional	number (double) \| null	SRM precursor matched.
`product_mz` optional	number (double) \| null	SRM product matched.
`intensity_unit` optional	string \| null	Signal unit.
`area_unit`	string	Unit of peak areas, e.g. `mAU·min`.
`points`	integer (uint64)	Samples in the chromatogram.
`method`	PeakMethod	How the peaks were found.
`peak_count`	integer (uint32)	Peaks found.
`total_area`	number (double)	Summed area.
`main_peak` optional	integer (uint32) \| null	Number of the largest peak.
`main_peak_area_percent` optional	number (double) \| null	Its area % (purity by area normalization).
`peaks`	array of Peak	The peak table.
`picked` optional	PickedPeak \| null	The expected peak (`--rt`).
`manual` optional	array of Peak	Manual integrations (`--integrate`), in request order.
`notes` optional	array of string	Anything the caller should know.

CompoundResult One result row: a compound in one file.

Field	Type	Meaning
`path`	string	The input file.
`compound`	string	Compound name.
`chromatogram`	string	Label of the chromatogram it was measured on.
`expected_rt_min` optional	number (double) \| null	Expected retention time, minutes.
`rt_window_min` optional	number (double) \| null	Window half-width, minutes.
`found`	boolean	True when a peak was found in the window.
`rt_min` optional	number (double) \| null	Apex retention time, minutes.
`rt_shift_min` optional	number (double) \| null	Apex − expected retention time, minutes.
`area` optional	number (double) \| null	Peak area (signal × `area_time_unit` of the method).
`height` optional	number (double) \| null	Peak height above the baseline.
`snr` optional	number (double) \| null	Height / noise σ.
`width_half_min` optional	number (double) \| null	Width at half height, minutes.
`tailing_factor` optional	number (double) \| null	USP tailing factor.
`start_min` optional	number (double) \| null	Integration start, minutes.
`end_min` optional	number (double) \| null	Integration end, minutes.
`baseline_code` optional	string \| null	Baseline code of the peak (`BB`, `BV`, …).
`area_percent` optional	number (double) \| null	Area % of the peak within its chromatogram.
`area_unit` optional	string \| null	Unit of `area`, e.g. `counts·min`, `mAU·s`.
`note` optional	string \| null	Why nothing was found, or anything else worth knowing.

Peak One integrated peak (a flat record: one row of a peak table).

Field	Type	Meaning
`number`	integer (uint32)	1-based peak number in retention-time order.
`rt_min`	number (double)	Retention time of the apex, minutes.
`start_min`	number (double)	Peak start (integration start), minutes.
`end_min`	number (double)	Peak end (integration end), minutes.
`height`	number (double)	Height of the apex above the baseline, signal units.
`area`	number (double)	Area above the baseline between start and end, signal units × `area_time_unit`.
`area_percent`	number (double)	Share of the summed area of all peaks in the table, %.
`width_half_min` optional	number (double) \| null	Width at half height, minutes (absent when the signal does not fall to half height before a drop line).
`width_10pct_min` optional	number (double) \| null	Width at 10 % height, minutes.
`width_5pct_min` optional	number (double) \| null	Width at 5 % height, minutes.
`width_base_min`	number (double)	End − start, minutes.
`tailing_factor` optional	number (double) \| null	USP tailing factor `W₀.₀₅ / 2f` (f: apex to the leading edge at 5 % height).
`asymmetry_factor` optional	number (double) \| null	Asymmetry factor `b/a` at 10 % height (a: leading half-width, b: trailing half-width).
`plates` optional	number (double) \| null	Theoretical plates, half-height method `5.54 (t_R / W½)²` (t_R from time zero).
`resolution` optional	number (double) \| null	Resolution to the previous peak, `1.18 (t₂ − t₁) / (W½₁ + W½₂)`.
`snr` optional	number (double) \| null	Height / noise σ (absent when the noise is 0).
`points`	integer (uint32)	Samples from start to end.
`baseline_code`	string	How each end meets the baseline: `B` baseline, `V` valley (drop line), `T` tangent skim, `M` manual (given boundaries); e.g. `BB`, `BV`, `VB`, `TT`.
`baseline_start`	number (double)	Baseline value at the start, signal units.
`baseline_end`	number (double)	Baseline value at the end, signal units.
`baseline_reason` optional	string \| null	`auto` baseline: why the baseline was drawn this way — `sloped_background` (an end was placed where the peak meets a sloped or drifting background), `drop_line` (fused with a neighbour: common baseline, vertical drop line at the valley), `baseline_penetration` (split from a neighbour where the signal dips below their common baseline), `isolated` (both ends on the baseline). The first that applies.

PeakMethod The method that produced a peak table, with every parameter actually used.

Field	Type	Meaning
`smoothing`	string	`savitzky_golay_quadratic` or `none`.
`smooth_window_points`	integer (uint32)	Smoothing window in points (1 = none).
`smooth_auto`	boolean	True when the window was chosen automatically.
`characteristic_width_points` optional	number (double) \| null	Median width at half height of the most prominent maxima, points (drives the automatic smoothing and baseline windows).
`noise`	number (double)	Noise σ, signal units.
`noise_method`	string	`segment_rms`, `segment_rms_nonzero`, `mad_first_difference`, `user` or `none`.
`min_snr`	number (double)	Detection threshold, S/N.
`min_height` optional	number (double) \| null	Detection threshold, signal units.
`min_width_min` optional	number (double) \| null	Smallest width at half height, minutes.
`min_points`	integer (uint32)	Fewest samples per peak.
`baseline`	string	`drop`, `valley` or `tangent`.
`skim_ratio` optional	number (double) \| null	`tangent` skim ratio.
`baseline_window_points`	integer (uint32)	Window of the running baseline, points.
`slope_noise` optional	number (double) \| null	`auto`: noise of the smoothed signal's derivative, signal units per minute (flanks end below [`AUTO_END_SLOPE_NOISE`] times it).
`look_ahead_points` optional	integer (uint32) \| null	`auto`: how far a flat stretch must go on without a valley to end a peak, points.
`rt_range_min` optional	array of number (double) \| null	Retention-time range searched, minutes.
`integration`	string	`trapezoid`.
`area_time_unit`	string	Time unit of `area`: `min` or `s`.
`points`	integer (uint64)	Samples analysed.

PickedPeak The expected peak of a chromatogram (--rt/--window).

Field	Type	Meaning
`expected_rt_min`	number (double)	Expected retention time, minutes.
`rt_window_min`	number (double)	Window half-width, minutes.
`rule`	string	`largest` or `nearest`.
`peak` optional	Peak \| null	The peak, when one has its apex in the window.

Region One integrated region of a spectrum.

Field	Type	Meaning
`number`	integer (uint32)	1-based region number in request order.
`from`	number (double)	Lower end asked for, axis units.
`to`	number (double)	Upper end asked for, axis units.
`x_first`	number (double)	Axis value of the first sample used.
`x_last`	number (double)	Axis value of the last sample used.
`points`	integer (uint32)	Samples used.
`baseline`	string	`linear` or `none`.
`baseline_start`	number (double)	Baseline at `x_first`, signal units.
`baseline_end`	number (double)	Baseline at `x_last`, signal units.
`area`	number (double)	Trapezoidal integral of (signal − baseline), signal units × axis units.
`area_no_baseline`	number (double)	Trapezoidal integral of the signal itself.
`max_x`	number (double)	Axis value of the region maximum (the sample of largest signal − baseline; of largest baseline − signal when bands are minima).
`max_height`	number (double)	Height of the maximum above the baseline (depth below it when bands are minima).
`max_value`	number (double)	Signal at the maximum.
`centroid` optional	number (double) \| null	(signal − baseline)-weighted mean axis value (absent when that integral is not positive).
`peaks` optional	array of integer (uint32)	Numbers of the detected bands whose apex lies in the region.
`peaks_area`	number (double)	Summed area of those bands (each above its own detection baseline).

SpectrumBands Bands and regions of one spectrum.

Field	Type	Meaning
`label`	string	Label (trace name).
`kind`	string	Always `spectrum`.
`source`	string	`trace N sweep S`.
`trace`	integer (uint32)	Trace index.
`sweep`	integer (uint32)	Sweep index.
`channel`	integer (uint32)	Channel of the signal.
`x_quantity`	string	Axis quantity: `wavenumber`, `raman_shift`, `wavelength`, `chemical_shift`, `points`, ….
`x_unit` optional	string \| null	Axis unit (`1/cm`, `nm`, `ppm`, …).
`y_quantity`	string	Signal quantity (`absorbance`, `intensity`, `transmittance`, …).
`intensity_unit` optional	string \| null	Signal unit.
`area_unit`	string	Unit of areas: signal unit (or quantity) × axis unit.
`points`	integer (uint64)	Samples in the spectrum.
`x_min`	number (double)	Smallest axis value.
`x_max`	number (double)	Largest axis value.
`bands_are_minima` optional	boolean	Bands are minima (transmittance, reflectance): detected on the negated signal.
`method`	BandMethod	How bands were found.
`peak_count`	integer (uint32)	Bands listed.
`peaks`	array of Band	Detected bands (with regions: only those with the apex in one), in order of x.
`regions` optional	array of Region	Integrated regions, in request order.
`notes` optional	array of string	Anything the caller should know.

peaks.schema.json · PeaksOutput

assay

openreadout analyze assay … --json data.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id of the input (`plate`, or `long-csv`).
`analysis`	string	The analysis run (`wells`, `curve`, `dose-response`, `kinetics`, `growth`, `qc`).
`table`	integer (uint32)	Table (plate) index.
`plate` optional	string \| null	Plate (table) name.
`read`	ReadSummary	The read analysed.
`reduce` optional	string \| null	How kinetic time courses were reduced to one value per well (endpoint analyses).
`layout`	LayoutSummary	Where the layout came from and what it assigns.
`blank` optional	BlankSummary \| null	Blank subtraction applied.
`outliers`	OutlierSummary	Outlier rule and flagged wells.
`wells` optional	array of WellRow	One row per well.
`samples` optional	array of SampleRow	One row per replicate group (sample, standard level, control, dose).
`curve` optional	CurveReport \| null	Standard-curve fit report (`curve`).
`compounds` optional	array of CompoundRow	One row per compound (`dose-response`).
`kinetics` optional	array of KineticRow	One row per well (`kinetics`).
`growth` optional	array of GrowthRow	One row per well (`growth`).
`quality` optional	QualityReport \| null	Assay quality from control wells (whenever positive and negative controls exist).
`written` optional	array of string	Files written (`--csv`, `--preview`).
`notes` optional	array of string	What was assumed or left out.
`warnings` optional	array of string	What may be wrong with the layout: role names read as samples, controls of unknown sign, role-map entries that matched no well.

Types used (15)

BlankSummary Blank subtraction applied.

Field	Type	Meaning
`method`	string	`mean` or `median`.
`wells`	array of string	Blank wells used.
`n`	integer (uint)	Number of blank wells used.
`value`	number (double)	The value subtracted (endpoint), or its mean over time points (kinetic: subtracted per time point).
`sd` optional	number (double) \| null	SD of the blank wells (endpoint).
`per_time_point` optional	boolean	Whether the blank was subtracted per time point.

CompoundRow Dose-response of one compound.

Field	Type	Meaning
`compound`	string	Compound name.
`kind`	string	`IC50` (response falls with dose) or `EC50`.
`ec50` optional	number (double) \| null	Concentration at the curve's midpoint (the 4PL/5PL parameter c).
`ec50_se` optional	number (double) \| null	Standard error of `ec50` (Wald, delta method).
`ec50_ci_low` optional	number (double) \| null	Lower confidence limit of `ec50`, from ln(c) ± t·SE(ln c).
`ec50_ci_high` optional	number (double) \| null	Upper confidence limit of `ec50`.
`log10_ec50` optional	number (double) \| null	log10 of `ec50`.
`absolute_ec50` optional	number (double) \| null	Concentration where the fitted curve crosses 50 % effect (`normalize: controls`).
`hill_slope` optional	number (double) \| null	Hill slope, GraphPad sign convention: positive when the response rises with dose.
`top` optional	number (double) \| null	The upper plateau: max(a, d).
`bottom` optional	number (double) \| null	The lower plateau: min(a, d).
`response_at_zero` optional	number (double) \| null	Response at zero dose (a).
`response_at_infinity` optional	number (double) \| null	Response at infinite dose (d).
`n_concentrations`	integer (uint)	Doses (distinct concentrations).
`min_concentration`	number (double)	Lowest and highest dose tested.
`max_concentration`	number (double)	Highest dose tested.
`extrapolated` optional	boolean	`ec50` lies outside the tested doses.
`fit` optional	FitReport \| null	The fit.
`error` optional	string \| null	Why no fit was made.

CurvePoint One point of a fit.

Field	Type	Meaning
`label`	string	Well (replicate fits) or group (fits on means).
`x`	number (double)	Concentration.
`y`	number (double)	Response.
`fitted`	number (double)	Fitted response.
`residual`	number (double)	y − fitted.

CurveReport Standard-curve report.

Field	Type	Meaning
`fit`	FitReport	The fit.
`fit_on`	string	`replicates` or `means`.
`range_low`	number (double)	Lowest standard concentration.
`range_high`	number (double)	Highest standard concentration.
`lloq` optional	number (double) \| null	Lower limit of quantification.
`uloq` optional	number (double) \| null	Upper limit of quantification.
`loq_rule`	string	How LLOQ/ULOQ were set.
`concentration_unit` optional	string \| null	Unit of the concentrations, when the layout states one.

FitReport A fitted curve.

