Upgrading

Names change between releases without aliases, so a script or prompt written for an older release can need the changes below. The changelog lists everything else.

From 0.3

The six plate-reader MCP tools are one, openreadout_assay, with analysis:

0.3	0.4
`openreadout_assay_wells`	`openreadout_assay` with `analysis: "wells"`
`openreadout_assay_curve`	`openreadout_assay` with `analysis: "curve"`
`openreadout_dose_response`	`openreadout_assay` with `analysis: "dose-response"`
`openreadout_kinetics`	`openreadout_assay` with `analysis: "kinetics"`
`openreadout_growth`	`openreadout_assay` with `analysis: "growth"`
`openreadout_assay_qc`	`openreadout_assay` with `analysis: "qc"`

The command line keeps analyze assay-wells, assay-curve, dose-response, kinetics, growth and assay-qc.

WebAssembly: preview() resolves to { meta, data, type } instead of { meta, png }, takes axes: "rulers" | "grid" | "none" instead of the axes and grid booleans, and draws at 768 px by default.

From 0.1 to 0.2

OpenReadout 0.2 renames several commands, MCP tools and flags so that the command line and the MCP server use the same names, and so that each command does one thing. The JSON output is schema_version 2. The old names have no aliases, so a script or prompt written for 0.1 needs the changes below.

Commands

0.1	0.2
`check --planes`	`planes`
`check A --against B`	`compare A B`
`check --report`	`report`
`spectra` (scan list)	`scans`
`spectra --scan N`, `--index I`, `--nth N` (one spectrum)	`spectrum --scan N`, `--spectrum I`, `--ms-level L --spectrum I` (zero-based)
`analyze assay wells`, `curve`, `dose-response`, `kinetics`, `growth`, `qc`	`analyze assay-wells`, `assay-curve`, `dose-response`, `kinetics`, `growth`, `assay-qc`
`export --attachment NAME`	`extract FILE NAME`
`batch summarize TABLE`	`summarize TABLE`
`search INDEX_DIR --health`	`health INDEX_DIR`
`search INDEX_DIR QUERY --export OUT`	`export-dataset INDEX_DIR QUERY OUT`
`index --health`	removed, use `health`

info, check, preview, stats, trace, table, the other analyze subcommands, export, batch, link, index, search, watch, self and mcp keep their names.

MCP tools

An MCP tool is now openreadout_ plus the command name, with - as _, and its arguments are the command’s long flags with - as _. The MCP tools page lists all of them.

0.1	0.2
`openreadout_analyze` with `kind`	one tool per analysis: `openreadout_peaks`, `openreadout_chromatogram`, `openreadout_nmr_peaks`, `openreadout_ephys_features`, `openreadout_spikes`, `openreadout_qpcr`, `openreadout_gate`
`openreadout_analyze` with `kind: assay` and `analysis`	`openreadout_assay_wells`, `openreadout_assay_curve`, `openreadout_dose_response`, `openreadout_kinetics`, `openreadout_growth`, `openreadout_assay_qc`
`openreadout_check` with `against`	`openreadout_compare`
`openreadout_check` with `report`	`openreadout_report`
`openreadout_spectra`	`openreadout_scans` and `openreadout_spectrum`
`openreadout_export` with `attachment`	`openreadout_extract`
`openreadout_batch` with `measure: summarize`	`openreadout_summarize`
`openreadout_formats`	the `openreadout://formats` resource
(none)	`openreadout_health`

The analysis options that 0.1 took in options are now arguments of each tool.

Flags and arguments

command	0.1	0.2 (command line / MCP)
`info`	vendor tree shown, `--no-vendor` to leave it out	left out, `--vendor` / `vendor` to include it
`info`	`--all-frames`	`--max-frames N` / `max_frames`
`stats`	planes listed, `--no-planes` to leave them out	left out, `--per plane` / `per: plane` to list them
`trace`	`--first`	`--first-sample` / `first_sample`
`table`	MCP `transform_parameters`	`--parameter` / `parameters`
`preview`	`--plain`, `--grid`	`--axes rulers\|grid\|none` / `axes`
`scans`	`--rt`, `--tol`, `--ppm`, `--filter`	`--rt-range`, `--precursor-tol`, `--precursor-ppm`, `--scan-filter`
`scans`	MCP `precursor_mz`	`--precursor` / `precursor`
`export`	`--to FORMAT`	`--format` / `format`. MCP also accepts `csv` now.
`batch`	MCP `inputs`, measure `spectra`	`paths`, measure `scans`
`watch`	MCP `stall_after_s`	`--stall-after` / `stall_after` (seconds)
`analyze nmr-peaks`	`--range A:B`	`--range-ppm` / `range_ppm`
`analyze ephys-features`	`--peak-threshold`	`--peak-threshold-mv` / `peak_threshold_mv`
`analyze spikes`	`--band`	`--band-hz` / `band_hz`
`analyze qpcr`	`--cq`, `--baseline START-END`, `--reference`, `--control`, `--undetermined-as`	`--compute-cq`, `--baseline-start` and `--baseline-end`, `--reference-target`, `--control-sample`, `--undetermined-cq`
plate assays	`--blank`, `--blank-subtraction` (MCP `blank`), `--positive`, `--negative`, `--empty`, `--wavelength`	`--blank-wells`, `--blank-subtraction` / `blank_subtraction`, `--positive-wells`, `--negative-wells`, `--empty-wells`, `--wavelength-nm`
`analyze growth`	`--threshold`	`--growth-threshold`
`analyze assay-curve`, `dose-response`	`--preview PNG` (MCP `plot`)	`--plot PNG` / `plot`
`info`, `stats`, `trace`, `table`, `batch`	`--samples`, `--layout`	`--sample-sheet` (the plate assays keep `--layout`)

JSON output

The envelope’s schema_version is "2". Besides the renames above, two defaults changed what a plain call returns: info --view full leaves out the vendor tree unless you add --vendor, and stats leaves out the per-plane list unless you ask for --per plane. LIF channels are named after their dye (DAPI, ALEXA 488) rather than their display colour. The schemas are on the JSON reference and in openreadout self schema.

Plugins and integrations

The Claude Code plugin now comes from its own repository, openreadout/agent-plugins. Add that marketplace and install the plugin from it:

/plugin marketplace add openreadout/agent-plugins
/plugin install openreadout@openreadout

Run openreadout self skill --install all again to replace an installed skill with the 0.2 version. The Python and