Field	Type	Meaning
`model`	string	`linear`, `4pl`, `5pl`.
`formula`	string	The formula in the parameter names.
`weighting`	string	`none`, `1/y`, `1/y2`, `1/x`, `1/x2`.
`parameters`	array of ParamRow	Parameters with standard errors and confidence limits.
`n_points`	integer (uint)	Points fitted.
`n_levels`	integer (uint)	Distinct concentrations.
`df`	integer (uint)	Residual degrees of freedom.
`r_squared`	number (double)	1 − SSE/SST.
`residual_se` optional	number (double) \| null	Residual standard error √(SSE/df).
`sse`	number (double)	Weighted sum of squared residuals.
`converged`	boolean	Whether the optimiser converged.
`iterations`	integer (uint)	Optimiser iterations.
`confidence`	number (double)	Confidence level of the limits.
`direction`	string	`increasing` or `decreasing` response with concentration.
`points`	array of CurvePoint	The points with fitted values and residuals.

GroupStats Statistics of a group of control wells.

Field	Type	Meaning
`wells`	array of string	Wells used.
`n`	integer (uint)	Count.
`mean`	number (double)	Mean.
`sd` optional	number (double) \| null	Sample SD.
`cv_percent` optional	number (double) \| null	CV %.
`min`	number (double)	Smallest value.
`max`	number (double)	Largest value.

GrowthRow Growth metrics of one well.

Field	Type	Meaning
`well`	string	Well name.
`role`	string	Role, or `unassigned`.
`sample` optional	string \| null	Sample name.
`n_points`	integer (uint)	Time points used.
`background` optional	number (double) \| null	The well's own minimum, subtracted as background when the layout has no blank wells (growthcurver's default); absent when blanks were subtracted or subtraction is off.
`window`	integer (uint)	Points per window of the log-scale fit.
`threshold`	number (double)	Values at or below this were left out of the log-scale fit.
`growth_rate_per_h` optional	number (double) \| null	Maximum specific growth rate µmax (per hour).
`doubling_time_h` optional	number (double) \| null	ln 2 / µmax, hours.
`doubling_time_min` optional	number (double) \| null	ln 2 / µmax, minutes.
`exp_phase_start_s` optional	number (double) \| null	First time of the exponential phase (s).
`exp_phase_end_s` optional	number (double) \| null	Last time of the exponential phase (s).
`exp_r_squared` optional	number (double) \| null	r² of ln(value) against time in the exponential phase.
`lag_time_s` optional	number (double) \| null	Lag time (s).
`max_value`	number (double)	Largest value.
`time_to_max_s`	number (double)	Time of the largest value (s).
`auc_h`	number (double)	Trapezoidal area under the curve (value × h).
`logistic_k` optional	number (double) \| null	Logistic fit: carrying capacity K.
`logistic_n0` optional	number (double) \| null	Logistic fit: N0 at the first time point.
`logistic_r_per_h` optional	number (double) \| null	Logistic fit: r (per hour).
`logistic_doubling_time_h` optional	number (double) \| null	Logistic fit: ln 2 / r (hours).
`logistic_t_mid_s` optional	number (double) \| null	Logistic fit: inflection time (s).
`logistic_sigma` optional	number (double) \| null	Logistic fit: residual SD.

KineticRow Kinetic metrics of one well.

Field	Type	Meaning
`well`	string	Well name.
`role`	string	Role, or `unassigned`.
`sample` optional	string \| null	Sample name.
`n_points`	integer (uint)	Time points used.
`window`	integer (uint)	Points per window.
`max_slope_per_min`	number (double)	Largest windowed slope, value units per minute (Vmax).
`max_slope_per_s`	number (double)	The same per second.
`max_slope_r_squared`	number (double)	r² of the max-slope window.
`time_at_max_slope_s`	number (double)	Mean time of the max-slope window (s).
`window_start_s`	number (double)	First time of the max-slope window (s).
`window_end_s`	number (double)	Last time of the max-slope window (s).
`lag_time_s` optional	number (double) \| null	Lag time (s).
`mean_slope_per_min`	number (double)	Least-squares slope over all points, value units per minute.
`mean_slope_r_squared`	number (double)	r² of the all-points line.
`max_value`	number (double)	Largest value.
`time_to_max_s`	number (double)	Time of the largest value (s).
`min_value`	number (double)	Smallest value.
`initial_value`	number (double)	First value.
`final_value`	number (double)	Last value.
`auc`	number (double)	Trapezoidal area under the curve (value × s).

LayoutSummary Layout summary.

Field	Type	Meaning
`sources`	array of string	Sources merged, in order (later ones win well by well): `embedded:<title>`, a file path, `text`, `--blank`, ….
`wells_assigned`	integer (uint)	Measured wells with a role.
`roles`	map of integer (uint)	Measured wells per role (`unassigned` for wells the layout does not name).
`concentration_unit` optional	string \| null	Unit of the concentrations, when the layout states one.

OutlierSummary Outlier rule and result.

Field	Type	Meaning
`rule`	string	`mad`, `grubbs` or `none`.
`threshold` optional	number (double) \| null	Modified z-score cut-off (mad) or alpha (grubbs).
`flagged`	array of string	Wells flagged.
`excluded`	boolean	Whether flagged wells were left out of means, fits and controls.

ParamRow One fitted parameter.

Field	Type	Meaning
`name`	string	Name (`a`, `b`, `c`, `d`, `g`; `slope`, `intercept`).
`value`	number (double)	Estimate.
`se` optional	number (double) \| null	Standard error (Wald).
`ci_low` optional	number (double) \| null	Lower confidence limit: value − t·SE.
`ci_high` optional	number (double) \| null	Upper confidence limit: value + t·SE.

QualityReport Assay quality of the plate (values as read, before blank subtraction).

Field	Type	Meaning
`positive` optional	GroupStats \| null	Positive-control wells.
`negative` optional	GroupStats \| null	Negative-control wells.
`blank` optional	GroupStats \| null	Blank wells.
`samples` optional	GroupStats \| null	Sample wells.
`z_prime` optional	number (double) \| null	Z′ = 1 − 3 (SDpos + SDneg) / \|mean pos − mean neg\| (Zhang, Chung & Oldenburg 1999).
`z_factor` optional	number (double) \| null	Z = 1 − 3 (SDsamples + SDneg) / \|mean samples − mean neg\|.
`signal_to_background` optional	number (double) \| null	Higher control mean / lower control mean.
`signal_to_noise` optional	number (double) \| null	\|mean pos − mean neg\| / SDneg.
`ssmd` optional	number (double) \| null	Strictly standardized mean difference (mean pos − mean neg) / √(SDpos² + SDneg²).
`median_replicate_cv_percent` optional	number (double) \| null	Median CV % over replicate groups of two or more wells.
`assessment` optional	string \| null	`excellent` (Z′ ≥ 0.5), `marginal` (0 < Z′ < 0.5) or `unusable` (Z′ ≤ 0).

ReadSummary The read analysed.

Field	Type	Meaning
`number`	integer (uint32)	1-based read number.
`label`	string	Label as the file writes it.
`mode` optional	string \| null	Detection mode.
`unit` optional	string \| null	Unit of the values.
`calculated` optional	boolean	Values the vendor software calculated (not measured).
`kinetic`	boolean	Whether the read has several time points per well.
`time_points` optional	integer (uint) \| null	Time points per well (kinetic reads).
`wavelength_nm` optional	number (double) \| null	The wavelength selected (spectral reads).
`wells_measured`	integer (uint)	Wells with values.

SampleRow One replicate group.

Field	Type	Meaning
`group`	string	Group name (the sample name, else role and concentration, else the well).
`role`	string	Role of the group.
`sample` optional	string \| null	Sample name.
`compound` optional	string \| null	Compound.
`concentration` optional	number (double) \| null	Nominal concentration.
`dilution` optional	number (double) \| null	Dilution factor.
`wells`	array of string	Wells of the group.
`metric`	string	What `mean`/`sd`/`cv_percent` summarise: `value` (blank-subtracted), or a kinetic/growth metric (`max_slope_per_min`, `doubling_time_h`).
`n`	integer (uint)	Wells in the group.
`n_used`	integer (uint)	Wells used (numbers, not excluded).
`mean` optional	number (double) \| null	Mean of the used wells.
`sd` optional	number (double) \| null	Sample SD (n − 1).
`cv_percent` optional	number (double) \| null	SD / \|mean\| × 100.
`outliers` optional	array of string	Outlier wells.
`back_calculated_mean` optional	number (double) \| null	`curve`: mean of the wells' back-calculated concentrations.
`back_calculated_sd` optional	number (double) \| null	`curve`: SD of the wells' back-calculated concentrations.
`back_calculated_cv_percent` optional	number (double) \| null	`curve`: CV % of the wells' back-calculated concentrations.
`back_calculated_of_mean` optional	number (double) \| null	`curve`: concentration back-calculated from the group's mean signal.
`final_concentration` optional	number (double) \| null	`back_calculated_mean` × dilution.
`flag` optional	string \| null	`curve`: range flag of `back_calculated_of_mean`.
`recovery_percent` optional	number (double) \| null	Standards: `back_calculated_mean` / nominal × 100.

WellRow One well.

Field	Type	Meaning
`well`	string	Well name (`A1`).
`row`	integer (uint32)	1-based row.
`col`	integer (uint32)	1-based column.
`role`	string	Role (`blank`, `standard`, `sample`, `positive`, `negative`, `control`, `empty`), or `unassigned`.
`group`	string	Replicate group this well belongs to.
`sample` optional	string \| null	Sample name.
`compound` optional	string \| null	Compound.
`concentration` optional	number (double) \| null	Nominal concentration (standards, doses).
`dilution` optional	number (double) \| null	Dilution factor.
`raw` optional	number (double) \| null	The value as read (after `reduce` for kinetic reads); null when the cell was not a number.
`value` optional	number (double) \| null	After blank subtraction (equal to `raw` without one).
`outlier`	boolean	Flagged as an outlier in its replicate group.
`excluded`	boolean	Left out of means and fits.
`back_calculated` optional	number (double) \| null	Concentration back-calculated from the standard curve (`curve`).
`final_concentration` optional	number (double) \| null	`back_calculated` × `dilution`.
`flag` optional	string \| null	`curve`: `in_range`, `below_range`, `above_range` (outside the standards' concentrations), `below_curve`, `above_curve` (beyond an asymptote: no concentration) or `not_computable`.
`quantifiable` optional	boolean \| null	`curve`: within [LLOQ, ULOQ].
`recovery_percent` optional	number (double) \| null	Standards: back-calculated / nominal × 100.
`percent_effect` optional	number (double) \| null	`dose-response` with `normalize: controls`: percent effect.
`extra` optional	map of string	Other layout columns.

assay.schema.json · AssayOutput

qpcr

Output of qpcr_report.

Field	Type	Meaning
`path`	string	The input file.
`format`	string	Format id.
`dialect`	string	Dialect (`rdml`, `eds-sds`, `eds-7500`, `eds-json`, `rex`).
`experiment` optional	string \| null	Experiment or run name.
`instrument` optional	string \| null	Instrument model.
`acquisition_temperature_c` optional	number (double) \| null	Temperature of the step that reads fluorescence during cycling (the annealing / extension temperature of a two-step PCR), °C.
`cycles` optional	integer (uint32) \| null	Number of PCR cycles in the program.
`reference_targets`	array of string	Reference targets used or recorded (endogenous controls).
`control_sample` optional	string \| null	Control (calibrator) sample used or recorded.
`record_count`	integer (uint64)	Records matching the filters.
`truncated`	boolean	True when `max_records` cut the list.
`records`	array of QpcrAssayRecord	The records.
`cq_counts`	CqCounts	Cq statuses over every record that matches the filters (not cut by `max_records`).
`targets`	array of TargetCqSummary	Per target: counts by Cq status and the mean Cq without the undetermined results.
`undetermined_cq` optional	number (double) \| null	Cq used for undetermined results in the aggregates, when the request gave one.
`cq_comparison` optional	CqComparison \| null	Our Cq against the vendor's (with `compute_cq`).
`relative_quantities`	array of RelativeQuantity	ΔΔCq results (with `relative`).
`standard_curves`	array of StandardCurveFit	Standard curves (with `standard_curve`).
`notes`	array of string	What to keep in mind.

Types used (6)

CqComparison Our threshold Cq against the vendor's, over every curve with a vendor result.

Field	Type	Meaning
`method`	string	How our Cq was computed.
`curves`	integer (uint64)	Curves compared.
`both_cq`	integer (uint64)	Both give a Cq.
`both_undetermined`	integer (uint64)	Both say there is no Cq.
`only_vendor`	integer (uint64)	Only the vendor gives a Cq.
`only_ours`	integer (uint64)	Only we give a Cq.
`vendor_threshold_used`	integer (uint64)	Curves where the threshold came from the file (the vendor's own).
`mean_difference` optional	number (double) \| null	Mean of (ours − vendor), cycles.
`mean_abs_difference` optional	number (double) \| null	Mean absolute difference, cycles.
`median_abs_difference` optional	number (double) \| null	Median absolute difference, cycles.
`max_abs_difference` optional	number (double) \| null	Largest absolute difference, cycles.
`within_0_1` optional	number (double) \| null	Fraction of `both_cq` within 0.1 cycles.
`within_0_5` optional	number (double) \| null	Fraction of `both_cq` within 0.5 cycles.
`pearson_r` optional	number (double) \| null	Pearson correlation of the two Cq lists.

CqCounts Cq statuses of a set of records.

Field	Type	Meaning
`records`	integer (uint64)	Records (well × target).
`determined`	integer (uint64)	With a Cq.
`undetermined`	integer (uint64)	Without a Cq because nothing amplified ("Undetermined").
`no_result`	integer (uint64)	Without any result (not analysed, setup only).
`excluded`	integer (uint64)	Excluded or omitted in the file (counted in the other fields too).

QpcrAssayRecord One well × target, with names resolved.

Field	Type	Meaning
`run`	string	Run (plate) name.
`well`	string	Well name (`A1`).
`row`	integer (uint32)	Plate row, 1-based.
`col`	integer (uint32)	Plate column, 1-based.
`sample` optional	string \| null	Sample name.
`target` optional	string \| null	Target (assay, detector, gene).
`dye` optional	string \| null	Reporter dye.
`task` optional	string \| null	Role of the well for this target: `unknown`, `standard`, `ntc`, `nac`, `ntp`, `nrt`, `positive`, ...
`quantity` optional	number (double) \| null	Given quantity (standards).
`cq` optional	number (double) \| null	Cq (Ct) as the vendor software or RDML file reports it.
`cq_undetermined`	boolean	True when the file says there is no Cq (Undetermined, `-1`, `NaN`, or an SDS/7500 `Ct` equal to the cycle count).
`cq_status`	string	`determined` (a Cq), `undetermined` (no amplification: `cq` is null) or `no result`.
`cq_stored` optional	number (double) \| null	The number the file stores for an undetermined result (SDS/7500 `.eds`: the cycle count, e.g. 40), kept for reference; never a Cq.
`cq_mean` optional	number (double) \| null	Mean Cq of the replicate group (vendor).
`cq_sd` optional	number (double) \| null	Standard deviation of the replicate group's Cq (vendor).
`tm`	array of number (double)	Melting temperatures of the product, °C (vendor; several when the curve has several peaks).
`threshold` optional	number (double) \| null	Threshold the Cq was called at (vendor).
`auto_threshold` optional	boolean \| null	Whether the vendor threshold was set automatically.
`baseline_start` optional	integer (uint32) \| null	First cycle of the baseline window (vendor).
`baseline_end` optional	integer (uint32) \| null	Last cycle of the baseline window (vendor).
`amp_status` optional	string \| null	Amplification status (vendor).
`cq_confidence` optional	number (double) \| null	Cq confidence (vendor).
`calculated_quantity` optional	number (double) \| null	Quantity calculated by the vendor software from a standard curve.
`efficiency` optional	number (double) \| null	Amplification efficiency of this reaction (fold per cycle), when the file has one.
`excluded` optional	string \| null	Why the result is excluded (omitted wells, RDML `excl`).
`flags`	array of string	Vendor QC flags.
`vendor_delta_cq` optional	number (double) \| null	ΔCq to the reference target as the vendor computed it (ΔΔCt experiments).
`vendor_rq` optional	number (double) \| null	Relative quantity as the vendor computed it.
`computed_cq` optional	number (double) \| null	Our threshold Cq (with `compute_cq`).
`computed_threshold` optional	number (double) \| null	Threshold our Cq used.
`computed_cq_status` optional	string \| null	`determined` or `undetermined` for our Cq (with `compute_cq`; a curve that never crosses the threshold, or crosses it only at the last read, is undetermined).
`cycles`	integer (uint32)	Number of cycles in the amplification curve.

RelativeQuantity ΔΔCq relative quantification of one sample × target.

Field	Type	Meaning
`sample`	string	Sample.
`target`	string	Target of interest.
`replicates`	integer (uint32)	Replicate wells averaged: those with a Cq (plus the undetermined ones when `undetermined_cq` is given).
`undetermined`	integer (uint32)	Replicate wells of this sample × target without a Cq (undetermined): left out of the mean, or counted at `undetermined_cq` when the request gives one.
`cq_mean`	number (double)	Mean Cq of the target in this sample.
`cq_sd` optional	number (double) \| null	Standard deviation of those Cqs.
`reference_cq_mean`	number (double)	Mean Cq of the reference target(s) in this sample (arithmetic mean over references).
`delta_cq`	number (double)	ΔCq = target − reference.
`delta_cq_sd` optional	number (double) \| null	SD of ΔCq (target and reference SDs combined in quadrature).
`delta_delta_cq` optional	number (double) \| null	ΔΔCq = ΔCq(sample) − ΔCq(control sample); `None` without a control.
`rq` optional	number (double) \| null	2^−ΔΔCq.
`rq_min` optional	number (double) \| null	2^−(ΔΔCq + SD).
`rq_max` optional	number (double) \| null	2^−(ΔΔCq − SD).
`efficiency_corrected_rq` optional	number (double) \| null	Efficiency-corrected ratio (Pfaffl) when every efficiency involved is known.
`vendor_delta_cq` optional	number (double) \| null	ΔCq the vendor software computed for these wells, when stored.
`vendor_rq` optional	number (double) \| null	Relative quantity the vendor software computed, when stored.

StandardCurveFit A standard curve fitted to the standard wells of one target.

Field	Type	Meaning
`target`	string	Target.
`points`	integer (uint32)	Standard wells used.
`levels`	integer (uint32)	Distinct quantities.
`slope`	number (double)	Slope of Cq against log10(quantity).
`intercept`	number (double)	Cq at quantity 1.
`r2`	number (double)	Coefficient of determination.
`efficiency_percent`	number (double)	Efficiency, percent: (10^(−1/slope) − 1) × 100.
`vendor_slope` optional	number (double) \| null	The vendor's slope for this target, when the file stores its standard curve.
`vendor_efficiency_percent` optional	number (double) \| null	The vendor's efficiency, percent.
`vendor_r2` optional	number (double) \| null	The vendor's r².

TargetCqSummary Per-target Cq summary over the records that match the filters.

Field	Type	Meaning
`target`	string	Target.
`counts`	CqCounts	Record counts by status (every task, excluded records included in the counts).
`averaged`	integer (uint64)	Records averaged: not excluded, with a Cq (plus the undetermined ones when `undetermined_cq` is given).
`cq_mean` optional	number (double) \| null	Mean Cq of those records; undetermined results are left out unless `undetermined_cq` is given.
`cq_sd` optional	number (double) \| null	Sample standard deviation of those Cqs.
`cq_min` optional	number (double) \| null	Smallest Cq.
`cq_max` optional	number (double) \| null	Largest Cq.

qpcr.schema.json · QpcrReport

nmr-peaks

Output of analyze nmr-peaks.

Field	Type	Meaning
`path`	string	The input path.
`format`	string	Format id.
`source`	string	`processed` (a spectrum the vendor software stored) or `fid` (processed here).
`trace`	integer (uint32)	Trace used (see `info` → `traces[]`).
`trace_name` optional	string \| null	Its name.
`sweep`	integer (uint32)	Sweep (row) used.
`nucleus` optional	string \| null	Observed nucleus, when known.
`processing` optional	ProcessingRecord \| null	How the FID was processed (`source` = `fid` only).
`axis`	PpmAxis	The chemical-shift axis of the spectrum.
`noise_sd`	number (double)	Robust noise standard deviation (same units as `height`).
`peak_options`	PeakOptions	Thresholds used.
`peak_count`	integer (uint)	Number of peaks found.
`main_peak` optional	Peak \| null	The tallest positive peak (named like `analyze peaks` → `main_peak` for chromatograms).
`peaks`	array of Peak	Peaks, high shift first.
`integrals` optional	array of Integral	Integrals of the requested regions.
`notes` optional	array of string	Remarks.

Types used (9)

Apodization Window function applied to the FID.

One of: object | object | object

BaselineMode Baseline correction choice.

One of: object | object | object

FidParameters What the processing needs to know about an acquisition.

Field	Type	Meaning
`spectral_width_hz`	number (double)	Spectral width (Hz): the complex sampling rate.
`carrier_frequency_mhz`	number (double)	Carrier (transmitter) frequency, MHz: the centre of the spectrum.
`reference_frequency_mhz`	number (double)	Frequency of 0 ppm, MHz (the referencing frequency).
`group_delay_points`	number (double)	Digital-filter group delay in points (0 when the data carry none).
`conjugate`	boolean	Complex-conjugate the FID before the transform (reverses the frequency axis).
`nucleus` optional	string \| null	Observed nucleus, e.g. `1H`, `13C`.

Integral One integral.

Field	Type	Meaning
`from_ppm`	number (double)	High-shift end of the region, ppm.
`to_ppm`	number (double)	Low-shift end of the region, ppm.
`value`	number (double)	Sum of the points × point spacing (intensity·ppm).
`normalized` optional	number (double) \| null	`value` rescaled so the reference region has the reference value (`None` when the reference integral is 0 or missing).
`points`	integer (uint)	Points summed.

Peak One picked peak.

Field	Type	Meaning
`ppm`	number (double)	Chemical shift, ppm (parabolic interpolation).
`hz`	number (double)	Frequency relative to 0 ppm, Hz.
`index`	integer (uint)	Index of the maximum point.
`height`	number (double)	Interpolated height (negative for negative peaks).
`width_hz` optional	number (double) \| null	Full width at half height, Hz (`None` when overlapping lines hide the half-height point).
`width_ppm` optional	number (double) \| null	Full width at half height, ppm.
`snr` optional	number (double) \| null	\|height\| / noise SD (`None` when the noise SD is 0).

PeakOptions Peak-picking thresholds.

Field	Type	Meaning
`min_snr`	number (double)	Minimum height as a multiple of the noise SD.
`min_height_fraction`	number (double)	Minimum height as a fraction of the tallest point in the searched range (0 = off).
`min_prominence_snr`	number (double)	Minimum prominence as a multiple of the noise SD.
`include_negative`	boolean	Also report negative peaks.
`range_ppm` optional	array of any \| null	Only search between these shifts (ppm, either order).
`max_peaks`	integer (uint)	Keep at most this many peaks (the tallest).

PpmAxis A regular chemical-shift axis: point k is at first_ppm + k · step_ppm.

Field	Type	Meaning
`first_ppm`	number (double)	Chemical shift of point 0 (the left, high-frequency edge), ppm.
`step_ppm`	number (double)	Increment per point, ppm (negative: shifts decrease left to right).
`size`	integer (uint)	Number of points.
`reference_frequency_mhz`	number (double)	Frequency of 0 ppm, MHz (converts ppm to Hz).

ProcessingRecord What was done, with the values actually used.

Field	Type	Meaning
`steps`	array of string	Steps in order, e.g. `zero_fill`, `group_delay`, `apodization`, `fft`, `phase`, `baseline`.
`fid_points`	integer (uint)	Complex points in the FID.
`size`	integer (uint)	Transform size, complex points.
`apodization` optional	Apodization \| null	Window applied.
`apodization_source`	string	Where the window width came from: `stored`, `default`, `option`.
`group_delay_points`	number (double)	Group delay removed, points.
`phase_mode`	string	Phase mode actually used: `stored`, `auto`, `manual`, `magnitude`, `none`.
`phase0_deg`	number (double)	Zero-order phase applied, degrees.
`phase1_deg`	number (double)	First-order phase applied, degrees.
`baseline`	BaselineMode	Baseline correction applied.
`parameters`	FidParameters	Parameters used.
`stored`	StoredProcessing	Stored processing values found (may be unused).
`notes` optional	array of string	Remarks (fallbacks, clamping).

StoredProcessing Processing parameters the vendor software stored with the data, in this crate's conventions.

Field	Type	Meaning
`source` optional	string \| null	Where they came from, e.g. `pdata/1/procs` or `procpar`.
`size` optional	integer (uint) \| null	Transform size in complex points.
`line_broadening_hz` optional	number (double) \| null	Exponential line broadening, Hz.
`phase0_deg` optional	number (double) \| null	Zero-order phase, degrees (`φ0` of the module docs).
`phase1_deg` optional	number (double) \| null	First-order phase across the whole spectrum, degrees (`φ1`).
`spectrum_stored` optional	boolean	True when the vendor software also stored a processed spectrum made with these values.
`first_point_factor` optional	number (double) \| null	Factor applied to the first FID point (Bruker `FCOR`); `None`: 0.5.
`time_domain_points` optional	integer (uint) \| null	Complex FID points the vendor processing used (Bruker `TDeff` / 2); `None`: all.

nmr-peaks.schema.json · NmrReport

ephys-features

Output of analyze ephys-features.

Field	Type	Meaning
`path`	string	Input path.
`format`	string	Format id.
`trace`	integer (uint32)	Trace analysed.
`channel`	ChannelRef	Channel analysed.
`clamp_mode`	string	`current_clamp`, `voltage_clamp` or `unknown` (from the channel and command units).
`sample_rate_hz`	number (double)	Sampling rate, Hz.
`settings`	ApSettings	Spike detection settings.
`stimulus` optional	StimulusInfo \| null	Stimulus from the protocol, when there is one.
`cell`	CellFeatures	Per-cell features.
`sweeps`	array of SweepFeatures	One row per sweep.
`spike_count_total`	integer (uint)	Total spikes detected.
`spikes`	array of Spike	One row per spike (at most `max_spikes`).
`spikes_truncated`	boolean	True when `spikes` was cut at `max_spikes`.
`notes` optional	array of string	Remarks.

Types used (9)

ApSettings Detection settings.

Field	Type	Meaning
`peak_threshold_mv`	number (double)	Voltage a spike must cross upward, mV.
`dvdt_threshold_v_per_s`	number (double)	`dV/dt` defining the onset, V/s.
`dvdt_window_samples`	integer (uint)	Consecutive samples the onset criterion must hold.

CellFeatures Per-cell summary.

Field	Type	Meaning
`resting_mv` optional	number (double) \| null	Median baseline (pre-stimulus) voltage over sweeps, mV.
`rheobase_pa` optional	number (double) \| null	Smallest depolarising step that evokes at least one spike during the stimulus, pA.
`rheobase_sweep` optional	integer (uint32) \| null	The sweep of that step.
`fi_curve`	array of FiPoint	f–I curve over depolarising steps.
`fi_slope_hz_per_pa` optional	number (double) \| null	Least-squares slope of rate vs current over steps that fire, Hz/pA.
`max_firing_rate_hz` optional	number (double) \| null	Highest firing rate, Hz.
`input_resistance_mohm` optional	number (double) \| null	Slope of steady-state deflection vs current over spike-free hyperpolarising steps, MΩ.
`tau_ms` optional	number (double) \| null	Median time constant over hyperpolarising steps, ms.
`capacitance_pf` optional	number (double) \| null	τ / R_in, pF.
`sag_ratio` optional	number (double) \| null	Sag ratio of the most hyperpolarising step.
`holding_current_pa` optional	number (double) \| null	Median holding current, pA (voltage clamp).
`access_resistance_mohm` optional	number (double) \| null	Median access resistance, MΩ (voltage clamp).
`membrane_resistance_mohm` optional	number (double) \| null	Median membrane resistance, MΩ (voltage clamp).
`membrane_capacitance_pf` optional	number (double) \| null	Median membrane capacitance from the test pulse, pF (voltage clamp).

ChannelRef The channel analysed.

Field	Type	Meaning
`index`	integer (uint32)	Channel index.
`name`	string	Name.
`unit` optional	string \| null	Unit as recorded.

FiPoint One point of the f–I curve.

Field	Type	Meaning
`sweep`	integer (uint32)	Sweep.
`current_pa`	number (double)	Injected current relative to holding, pA.
`rate_hz`	number (double)	Firing rate during the stimulus, Hz.
`spike_count`	integer (uint)	Spikes during the stimulus.

Spike One action potential.

Field	Type	Meaning
`sweep`	integer (uint32)	Sweep index.
`index`	integer (uint32)	Spike number within the sweep (0-based).
`peak_sample`	integer (uint64)	Sample index of the peak within the sweep.
`peak_time_s`	number (double)	Peak time from the sweep start, s.
`peak_mv`	number (double)	Peak voltage, mV.
`threshold_time_s`	number (double)	Onset time, s.
`threshold_mv`	number (double)	Onset voltage, mV.
`threshold_from_dvdt`	boolean	True when the onset met the dV/dt criterion.
`amplitude_mv`	number (double)	Peak − onset voltage, mV.
`half_width_ms` optional	number (double) \| null	Width at half amplitude, ms.
`rise_time_ms`	number (double)	Onset to peak, ms.
`decay_time_ms` optional	number (double) \| null	Peak to the return to the onset voltage, ms.
`ahp_mv` optional	number (double) \| null	After-hyperpolarisation minimum, mV.
`ahp_depth_mv` optional	number (double) \| null	Onset − AHP minimum, mV.
`upstroke_v_per_s`	number (double)	Largest rising dV/dt, V/s.
`downstroke_v_per_s` optional	number (double) \| null	Largest falling dV/dt (negative), V/s.
`isi_ms` optional	number (double) \| null	Time since the previous spike's peak, ms.

StepResponse Passive response to one current step.

Field	Type	Meaning
`baseline_mv` optional	number (double) \| null	Baseline voltage, mV.
`steady_state_mv` optional	number (double) \| null	Steady-state voltage at the end of the step, mV.
`extreme_mv` optional	number (double) \| null	Extreme voltage during the step (minimum for hyperpolarising steps), mV.
`input_resistance_mohm` optional	number (double) \| null	(steady − baseline) / ΔI, MΩ.
`tau_ms` optional	number (double) \| null	Membrane time constant, ms.
`sag_ratio` optional	number (double) \| null	(steady − min) / (baseline − min) (eFEL sag_ratio1), hyperpolarising steps.
`steady_fraction` optional	number (double) \| null	(baseline − steady) / (baseline − min) (eFEL sag_ratio2), hyperpolarising steps.

StimulusInfo The stimulus found in the protocol.

Field	Type	Meaning
`output`	string	Command output name.
`unit` optional	string \| null	Command unit.
`holding`	number (double)	Holding level, in `unit`.
`epoch` optional	integer (uint32) \| null	Epoch index used as the stimulus.

SweepFeatures One sweep.

Field	Type	Meaning
`sweep`	integer (uint32)	Sweep index.
`stimulus_start_s` optional	number (double) \| null	Stimulus start, s from the sweep start.
`stimulus_end_s` optional	number (double) \| null	Stimulus end, s.
`stimulus_pa` optional	number (double) \| null	Injected current relative to holding, pA (current clamp).
`stimulus_mv` optional	number (double) \| null	Command step relative to holding, mV (voltage clamp).
`spike_count`	integer (uint)	Spikes in the whole sweep.
`spike_count_stimulus` optional	integer (uint) \| null	Spikes whose peak falls inside the stimulus.
`firing_rate_hz` optional	number (double) \| null	Spikes in the stimulus / stimulus duration, Hz.
`first_spike_latency_ms` optional	number (double) \| null	First spike peak after stimulus onset, ms.
`isi_mean_ms` optional	number (double) \| null	Mean inter-spike interval inside the stimulus, ms.
`isi_cv` optional	number (double) \| null	ISI coefficient of variation inside the stimulus.
`adaptation_index` optional	number (double) \| null	ISI adaptation index inside the stimulus.
`half_width_mean_ms` optional	number (double) \| null	Mean spike half-width, ms.
`amplitude_mean_mv` optional	number (double) \| null	Mean spike amplitude (peak − onset), mV.
`passive` optional	StepResponse \| null	Passive response (current clamp, spike-free sweeps; baseline always).
`test_pulse` optional	TestPulse \| null	Test-pulse metrics (voltage clamp).

TestPulse Voltage-clamp test-pulse metrics (module docs).

Field	Type	Meaning
`delta_mv`	number (double)	Voltage step, mV.
`holding_current_pa` optional	number (double) \| null	Current before the step, pA.
`peak_current_pa` optional	number (double) \| null	Transient peak minus baseline, pA.
`steady_current_pa` optional	number (double) \| null	Steady state minus baseline, pA.
`access_resistance_mohm` optional	number (double) \| null	ΔV / peak, MΩ.
`membrane_resistance_mohm` optional	number (double) \| null	ΔV / steady − access, MΩ.
`total_resistance_mohm` optional	number (double) \| null	ΔV / steady, MΩ.
`tau_ms` optional	number (double) \| null	Decay time constant of the transient, ms.
`capacitance_pf` optional	number (double) \| null	Q/ΔV · ((Ra + Rm)/Rm)² from the transient's charge, pF.

ephys-features.schema.json · CellReport

spikes

Output of analyze spikes.

Field	Type	Meaning
`path`	string	Input path.
`format`	string	Format id.
`trace`	integer (uint32)	Trace analysed.
`sample_rate_hz`	number (double)	Sampling rate, Hz.
`settings`	DetectSettings	Settings used (the high edge after clamping to 0.45 × the sampling rate).
`sweeps`	array of integer (uint32)	Sweeps analysed.
`channels`	array of ChannelSpikes	One entry per channel.
`spike_count_total`	integer (uint)	Spikes on all channels.
`notes` optional	array of string	Remarks.

Types used (4)

ChannelSpikes Detection results of one channel.

Field	Type	Meaning
`channel`	integer (uint32)	Channel index.
`name`	string	Channel name.
`unit` optional	string \| null	Unit of `noise` and `threshold`.
`noise`	number (double)	Noise (MAD / 0.6745 of the filtered signal; the first sweep analysed).
`threshold`	number (double)	Detection threshold (`threshold × noise`).
`spike_count`	integer (uint)	Spikes detected, all sweeps.
`rate_hz`	number (double)	Spikes per second of analysed signal.
`duration_s`	number (double)	Seconds analysed.
`times`	array of SpikeTime	Spike times, s from each sweep's start, with the sweep (at most `max_times`).
`times_truncated`	boolean	True when `times` was cut.

DetectSettings Detection settings.

Field	Type	Meaning
`low_hz`	number (double)	Band-pass low edge, Hz.
`high_hz`	number (double)	Band-pass high edge, Hz (clamped to 0.45 × the sampling rate).
`order`	integer (uint)	Butterworth order.
`threshold`	number (double)	Threshold in noise units.
`sign`	PeakSign	Direction.
`exclude_ms`	number (double)	Exclusion half-window, ms.

PeakSign Which deflections count.

One of: "neg" | "pos" | "both"

SpikeTime One spike time.

Field	Type	Meaning
`sweep`	integer (uint32)	Sweep/segment.
`sample`	integer (uint64)	Sample within the sweep.
`time_s`	number (double)	Seconds from the sweep start.
`amplitude`	number (double)	Filtered amplitude at the peak (in the channel unit).

spikes.schema.json · SpikesReport

gate

Output of analyze gate.

Field	Type	Meaning
`path` optional	string \| null	The FCS file gated; absent when only the gating file was described.
`gating_file`	string	The gating file (FlowJo workspace or Gating-ML document).
`gating_format`	string	`flowjo-wsp` or `gating-ml`.
`workspace` optional	WorkspaceSummary \| null	Workspace-level facts (FlowJo only).
`sample` optional	SampleSummary \| null	The workspace sample whose gates were used (FlowJo only).
`table` optional	integer (uint32) \| null	FCS data set (table) gated.
`event_count` optional	integer (uint64) \| null	Events in the data set.
`compensation`	array of CompensationSummary	Compensation matrices the gating file defines (and whether any gate used them).
`transforms`	array of TransformSummary	Transforms by id (FlowJo: by parameter name).
`populations`	array of PopulationRow	One row per population, parents before children.
`tree`	array of PopulationNode	The same populations as a tree (quadrant gates appear as grouping nodes without a count).
`notes` optional	array of string	Caveats: skipped populations, disagreements with counts stored in the workspace, scaling.

Types used (8)

CompensationSummary A compensation or unmixing matrix.

Field	Type	Meaning
`name`	string	Matrix name or id; `$SPILLOVER`/`$SPILL`/`SPILL` for the FCS file's own.
`source`	string	Where it comes from: `workspace`, `gating-ml`, `fcs` or `command-line`.
`detectors`	array of string	Detectors (columns), `$PnN`.
`fluorochromes`	array of string	Rows: fluorochromes, or the detectors that receive the unmixed values.
`matrix`	array of array of number (double)	Row-major coefficients (spillover fractions).
`spectral`	boolean	More detectors than rows: unmixed by ordinary least squares.
`used`	boolean	Whether a gate (or the table) used it.

GateDimension One gate axis.

Field	Type	Meaning
`parameter`	string	Parameter (`$PnN`, fluorochrome) or ratio id.
`compensation`	string	`uncompensated`, `FCS` or a matrix name.
`transform` optional	string \| null	Transform id, if any.
`min` optional	number (double) \| null	Lower bound (inclusive), as stored.
`max` optional	number (double) \| null	Upper bound (exclusive), as stored.

GroupSummary A workspace group.

Field	Type	Meaning
`name`	string	Group name.
`samples`	array of string	Sample names in the group.

PopulationNode A node of the population tree.

Field	Type	Meaning
`name`	string	Population name.
`path`	string	`/`-separated path from the root (`/Lymphocytes/Single Cells/CD3+`).
`gate_type`	string	Gate type, or `quadrant-gate` for the node grouping a quadrant gate's quadrants.
`count` optional	integer (uint64) \| null	Events (absent without an FCS file, and for quadrant-gate grouping nodes).
`children` optional	array of PopulationNode	Child populations.

PopulationRow One population.

Field	Type	Meaning
`path`	string	`/`-separated path from the root (`/Lymphocytes/Single Cells/CD3+`).
`name`	string	Population name.
`parent` optional	string \| null	Parent path; absent for populations of all events.
`gate_type`	string	`rectangle`, `polygon`, `ellipsoid`, `quadrant` or `boolean`.
`dimensions`	array of GateDimension	Gate axes.
`gate`	any	Gate geometry as stored: `vertices`, `mean`/`covariance`/`distance_square`, `foci`/`edge`, or `op`/`operands` (paths, with `complement`).
`complement`	boolean	Events outside the gate form the population (FlowJo `eventsInside="0"`).
`coordinates`	string	Coordinates are stored before the transform (`untransformed`, FlowJo) or after it.
`count` optional	integer (uint64) \| null	Events in the population (absent when no FCS file was given).
`percent_of_parent` optional	number (double) \| null	Percent of the parent population's events.
`percent_of_total` optional	number (double) \| null	Percent of all events.
`stored_count` optional	integer (uint64) \| null	The count the gating software stored (FlowJo `count`), for comparison.
`medians` optional	map of number (double)	Median fluorescence (or scatter) of the population's events for each parameter asked for (`analyze gate --median`), keyed by the name as asked: scale values (after `$PnE`/`$PnG`), compensated when the name carries the workspace's `Comp-` prefix. Absent for an empty population.

SampleSummary A workspace sample.

Field	Type	Meaning
`id`	string	FlowJo sample id.
`name`	string	Sample name.
`uri` optional	string \| null	Where FlowJo found the FCS file.
`event_count` optional	integer (uint64) \| null	Event count FlowJo stored.
`groups`	array of string	Groups the sample belongs to.
`population_count`	integer (uint)	Populations in the sample's gate tree.
`compensation` optional	string \| null	Name of the sample's compensation matrix.
`keywords` optional	map of string	Keywords FlowJo stored with the sample (FCS TEXT plus its own).

TransformSummary A parameter transform defined in the gating file.

Field	Type	Meaning
`id`	string	Id (FlowJo: the parameter it applies to).
`kind`	string	`linear`, `log`, `arcsinh`, `logicle`, `hyperlog`, `ratio`, `flowjo-log`, `flowjo-biex`, `arcsinh-cofactor`, or the element name of an unsupported FlowJo transform.
`parameters`	map of number (double)	Parameters (`T`, `W`, `M`, `A`, `offset`, `decades`, `neg`, `width`, `pos`, `maxRange`, …).
`supported`	boolean	False for transforms this reader does not evaluate.

WorkspaceSummary Facts about a FlowJo workspace.

Field	Type	Meaning
`version` optional	string \| null	Workspace format version (`20.0`).
`flowjo_version` optional	string \| null	FlowJo release that saved it.
`modified` optional	string \| null	Modification date as written.
`groups`	array of GroupSummary	Groups and their member sample names.
`samples`	array of SampleSummary	Every sample in the workspace.

gate.schema.json · GateOutput

batch-table

Output of a batch command in table mode.

Field	Type	Meaning
`measure`	string	Measure (`stats`, `trace`, `table`, `gate`, `info`, …).
`grain`	array of string	Columns that identify a row within its data set.
`inputs`	InputReport	How the inputs became data sets.
`joins` optional	array of JoinReport	Sample sheets and layouts joined, in order.
`columns`	array of Column	Columns of `rows`, with type, unit and role (`id`, `key`, `metadata`, `annotation`, `value`, `error`).
`total_rows`	integer (uint64)	Rows in the whole table.
`offset`	integer (uint64)	Index of the first row in `rows`.
`returned_rows`	integer (uint64)	Rows returned here.
`truncated`	boolean	True when the table has rows after the last one returned (page with `offset`, or read the full table from `output`).
`rows`	array of array of Value	Rows as arrays in column order.
`summary` optional	SummaryOutput \| null	The group summary (`--by`).
`output` optional	WrittenFile \| null	The file the full table was written to (`-o`).
`warnings` optional	array of string	Things to check: skipped inputs, grouping, join results.

Types used (14)

Column One column.

Field	Type	Meaning
`name`	string	Name (stable; units that never change are part of it, e.g. `sample_rate_hz`).
`type`	ColumnType	Inferred type.
`unit` optional	string \| null	Unit of every value in the column, when fixed.
`role`	Role	What the column holds.
`description` optional	string \| null	One line on its meaning.

ColumnType Column type, inferred from the cells.

One of: "string" | "integer" | "float" | "boolean"

InputReport How the inputs turned into data sets.

Field	Type	Meaning
`datasets`	integer (uint64)	Data sets measured (rows come from these), including those that failed.
`ok`	integer (uint64)	Data sets measured without error.
`failed`	integer (uint64)	Data sets that failed (their rows carry `error`).
`skipped_unknown`	integer (uint64)	Files found by walking a directory that no reader recognises (not in the table).
`skipped_format`	integer (uint64)	Data sets of other formats left out by the format filter.
`skipped_sheets`	integer (uint64)	Sample sheets and layouts found among the inputs (never measured).
`grouped_members`	integer (uint64)	Files that belong to another input's multi-file data set (measured once, with it).
`skipped_examples` optional	array of string	A few of the skipped paths, with why.
`reused` optional	integer (uint64)	Data sets whose rows were reused from the journal of an interrupted run.

JoinReport What a join did.

Field	Type	Meaning
`sheet`	SampleSheet	The sheet read.
`key`	array of KeyCandidate	The key used: one or more (sheet column, field) pairs, all of which must agree.
`auto`	boolean	True when the key was chosen from the data (no `--key`).
`alternatives` optional	array of KeyCandidate	The next best keys (auto only), to judge how clear the choice was.
`annotations`	array of string	Columns added to the table.
`matched_rows`	integer (uint64)	Table rows that got annotations.
`rows`	integer (uint64)	Rows in the table.
`matched_datasets`	integer (uint64)	Data sets with at least one annotated row.
`datasets`	integer (uint64)	Data sets in the table.
`unmatched_datasets`	array of string	Data sets no sheet row matched (first 20).
`unmatched_datasets_count`	integer (uint64)	How many data sets no sheet row matched.
`unmatched_sheet_rows`	array of string	Sheet rows that matched no table row, by their key values (first 20).
`unmatched_sheet_rows_count`	integer (uint64)	How many sheet rows matched nothing.
`ambiguous`	array of string	Table rows that matched several sheet rows that disagree (first 20); left without annotations.
`ambiguous_count`	integer (uint64)	How many rows were ambiguous.
`warnings` optional	array of string	Things to check.

KeyCandidate One key pair tried.

Field	Type	Meaning
`sheet_column`	string	Sheet column.
`field`	KeyField	Table key.
`matched_rows`	integer (uint64)	Table rows it matches.
`matched_datasets`	integer (uint64)	Data sets it matches.

KeyField A key of the table's rows a sheet column can match.

Role What a column holds.

SampleSheet A sample sheet or plate layout in long form.

Field	Type	Meaning
`path`	string	The file.
`worksheet` optional	string \| null	Worksheet read (workbooks only).
`kind`	SheetKind	Table or plate layout.
`columns`	array of string	Column names (a layout: `well`, then one per grid).
`plate_wells` optional	integer (uint32) \| null	Plate format of a layout (96, 384, 1536, …).
`notes` optional	array of string	What was assumed while reading.

SheetKind How the sheet was laid out.

One of: "table" | "plate_layout"

SummaryOutput A summary: one row per group and value column.

Field	Type	Meaning
`group_by`	array of string	Columns that define a group: `by` plus the measurement dimensions added.
`added_dimensions` optional	array of string	Dimensions added automatically.
`values`	array of string	Value columns summarized.
`replicate` optional	string \| null	Replicate column, if any.
`test` optional	string \| null	Test and control, if any.
`control` optional	string \| null	The control group (value of the first `by` column).
`rows_used`	integer (uint64)	Table rows used / left out (errors, filters, missing values).
`rows_excluded`	integer (uint64)	Rows left out by filters or errors.
`table`	Table	The summary table.
`notes` optional	array of string	Things to know.

Table A table: columns and rows of cells in column order.

Field	Type	Meaning
`columns`	array of Column	Columns.
`rows`	array of array of Value	Rows; each has one cell per column.

TableFormat A table file format.

One of: "csv" | "tsv" | "jsonl" | "json" | "parquet"

Value One cell.

One of: boolean | integer (int64) | number (double) | string | null

WrittenFile What was written.

Field	Type	Meaning
`path`	string	The file.
`format`	TableFormat	Its format.
`rows`	integer (uint64)	Data rows.
`columns`	integer (uint64)	Columns.
`bytes`	integer (uint64)	Size in bytes.
`verified`	boolean	Read back and checked before it was renamed into place.

batch-table.schema.json · BatchOutput

batch-summary

Output of batch summarize.

Field	Type	Meaning
`input`	string	The table summarized.
`summary`	SummaryOutput	The summary.
`output` optional	WrittenFile \| null	Where it was written (`-o`).

Types used (8)

Column One column.

Field	Type	Meaning
`name`	string	Name (stable; units that never change are part of it, e.g. `sample_rate_hz`).
`type`	ColumnType	Inferred type.
`unit` optional	string \| null	Unit of every value in the column, when fixed.
`role`	Role	What the column holds.
`description` optional	string \| null	One line on its meaning.

ColumnType Column type, inferred from the cells.

One of: "string" | "integer" | "float" | "boolean"

Role What a column holds.

SummaryOutput A summary: one row per group and value column.

Field	Type	Meaning
`group_by`	array of string	Columns that define a group: `by` plus the measurement dimensions added.
`added_dimensions` optional	array of string	Dimensions added automatically.
`values`	array of string	Value columns summarized.
`replicate` optional	string \| null	Replicate column, if any.
`test` optional	string \| null	Test and control, if any.
`control` optional	string \| null	The control group (value of the first `by` column).
`rows_used`	integer (uint64)	Table rows used / left out (errors, filters, missing values).
`rows_excluded`	integer (uint64)	Rows left out by filters or errors.
`table`	Table	The summary table.
`notes` optional	array of string	Things to know.

Table A table: columns and rows of cells in column order.

Field	Type	Meaning
`columns`	array of Column	Columns.
`rows`	array of array of Value	Rows; each has one cell per column.

TableFormat A table file format.

One of: "csv" | "tsv" | "jsonl" | "json" | "parquet"

Value One cell.

One of: boolean | integer (int64) | number (double) | string | null

WrittenFile What was written.

Field	Type	Meaning
`path`	string	The file.
`format`	TableFormat	Its format.
`rows`	integer (uint64)	Data rows.
`columns`	integer (uint64)	Columns.
`bytes`	integer (uint64)	Size in bytes.
`verified`	boolean	Read back and checked before it was renamed into place.

batch-summary.schema.json · SummarizeOutput

link

Output of link.

Field	Type	Meaning
`inputs`	InputReport	How the inputs became data sets.
`min_confidence`	Confidence	Minimum confidence of links that form groups.
`groups`	array of LinkGroup	Groups of two or more data sets.
`unlinked`	integer (uint64)	Data sets in no group.
`unlinked_examples` optional	array of string	Some of them.
`weak_links` optional	array of Link	Links below `min_confidence` (not grouped), strongest first (first 50).
`shared_identifiers` optional	array of SharedIdentifier	Identifiers treated as weak evidence.
`notes` optional	array of string	Things to know.

Types used (7)

Confidence How sure a link is.

One of: "low" | "medium" | "high"

Evidence One piece of evidence.

Field	Type	Meaning
`kind`	string	Kind (`same_sample_id`, `same_acquisition`, …; see the module documentation).
`detail`	string	The values compared, and where they came from.
`confidence`	Confidence	Confidence of this evidence alone.

InputReport How the inputs turned into data sets.

Field	Type	Meaning
`datasets`	integer (uint64)	Data sets measured (rows come from these), including those that failed.
`ok`	integer (uint64)	Data sets measured without error.
`failed`	integer (uint64)	Data sets that failed (their rows carry `error`).
`skipped_unknown`	integer (uint64)	Files found by walking a directory that no reader recognises (not in the table).
`skipped_format`	integer (uint64)	Data sets of other formats left out by the format filter.
`skipped_sheets`	integer (uint64)	Sample sheets and layouts found among the inputs (never measured).
`grouped_members`	integer (uint64)	Files that belong to another input's multi-file data set (measured once, with it).
`skipped_examples` optional	array of string	A few of the skipped paths, with why.
`reused` optional	integer (uint64)	Data sets whose rows were reused from the journal of an interrupted run.

Link A link between two data sets.

Field	Type	Meaning
`a`	string	One data set.
`b`	string	The other.
`confidence`	Confidence	The strongest evidence's confidence.
`evidence`	array of Evidence	All evidence found.

LinkGroup Data sets that measured the same sample.

Field	Type	Meaning
`group`	integer (uint32)	Group number (from 1, in the order of the first member).
`confidence`	Confidence	The weakest link that holds the group together (low when the group has a conflict).
`sample` optional	string \| null	The sample id the members share, when they do.
`members`	array of LinkMember	Members in input order.
`links`	array of Link	The links, with evidence.
`conflicts` optional	array of string	Disagreements inside the group (different sample ids).

LinkMember A member of a group.

Field	Type	Meaning
`path`	string	The data set.
`format` optional	string \| null	Format id.
`sample_id` optional	string \| null	Recorded sample id.
`well` optional	string \| null	Recorded well.
`barcode` optional	string \| null	Recorded barcode.
`started_at` optional	string \| null	Acquisition start.

SharedIdentifier An identifier shared by many data sets or naming a control.

Field	Type	Meaning
`field`	string	Field (`sample_id`, `sample_name`, `barcode`).
`value`	string	Value.
`datasets`	integer (uint64)	Data sets recording it.
`reason`	string	Why it was treated as weak.

link.schema.json · LinkOutput

sidecar

Output of info --view full --sidecar for one input.

Field	Type	Meaning
`input`	string	The input file.
`output`	string	The sidecar path.
`status`	string	`written` or `unchanged` (an up-to-date sidecar was already there).
`format` optional	string \| null	Format id of the input (absent when the sidecar was unchanged and the file not opened).
`bytes`	integer (uint64)	Size of the sidecar in bytes.
`verified`	boolean	True when a written sidecar was read back and matched.

sidecar.schema.json · SidecarReport

sidecar file

The content of a .openreadout.json sidecar: the info --view full --json envelope plus sidecar.

Field	Type	Meaning
`ok`	boolean	Always true.
`schema_version`	string	The envelope schema version.
`tool`	ToolId	The producing tool and its version.
`sidecar`	SidecarMeta	What the sidecar was made from.
`data`	Dump	The `info --view full` output.

Types used (49)

Acquisition When and by whom.

Field	Type	Meaning
`started_at` optional	string \| null	ISO-8601 start (same zone rules as the rest of the model).
`ended_at` optional	string \| null	ISO-8601 end, when recorded.
`operator` optional	string \| null	Operator or user name as recorded.
`duration_s` optional	number (double) \| null	Length of the acquisition (run length, recording length, time-lapse span) in seconds.
`comment` optional	string \| null	Free-text comment saved with the acquisition (ABF file comment, FCS `$COM`, Thermo sequence comment, ANDI sample comments), as recorded.
`saved_at` optional	string \| null	ISO-8601 time the file was last saved or exported, when that is the only time it records (a SoftMax Pro text export's `Date Last Saved`). It follows the measurement and is not its start: `started_at` stays empty.

Acquisition2 acquisition in info, info --view structure, check and check --planes: present only for

acquisition in info, info --view structure, check and check --planes: present only for files that are not finished. See book/src/guides/lab-shares.md.

Field	Type	Meaning
`state`	AcquisitionState	`in_progress` or `interrupted`.
`complete_planes`	integer (uint64)	Planes whose data is entirely on disk.
`expected_planes` optional	integer (uint64) \| null	Planes the finished file will hold, when the metadata written so far says so.
`modified_ago_s`	number (double)	Seconds since the file (or the newest member of a directory store) was modified.
`window_s`	number (double)	The live window used for the decision, in seconds.
`missing`	array of string	Structures written at the end of an acquisition that are absent.
`tail_bytes`	integer (uint64)	Bytes after the last complete unit (a unit still being written).
`evidence`	array of string	The observations behind the decision.

AcquisitionState Whether an incomplete file is still being written.

One of: "in_progress" | "interrupted"

Assumed A value the reader assumed (a default, a guess from context) instead of reading it.

Field	Type	Meaning
`field`	string	JSON path of the value in `info` (e.g. `traces[0].channels[1].unit`).
`detail`	string	Why it was assumed and from what.

Assurance The per-file assurance block of info (every view) and check.

Field	Type	Meaning
`level`	AssuranceLevel	`validated`, `partially_validated` or `unvalidated`.
`summary`	string	One line for people and agents.
`fingerprint`	string	The variant fingerprint: `format_id` then `kind=value` for each feature, sorted.
`variant`	array of VariantFeature	Each feature with its corpus evidence.
`reasons` optional	array of string	Why the level is not `validated`, one reason per line.
`undecoded` optional	array of Undecoded	Structures met but not decoded.
`assumed` optional	array of Assumed	Values assumed instead of read.
`calibrations` optional	array of Calibration	Vendor calibrations and corrections the file carries, and whether they were applied.
`inferred_fields` optional	InferredFields	Normalized fields whose meaning is inferred rather than specified.
`inferred` optional	array of InferredValue	Values derived by a rule instead of read, with the evidence for each rule.
`strict_refuses` optional	array of Scope	Outputs `--strict` (MCP `strict: true`) refuses to return for this file.
`strict_withholds` optional	array of Withheld	Fields `--strict` withholds (returned as null; asking for one with `--only` exits 6) while the rest of the output is returned.
`reader_confidence`	Confidence	The reader's overall confidence (evidence rubric), for context.

AssuranceLevel How far a file lies inside what its reader has been validated on.

One of: "validated" | "partially_validated" | "unvalidated"

Calibration A vendor calibration or correction the file carries.

Field	Type	Meaning
`name`	string	What it calibrates (`m/z (MzCalibration)`, `ADC to µV`, `spillover compensation`).
`status`	CalibrationStatus	Applied, not applied, or available on request.
`scope` optional	array of Scope	Outputs it applies to.
`detail`	string	How it is (or is not) applied and how to get calibrated values.

CalibrationStatus Whether a vendor calibration or correction stored in the file was applied.

One of: "applied" | "not_applied" | "available"

ChannelInfo One acquisition channel.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based channel index (the `c` of a plane).
`name` optional	string \| null	Channel name as the acquisition software shows it.
`fluorophore` optional	string \| null	Fluorescent dye or protein imaged in this channel (e.g. `DAPI`, `GFP`), if recorded.
`excitation_nm` optional	number (double) \| null	Excitation wavelength in nanometres: the light used to make the sample fluoresce.
`emission_nm` optional	number (double) \| null	Emission wavelength in nanometres: the light collected from the sample. What the file records varies by format (a dye's emission peak, a filter's centre, the start of a spectral detection window for Leica λ scans); `docs/formats/<fmt>.md` says which. When a detection band is known, `emission_band_*_nm` give it explicitly.
`emission_range_nm` optional	array of number (double) \| null	Detection band `[start_nm, end_nm]` when the instrument records a range instead of a single emission wavelength.
`emission_band_start_nm` optional	number (double) \| null	Short-wavelength edge of the detection band in nanometres (spectral detector window or emission filter), when the file records the band.
`emission_band_end_nm` optional	number (double) \| null	Long-wavelength edge of the detection band in nanometres.
`emission_band_center_nm` optional	number (double) \| null	Centre of the detection band in nanometres: (start + end) / 2.
`color` optional	string \| null	Display colour as `#RRGGBB` if the file records one.
`acquisition_mode` optional	string \| null	Acquisition mode as a readable label, `<technique>[ <contrast>]` (e.g. `Laser Scanning Confocal`, `Widefield Fluorescence`, `Brightfield`, `Phase Contrast`); OME enumeration tokens (`WideField`) are turned into these labels, other vendor wording is kept.
`exposure_ms` optional	number (double) \| null	Exposure (integration) time of the detector in milliseconds.

ColumnInfo A column of a tabular dataset (e.g. an FCS parameter).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based column index.
`name`	string	Short name (FCS `$PnN`).
`label` optional	string \| null	Descriptive label (FCS `$PnS`), if any.
`dtype`	string	NumPy-style dtype of the values as returned by `read_table` (`float32`, `float64`, `uint32`, ...).
`unit` optional	string \| null	Physical unit of the values, if the format records one.
`range` optional	array of number (double) \| null	Nominal `[min, max]` range when the format declares one.
`extra` optional	object	Format-specific column metadata in the reader's documented vocabulary.

Confidence Per-format confidence summary shown by info and self formats.

One of: "high" | "medium" | "low"

Dump Output of info --view full.

Field	Type	Meaning
`file`	InfoOutput	What `info` reports, including the derived `experiment`.
`vendor` optional	any	The vendor's own metadata tree, converted to JSON without renaming anything.
`provenance`	map of Source	Where each normalized field came from. Keys are JSON paths into `file`.

Experiment The experiment a file records: sample, instrument, method, acquisition and measurements.

Field	Type	Meaning
`sample` optional	Sample \| null	What was measured on.
`instrument` optional	ExperimentInstrument \| null	What it was measured with.
`method` optional	Method \| null	How.
`acquisition` optional	Acquisition \| null	When and by whom.
`measurements` optional	array of Measurement	What was measured, one entry per kind of data block.
`notes` optional	array of string	Things to know when reading the fields above (several samples in one file, ...).
`provenance` optional	map of Origin	Origin of every value, keyed by its path in this object (`sample.id`, `method.parameters.nucleus`, `measurements[0]`).

ExperimentInstrument The instrument that made the measurement.

Field	Type	Meaning
`vendor` optional	string \| null	Manufacturer.
`model` optional	string \| null	Model (microscope stand, mass spectrometer, cytometer, plate reader, detector module).
`serial` optional	string \| null	Serial number.
`software` optional	string \| null	Acquisition software.
`software_version` optional	string \| null	Version of the acquisition software.
`kind` optional	Term \| null	Kind of instrument (OBI term: `microscope`, `mass spectrometer`, `flow cytometer`, ...).

FeatureKind What a variant feature describes.

FeatureStatus How the corpus covers one feature value.

One of: "validated" | "seen" | "unseen"

FormatDescriptor Static description of a format as the tool understands it.

Field	Type	Meaning
`id`	string	Short id used on the command line, e.g. `czi`.
`name`	string	Human name, e.g. `Zeiss CZI`.
`vendor`	string	Vendor (nominative use only).
`extensions`	array of string	File extensions, lowercase, without the dot.
`family`	string	Family: `microscopy`, `mass-spectrometry`, `flow-cytometry`, ...
`can_read`	boolean	True when the tool can read this format.
`can_write`	boolean	True when `export` can also write this format (e.g. mzML, OME-Zarr).
`confidence`	Confidence	Overall confidence in this reader.
`known_gaps`	array of string	Things this reader knowingly does not handle yet.

ImageInfo One image (a scene, series, or position) inside the file.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based index used by `--image`.
`name` optional	string \| null	Image (scene, series or position) name, if recorded.
`size_x`	integer (uint32)	Width in pixels.
`size_y`	integer (uint32)	Height in pixels.
`size_z`	integer (uint32)	Number of Z planes (focal slices).
`size_c`	integer (uint32)	Number of channels.
`size_t`	integer (uint32)	Number of time points.
`dimension_order`	string	Storage order of planes, e.g. `XYCZT` (X and Y always first).
`pixel_type`	PixelType	Sample type of every plane.
`samples_per_pixel`	integer (uint32)	1 for grayscale channels, 3 for interleaved RGB.
`physical_size`	PhysicalSize	Physical size of one pixel (and the Z step).
`time_increment_s` optional	number (double) \| null	Interval between time points in seconds.
`channels`	array of ChannelInfo	One entry per channel, in channel order.
`objective` optional	ObjectiveInfo \| null	The objective lens, if recorded.
`instrument` optional	InstrumentInfo \| null	Instrument and software, if recorded.
`acquired_at` optional	string \| null	ISO-8601 acquisition start, if recorded.
`mosaic` optional	MosaicInfo \| null	Tile layout when the image was acquired as a mosaic.
`pyramid_levels`	integer (uint32)	Number of resolution levels stored (1 = no pyramid).
`resolution_levels` optional	array of ResolutionLevel	Size, downsampling and stored tile size of every resolution level, level 0 first. Filled by readers of pyramidal or tiled images (read a level with `--level N`, a rectangle with `--region X,Y,W,H`); empty otherwise.
`plane_count`	integer (uint64)	`size_z * size_c * size_t`.
`extra` optional	object	Format-specific extras that have no OME equivalent, in our own vocabulary.

InferredFields Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a

Fields whose meaning was inferred (reverse-engineered from corpus files), not read from a specification: the inferred entries of the reader's provenance map.

Field	Type	Meaning
`count`	integer (uint32)	How many normalized fields have inferred meaning.
`of`	integer (uint32)	How many normalized fields carry provenance at all.
`examples` optional	array of string	Up to 12 of their JSON paths (`info --view full` → `provenance` has all).

InferredValue A value derived by a rule, with the corpus evidence for the rule.

Field	Type	Meaning
`field`	string	JSON path of the value in `info`.
`rule`	string	The rule that derived it.
`status`	FeatureStatus	`validated` when development files' oracles confirmed values derived by this rule.
`detail`	string	What was derived from what.

InfoOutput What info prints: the normalized [FileInfo] plus the derived [Experiment] under the

What info prints: the normalized [FileInfo] plus the derived [Experiment] under the additive experiment key. Dereferences to the FileInfo.

Field	Type	Meaning
`path`	string	The path as given by the caller.
`size_bytes`	integer (uint64)	Size in bytes (for directory formats such as Bruker `.d`, the files that were read).
`format`	FormatDescriptor	The format that read the file.
`format_version` optional	string \| null	Version of the container format as written in the file, if any.
`images`	array of ImageInfo	Images in the file (empty for tables, spectra and traces).
`tables` optional	array of TableInfo	Tabular datasets (flow cytometry events, ...). Empty for image formats.
`spectra` optional	array of SpectraInfo	Mass-spectrometry runs. Empty for other formats.
`traces` optional	array of TraceInfo	Sampled-signal blocks (electrophysiology, chromatography, NMR). Empty for other formats.
`plane_count`	integer (uint64)	Total planes across all images.
`notes` optional	array of string	Notes the reader wants the caller to see (e.g. "pyramid levels skipped").
`experiment` optional	Experiment \| null	Sample, instrument, method, acquisition and measurements, each value with its origin (`book/src/guides/metadata.md`). Absent when nothing is known.
`acquisition` optional	Acquisition2 \| null	Present when the file is not finished: still being written (`in_progress`, with the number of complete planes) or stopped before the end (`interrupted`). See `book/src/guides/lab-shares.md`.
`plate` optional	PlateSummary \| null	Multi-well plates (high-content screening): the plate id and type, rows and columns, the imaged wells with the images (fields) of each, and how many planes the copy on disk is missing (`docs/formats/hcs.md`). Absent for other files.
`images_total` optional	integer (uint64) \| null	Set when `images` lists only the first few images ([`InfoOutput::cap_images`]: screening plates by default, whose field images are all alike, or `--max-images N`): how many images the file holds. `plate.wells[].images` still indexes every field, the image commands take any index, and `--max-images 0` (MCP `max_images: 0`) lists them all.
`assurance` optional	Assurance \| null	Whether this file lies inside what its reader has been validated on: the variant fingerprint with the corpus evidence for each feature, structures not decoded, values assumed, vendor calibrations, and the outputs `--strict` refuses (`docs/assurance.md`).

InstrumentInfo The instrument and software that produced the file.

Field	Type	Meaning
`manufacturer` optional	string \| null	Instrument manufacturer.
`model` optional	string \| null	Instrument model (e.g. microscope stand or mass spectrometer).
`software` optional	string \| null	Acquisition software.
`software_version` optional	string \| null	Version of the acquisition software.
`detector` optional	string \| null	Detector (camera or photomultiplier) name.

Measurement One thing that was measured, in scientific words.

Field	Type	Meaning
`kind`	MeasurementKind	Which array of the file it describes.
`indices`	array of integer (uint32)	Indices into that array (images, tables, traces or runs) this entry covers.
`what`	string	What was measured, e.g. `fluorescence, 3 channels (DAPI, GFP, mCherry), 21 z-slices` or `LC-MS, negative mode, 2,031 scans, MS1`.
`technique` optional	Term \| null	The technique (CHMO, FBbi, OBI or PSI-MS term).
`terms` optional	array of Term	Further terms: polarity, spectrum types, detectors, acquisition modes.
`parameters` optional	map of Quantity	Counts and settings with units (`scans`, `wells`, `wavelength`, `z_slices`).

MeasurementKind Which part of the file a measurement describes.

One of: "image" | "table" | "trace" | "spectra"

Method How the measurement was made.

Field	Type	Meaning
`name` optional	string \| null	Name of the acquisition method, protocol or experiment as the software saved it.
`technique` optional	Term \| null	The technique (CHMO, FBbi or OBI term: `liquid chromatography-mass spectrometry`, ...).
`assay` optional	Term \| null	The kind of assay (OBI term).
`parameters` optional	map of Quantity	Method settings, keyed by our own snake_case names (`nucleus`, `polarity`, `z_step`).

MosaicInfo Mosaic (tiled/stitched) acquisition summary.

Field	Type	Meaning
`tile_count`	integer (uint32)	Number of tiles (fields of view) in the mosaic.
`tile_width` optional	integer (uint32) \| null	Width of one tile in pixels, when all tiles share it.
`tile_height` optional	integer (uint32) \| null	Height of one tile in pixels, when all tiles share it.
`stitched_on_read`	boolean	Whether the reader stitches tiles into a single plane on read.

ObjectiveInfo The objective lens.

Field	Type	Meaning
`model` optional	string \| null	Objective model name as the vendor records it.
`nominal_magnification` optional	number (double) \| null	Nominal magnification (e.g. `63` for a 63× lens).
`lens_na` optional	number (double) \| null	Numerical aperture.
`immersion` optional	string \| null	Immersion medium between lens and sample (`Oil`, `Water`, `Air`, ...).

Origin Where one experiment value came from.

Field	Type	Meaning
`source`	Source	How the meaning of the source field is known (the reader's provenance for that field; `inferred` for our own mapping and derived text).
`from`	string	The field it was taken from: a path into the `info` JSON (`spectra[0].extra.vial`), or a vendor file inside the dataset (`pdata/1/title`).

PhysicalSize Physical pixel size in micrometres (the OME default unit). Every present value is > 0.

Field	Type	Meaning
`x` optional	number (double) \| null	Pixel width in µm (the distance between neighbouring columns).
`y` optional	number (double) \| null	Pixel height in µm (the distance between neighbouring rows).
`z` optional	number (double) \| null	Spacing between Z planes (focal slices) in µm.
`unit`	string	Always `µm` in this schema version.

PixelType Sample type of one channel value. Names follow OME-XML PixelType values.

PlateSummary Layout of a multi-well plate (high-content screening): info → plate.

Field	Type	Meaning
`id` optional	string \| null	Plate identifier or barcode as the acquisition software recorded it.
`name` optional	string \| null	Plate name, when recorded besides the id.
`plate_type` optional	string \| null	Plate type (product) as recorded, e.g. `384 PerkinElmer CellCarrier Ultra`.
`rows`	integer (uint32)	Number of rows of the plate (8 for a 96-well plate).
`columns`	integer (uint32)	Number of columns of the plate (12 for a 96-well plate).
`wells`	array of PlateWell	The imaged wells, row by row.
`field_count`	integer (uint32)	Most fields of view in one well.
`planes_expected`	integer (uint64)	Planes the plate's index lists (every image's `plane_count`).
`planes_absent` optional	integer (uint64)	Planes the instrument never acquired or recorded (they read as blank and are left out of statistics; `images[].extra.absent_planes`).
`planes_missing` optional	integer (uint64)	Planes whose files the index names but that are not on disk (`check` lists them).
`complete`	boolean	True when every plane the index names is on disk.
`extra` optional	object	Format-specific plate facts in the reader's documented vocabulary.

PlateWell One imaged well of a plate.

Field	Type	Meaning
`well`	string	Well name, e.g. `C05` (row letters, column zero-padded to two digits).
`row`	string	Row letters (`C`).
`column`	integer (uint32)	Column number, 1-based (`5`).
`row_index`	integer (uint32)	Zero-based row index (`C` = 2).
`column_index`	integer (uint32)	Zero-based column index.
`images`	array of integer (uint32)	Indices of the images (fields of view) of this well, in field order.
`planes_missing` optional	integer (uint64)	Planes of this well whose files are not on disk (0 when the well is complete).

Quantity A value with an optional unit: {"value": 19, "unit": "min", "ucum": "min"}.

Field	Type	Meaning
`value`	any	A number, a string, or a list of them.
`unit` optional	string \| null	Unit as written for people (`µm`, `°C`), when the value has one.
`ucum` optional	string \| null	UCUM code of `unit` (`um`, `Cel`).

ResolutionLevel Geometry of one resolution level of an image.

Field	Type	Meaning
`level`	integer (uint32)	Level index: 0 is full resolution, larger is more downsampled (`--level`).
`size_x`	integer (uint32)	Width in pixels.
`size_y`	integer (uint32)	Height in pixels.
`downsample_x`	number (double)	Level-0 width over this level's width (1 for level 0; 2, 4, ... for a halving pyramid).
`downsample_y`	number (double)	Level-0 height over this level's height.
`tile_width` optional	integer (uint32) \| null	Width of the tiles (subblocks, chunks) the level is stored in, when it is tiled: region reads aligned to this grid decode each tile once.
`tile_height` optional	integer (uint32) \| null	Height of the stored tiles.
`size_z` optional	integer (uint32) \| null	Number of z planes at this level, when it differs from the image's `size_z` (Imaris downsamples z as well).

Sample What was measured: the sample's identity as the file records it.

Field	Type	Meaning
`id` optional	string \| null	The sample's identifier, from the field named in `source_field`.
`name` optional	string \| null	A descriptive sample name when the file records one besides the id.
`well` optional	string \| null	Plate well (`B2`, `A01`).
`barcode` optional	string \| null	Plate or tube barcode.
`sequence_position` optional	string \| null	Position in the autosampler sequence or tray (vial `D:35`, `2:A,8`).
`source_field` optional	string \| null	Path of the field `id` came from (`spectra[0].extra.sample_name`, `tables[0].extra.specimen`, `pdata/1/title`).

Scope Which outputs of a file a feature, a structure or a calibration affects.

One of: "metadata" | "pixels" | "spectra" | "traces" | "tables"

SidecarMeta Sidecar bookkeeping: what it was made from and when.

Field	Type	Meaning
`source`	SidecarSource	The source's fingerprint (compared to decide whether to rewrite).
`options`	SidecarOptions	The options used.
`written_at`	string	When the sidecar was written (ISO-8601 UTC).

SidecarOptions The info --view full options the sidecar was written with.

Field	Type	Meaning
`vendor`	boolean	The vendor metadata tree is included.
`provenance`	boolean	The provenance map is included.
`all_frames`	boolean	Every per-frame record is included (`--all-frames`).

SidecarSource The source a sidecar describes, as it was when the sidecar was written.

Field	Type	Meaning
`name`	string	File (or directory) name of the source.
`size_bytes`	integer (uint64)	Size in bytes (a directory data set: the sum of its files).
`modified_ns`	integer (uint64)	Modification time in nanoseconds since the Unix epoch (a directory: the newest file).

SignalChannelInfo One channel of a sampled-signal dataset.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based channel index.
`name`	string	Channel name as recorded.
`unit` optional	string \| null	Physical unit of the scaled values (`pA`, `mV`, `AU`, ...).
`dtype`	string	NumPy-style dtype of the raw stored samples.
`scale`	number (double)	`value = raw * scale + offset` when the file stores integers.
`offset`	number (double)	Added after scaling; see `scale`.
`extra` optional	object	Format-specific channel metadata in the reader's documented vocabulary.

Source How we learned what a field means. Ordered from most to least authoritative.

One of: "spec" | "vendor-impl" | "prior-art" | "inferred"

SpectraInfo A collection of mass spectra (one acquisition run).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based run index.
`name` optional	string \| null	Run name, if the file records one.
`scan_count`	integer (uint64)	Number of spectra (scans) in the run.
`ms_levels`	array of integer (uint32)	MS levels present (1 = full scans, 2 = MS/MS, ...).
`rt_range_s` optional	array of number (double) \| null	Retention-time range in seconds.
`instrument` optional	InstrumentInfo \| null	Instrument and software, if recorded.
`extra` optional	object	Format-specific run metadata in the reader's documented vocabulary.

TableInfo A tabular dataset inside the file (rows × columns), e.g. FCS events.

Field	Type	Meaning
`index`	integer (uint32)	Zero-based table index.
`name` optional	string \| null	Table name, if the format has one.
`row_count`	integer (uint64)	Number of rows (e.g. recorded events).
`columns`	array of ColumnInfo	One entry per column.
`extra` optional	object	Format-specific table metadata in the reader's documented vocabulary.

Term An ontology term: its id (CURIE, e.g. CHMO:0000524) and label.

Field	Type	Meaning
`id`	string	Compact id, `PREFIX:local` (`MS:1000130`, `CHMO:0000591`, `FBbi:00000246`, `OBI:0000916`).
`label`	string	The term's label in its ontology (`positive scan`).

ToolId Identifies the producing tool so consumers can reason about compatibility.

Field	Type	Meaning
`name`	string	Always `openreadout`.
`version`	string	The tool's version (`CARGO_PKG_VERSION`).

TraceInfo A block of uniformly sampled signals (a sweep, a chromatogram run, an FID).

Field	Type	Meaning
`index`	integer (uint32)	Zero-based trace index.
`name` optional	string \| null	Trace name, if the format has one.
`sample_rate_hz`	number (double)	Samples per second.
`sample_count`	integer (uint64)	Samples per sweep (the longest sweep when sweeps differ; see `extra.sweep_sample_counts`).
`sweep_count`	integer (uint32)	Number of sweeps/episodes stored back to back (1 for continuous recordings).
`channels`	array of SignalChannelInfo	One entry per channel.
`start_s` optional	number (double) \| null	Time of the first sample relative to the recording start, seconds.
`extra` optional	object	Format-specific trace metadata in the reader's documented vocabulary.

Undecoded A structure the reader met in the file but did not decode.

Field	Type	Meaning
`structure`	string	What the structure is, in the format notes' vocabulary.
`scope` optional	array of Scope	Outputs that may be incomplete or wrong because of it. Empty: it is left out and the values returned do not depend on it.
`detail`	string	What is known about it and what the reader does instead.

VariantFeature One feature of the file's fingerprint, with the corpus evidence for it.

Field	Type	Meaning
`kind`	FeatureKind	What the feature describes.
`value`	string	Its value.
`scope` optional	array of Scope	Outputs whose decoding depends on it (empty: descriptive only).
`status`	FeatureStatus	`validated`, `seen` or `unseen`.
`corpus_files`	integer (uint32)	Development-corpus files with this value confirmed by an independent reader.
`sources`	integer (uint32)	Distinct depositors among them.

Withheld A field --strict withholds: it is present, but its value was assumed, derived by a rule no

A field --strict withholds: it is present, but its value was assumed, derived by a rule no independent reader confirmed, or never compared with an independent reader.

Field	Type	Meaning
`field`	string	JSON path pattern in `info` (`[]` matches any index).
`reason`	string	Why it is not validated.

sidecar-file.schema.json · SidecarFile

index

index.json.

Field	Type	Meaning
`schema_version`	string	[`INDEX_SCHEMA_VERSION`].
`tool`	ToolInfo	The tool and version that wrote it.
`index_dir`	string	Absolute path of the index directory.
`roots`	array of string	The directories (or files) crawled, absolute.
`settings`	IndexSettings	Options of the crawl.
`complete`	boolean	True when the crawl walked every root to the end. False after a cap (`--max-files`, `--max-seconds`) or an interruption: the tables then hold what was read so far plus the previous run's records for the rest, and rerunning the same command continues.
`started_at`	string	When this run started (ISO-8601 UTC).
`updated_at`	string	When the tables were written.
`tables`	map of TableManifest	The tables.
`datasets`	integer (uint64)	Data sets (rows of `experiments.parquet`) after multi-file grouping.
`files`	integer (uint64)	Rows of `files.parquet`.
`bytes`	integer (uint64)	Bytes of every file seen.
`formats`	map of Tally	Data sets and bytes per format id.
`families`	map of Tally	Data sets and bytes per family.
`years`	map of Tally	Data sets per acquisition year (`unknown` when the file records no date).
`unknown_extensions`	map of Tally	Files no reader recognises, per lower-case extension (`(none)` for no extension).
`check_status`	map of integer (uint64)	Data sets per check status.
`problems`	map of integer (uint64)	Problems per category (`integrity`, `readability`, `walk`, `pii`).
`pii`	PiiTotals	Personal-data totals.
`changes`	map of integer (uint64)	Data sets per change (`new`, `changed`, `unchanged`, `moved`) and `removed`.
`crawl`	CrawlStats	Crawl counters, cumulative over resumed sessions.
`files_per_s`	number (double)	Items per second over the crawl's wall time.
`next` optional	string \| null	What to do next, when the crawl is not complete.

Types used (7)

CrawlStats Counters of one crawl (cumulative over resumed sessions of the same run).

Field	Type	Meaning
`items`	integer (uint64)	Walk items processed: files and directory data sets.
`files_seen`	integer (uint64)	Files seen, counting every file inside directory data sets.
`recognised`	integer (uint64)	Items a reader recognised (before multi-file grouping).
`unknown`	integer (uint64)	Items no reader recognises.
`unreadable`	integer (uint64)	Recognised items that could not be opened or summarized.
`new`	integer (uint64)	Items read for the first time.
`changed`	integer (uint64)	Items read again (size, time or tool version changed).
`unchanged`	integer (uint64)	Items reused from the previous run without being opened.
`removed`	integer (uint64)	Items of the previous run that are gone.
`bytes_seen`	integer (uint64)	Bytes of every file seen.
`bytes_read`	integer (uint64)	Bytes the crawler itself read (sniffing and fingerprints); the readers' own header reads are not counted.
`elapsed_s`	number (double)	Wall time of the crawl, seconds (all sessions of a resumed run).
`sessions`	integer (uint32)	Sessions this run took (1 plus the number of resumes).
`walk`	WalkStats	What the walk skipped.

IndexSettings Crawl options that shape the index.

Field	Type	Meaning
`check`	string	`headers`, `full` or `none`.
`follow_symlinks`	boolean	Symbolic links followed.
`exclude` optional	array of string	`--exclude` patterns.
`pii`	boolean	Personal-data detection on.

PiiTotals Personal-data totals.

Field	Type	Meaning
`datasets_flagged`	integer (uint64)	Data sets with at least one flag.
`flags`	integer (uint64)	Flags.
`by_kind`	map of integer (uint64)	Flags per kind (`person_name`, `email`, ...).

TableManifest One table of the index.

Field	Type	Meaning
`file`	string	File name inside the index directory.
`rows`	integer (uint64)	Rows.

Tally A count and a byte total.

Field	Type	Meaning
`count`	integer (uint64)	How many.
`bytes`	integer (uint64)	Bytes.

ToolInfo The tool that wrote the index.

Field	Type	Meaning
`name`	string	`openreadout`.
`version`	string	Its version.

WalkStats Counters of what the walk skipped.

Field	Type	Meaning
`directories`	integer (uint64)	Directories listed.
`hidden_skipped`	integer (uint64)	Hidden entries (`.name`) skipped.
`symlinks_skipped`	integer (uint64)	Symbolic links skipped (not followed).
`excluded`	integer (uint64)	Entries skipped by `--exclude` (and the index directory).
`unreadable_directories`	integer (uint64)	Directories that could not be listed.

index.schema.json · IndexManifest

search

Search results.

Field	Type	Meaning
`index_dir`	string	The index directory searched.
`query`	string	The query as given.
`index_complete`	boolean	Whether the index covers every root to the end (see `index.json`).
`total`	integer (uint64)	Data sets matching.
`returned`	integer (uint)	Results returned.
`truncated`	boolean	True when `total` > `returned`.
`fields`	array of string	The columns of each result.
`results`	array of object	One object per matching data set, with the requested columns.

search.schema.json · SearchOutput

search-health

openreadout search INDEX --health.

Field	Type	Meaning
`index_dir`	string	The index directory.
`index_complete`	boolean	Whether the index covers every root to the end.
`roots`	array of string	The roots of the index.
`index_updated_at`	string	When the index was last written.
`generated_at`	string	When this report was made.
`totals`	Totals	Totals.
`by_format`	array of NamedTally	Data sets and bytes per format.
`by_family`	array of NamedTally	Per family.
`by_year`	array of NamedTally	Per acquisition year.
`integrity`	Integrity	Truncated and corrupt data sets.
`unreadable`	Unreadable	Unreadable formats and unrecognised files.
`duplicates`	Duplicates	Byte-identical copies.
`near_duplicates`	NearDuplicates	The same experiment stored more than once.
`at_risk`	AtRisk	Vendor-only formats with no open export.
`pii`	PiiSection	Personal data.

Types used (14)

AtRisk At-risk section: vendor-only formats with no open export next to them.

Field	Type	Meaning
`count`	integer (uint64)	Data sets at risk.
`bytes`	integer (uint64)	Their bytes.
`legacy`	integer (uint64)	Of which in legacy formats (vendor software discontinued).
`by_format`	array of NamedTally	Per format.
`datasets`	array of AtRiskEntry	The largest.
`with_open_export`	integer (uint64)	Vendor/legacy data sets that do have an open export.

AtRiskEntry A data set at risk.

Field	Type	Meaning
`path`	string	Path.
`format`	string	Format id.
`preservation`	string	`vendor` or `legacy`.
`size_bytes`	integer (uint64)	Bytes.

DuplicateGroup A group of identical data sets.

Field	Type	Meaning
`size_bytes`	integer (uint64)	Bytes of one copy.
`sha256` optional	string \| null	SHA-256 of the content (null when not confirmed by hashing).
`paths`	array of string	The copies, in walk order.

Duplicates Duplicates section.

Field	Type	Meaning
`confirmed`	boolean	True when every group was confirmed by a full-content hash.
`group_count`	integer (uint64)	Groups of identical data sets.
`redundant_bytes`	integer (uint64)	Bytes that extra copies take.
`candidates_hashed`	integer (uint64)	Candidate data sets hashed.
`bytes_hashed`	integer (uint64)	Bytes read to hash them.
`groups`	array of DuplicateGroup	The largest groups.

Integrity Integrity section.

Field	Type	Meaning
`status`	map of integer (uint64)	Data sets per check status.
`problem_count`	integer (uint64)	Data sets that are truncated, corrupt, unreadable or unsupported.
`problems`	array of IntegrityEntry	The first of them.

IntegrityEntry A data set with an integrity problem.

Field	Type	Meaning
`path`	string	Path.
`format` optional	string \| null	Format id.
`status`	string	`truncated`, `corrupt`, `unreadable` or `unsupported`.
`codes`	array of string	Finding or error codes.
`message` optional	string \| null	The error message, when it could not be opened.

NamedTally A count and bytes under a name.

Field	Type	Meaning
`name`	string	The format id, family, year or extension.
`count`	integer (uint64)	How many.
`bytes`	integer (uint64)	Bytes.

NearDuplicateGroup The same experiment stored more than once (not byte-identical).

Field	Type	Meaning
`reason`	string	Why they were grouped: `same acquisition time and dimensions` or `same name and dimensions`.
`paths`	array of string	The members, in walk order.
`formats`	array of string	Their formats, same order.
`exported_twice`	boolean	True when two or more members are open exports (the experiment was exported twice).

NearDuplicates Near-duplicate section.

Field	Type	Meaning
`group_count`	integer (uint64)	Groups found.
`exported_twice`	integer (uint64)	Groups with two or more open exports.
`groups`	array of NearDuplicateGroup	The first groups.

PiiEntry A flagged data set.

Field	Type	Meaning
`path`	string	Path.
`kinds`	array of string	Kinds flagged.
`fields`	array of string	Fields flagged.

PiiSection Personal-data section (field paths and kinds only; never values).

Field	Type	Meaning
`datasets_flagged`	integer (uint64)	Data sets with a flag.
`flags`	integer (uint64)	Flags.
`by_kind`	map of integer (uint64)	Flags per kind.
`by_rule`	map of integer (uint64)	Flags per rule.
`by_field`	array of NamedTally	Flags per field path (array indices removed), most frequent first.
`datasets`	array of PiiEntry	The first flagged data sets with their kinds.

Totals Totals.

Field	Type	Meaning
`datasets`	integer (uint64)	Data sets.
`dataset_bytes`	integer (uint64)	Bytes in data sets.
`files`	integer (uint64)	Files seen (all roles).
`unknown_files`	integer (uint64)	Files no reader recognises.
`unknown_bytes`	integer (uint64)	Their bytes.

Unreadable Unreadable section.

Field	Type	Meaning
`formats`	array of UnreadableFormat	Recognised formats that could not be opened, per format and error.
`unknown_extensions`	array of NamedTally	Files no reader recognises, per extension (largest counts first).

UnreadableFormat Formats recognised but not readable, per error.

Field	Type	Meaning
`format`	string	Format id.
`error_code`	string	Error code (`unsupported_feature`, `corrupt_file`, `io`).
`count`	integer (uint64)	Data sets.

search-health.schema.json · HealthReport

search-export

datasheet.json, and the payload of search --export --json.

Field	Type	Meaning
`schema_version`	string	Datasheet schema version.
`output`	string	The output directory.
`created_at`	string	When the export finished.
`tool`	string	Tool and version.
`query`	string	The query.
`index_dir`	string	The index it came from.
`index_roots`	array of string	The index's roots.
`index_updated_at`	string	When the index was written.
`table_format`	TableFormat	Tables written as `parquet` or `csv`.
`redaction`	string	Whether personal data was redacted, and how.
`counts`	map of integer (uint64)	Totals over the exported data sets.
`formats`	map of integer (uint64)	Data sets per source format.
`licenses`	map of integer (uint64)	Data sets per licence (`unknown` when none was found).
`exported_now`	integer (uint64)	Data sets exported in this run (the rest were already done).
`resumed`	integer (uint64)	Data sets reused from an earlier, interrupted run.
`datasets`	array of ExportedDataset	Every exported data set.
`skipped`	array of SkippedDataset	Data sets that could not be exported.
`verified`	boolean	Every output verified.

Types used (6)

ExportedDataset One exported data set.

Field	Type	Meaning
`id`	string	Output id (file-name prefix).
`source`	string	Source path.
`format`	string	Source format id.
`family`	string	Source family.
`size_bytes`	integer (uint64)	Source bytes.
`fingerprint` optional	string \| null	Source content fingerprint (from the index).
`counts`	map of integer (uint64)	Images, planes, tables, table rows, traces, trace samples, spectra runs, spectra.
`outputs`	array of OutputFile	Files written.
`experiment` optional	any	The experiment (redacted when asked), with provenance.
`license` optional	LicenseInfo \| null	Licence, when known.
`pii` optional	array of PiiFlag	Personal-data flags (field, kind, rule).
`redacted_values`	integer (uint64)	Values replaced by redaction.
`notes` optional	array of string	Things to know (parts that could not be exported).

LicenseInfo The licence of a data set, when known.

Field	Type	Meaning
`spdx` optional	string \| null	SPDX id, when recognised (`CC-BY-4.0`, `CC0-1.0`, `MIT`, ...).
`source`	string	Where it came from: `user` (`--license`) or the licence file's path.

OutputFile One written file.

Field	Type	Meaning
`file`	string	Path relative to the output directory.
`kind`	string	`metadata`, `image`, `table`, `trace` or `spectra`.
`rows`	integer (uint64)	Rows (tables, traces, spectra) or planes (images).
`columns` optional	array of string	Columns written (tables, traces, spectra).
`bytes`	integer (uint64)	Bytes on disk.
`digest` optional	string	xxh3-64 digest of every value written (rows in order), hex; empty for images.
`verified`	boolean	Read back and compared.

PiiFlag One personal-data flag: which field, what kind, which rule. The value itself is never

One personal-data flag: which field, what kind, which rule. The value itself is never stored in the index.

Field	Type	Meaning
`field`	string	Path of the field in the `info` JSON (`experiment.acquisition.operator`, `tables[0].extra.vendor_keywords.EXPORT.EXPORT USER NAME`).
`kind`	string	`person_name`, `email`, `phone`, `patient_id`, `date_of_birth` or `free_text`.
`rule`	string	The rule that fired (`book/src/guides/lab-shares.md#personal-data`).

SkippedDataset A data set that could not be exported.

Field	Type	Meaning
`source`	string	Source path.
`reason`	string	Why.

TableFormat File format for tables, traces and spectra.

One of: "parquet" | "csv"

search-export.schema.json · ExportDatasetReport

watch

One line of watch output.

Field	Type	Meaning
`seq`	integer (uint64)	Sequence number, increasing by one per event within a watcher (the MCP cursor).
`event`	EventKind	What happened.
`ts`	string	When the event was emitted (ISO-8601 UTC, milliseconds).
`path`	string	The data set (a file, or a directory store).
`format` optional	string \| null	Format id, once known.
`state` optional	string \| null	`in_progress`, `interrupted` or `complete`.
`image` optional	integer (uint32) \| null	Image index (plane events).
`c` optional	integer (uint32) \| null	Channel index (plane events).
`z` optional	integer (uint32) \| null	Z index (plane events).
`t` optional	integer (uint32) \| null	Time index (plane events).
`run` optional	integer (uint32) \| null	Run (spectra) or trace index.
`index` optional	integer (uint64) \| null	Zero-based position of the plane, scan or sweep among those reported for the data set.
`complete` optional	integer (uint64) \| null	Planes (or scans) complete so far.
`expected` optional	integer (uint64) \| null	Planes the finished data set will hold, when known.
`size_bytes` optional	integer (uint64) \| null	Size of the data set in bytes when the event was produced.
`mtime` optional	string \| null	Modification time of the data set (ISO-8601 UTC).
`idle_s` optional	number (double) \| null	Seconds since the data set last grew (`dataset_stalled`).
`qc` optional	QcFinding \| null	The fired rule (`qc`).
`error` optional	ErrorBody \| null	What went wrong (`error`).

Types used (4)

ErrorBody Structured error body. hint is meant to be actionable by an agent.

Field	Type	Meaning
`code`	string	Stable code: `unknown_format`, `unsupported_feature`, `corrupt_file`, `usage`, `io`, `error`, `internal_panic` (a bug: the tool panicked; please report it).
`message`	string	Human-readable description of the failure.
`hint` optional	string \| null	What to try next, when the tool knows.
`exit_code`	integer (int32)	The process exit code for this error (see the crate docs).

EventKind Kinds of events.

Metric A QC metric.

One of: "saturated_fraction" | "sharpness_ratio" | "interval_ratio" | "tic_ratio"

QcFinding A fired rule.

Field	Type	Meaning
`rule`	string	Rule name.
`metric`	Metric	Metric measured.
`value`	number (double)	Measured value.
`bound`	string	`min` or `max`: which bound was crossed.
`threshold`	number (double)	The bound's value.
`description` optional	string \| null	The rule's description.
`saturation_level` optional	number (double) \| null	`saturated_fraction` only: the sample value counted as saturated (2^bits − 1 from the file's recorded bit depth, else the pixel type's maximum).

watch.schema.json · WatchEvent

formats

Output of self formats.

Field	Type	Meaning
`formats`	array of FormatDescriptor	Every registered format, in detection order.

Types used (2)

Confidence Per-format confidence summary shown by info and self formats.

One of: "high" | "medium" | "low"

FormatDescriptor Static description of a format as the tool understands it.

Field	Type	Meaning
`id`	string	Short id used on the command line, e.g. `czi`.
`name`	string	Human name, e.g. `Zeiss CZI`.
`vendor`	string	Vendor (nominative use only).
`extensions`	array of string	File extensions, lowercase, without the dot.
`family`	string	Family: `microscopy`, `mass-spectrometry`, `flow-cytometry`, ...
`can_read`	boolean	True when the tool can read this format.
`can_write`	boolean	True when `export` can also write this format (e.g. mzML, OME-Zarr).
`confidence`	Confidence	Overall confidence in this reader.
`known_gaps`	array of string	Things this reader knowingly does not handle yet.

formats.schema.json · FormatsOutput

doctor

Output of doctor.

Field	Type	Meaning
`ok`	boolean	True when every check passed (exit 0; otherwise exit 1).
`version`	string
`target`	string	Target triple the binary was built for.
`profile`	string	`release` or `debug`.
`features`	array of string	Cargo features compiled in.
`mcp`	boolean	Whether `openreadout mcp` can serve (the `mcp` feature).
`mcp_tools`	array of string	The MCP tools the server offers (empty without the `mcp` feature).
`threads`	integer (uint)	Worker threads for plane decoding (`--threads`).
`formats`	array of string	Registered format readers, in detection order.
`stdout_is_terminal`	boolean
`stderr_is_terminal`	boolean
`environment`	array of string	Environment variables that change behaviour, when set.
`checks`	array of DoctorCheck

Types used (1)

DoctorCheck One self-test step.

Field	Type	Meaning
`name`	string
`ok`	boolean
`detail`	string

doctor.schema.json · DoctorReport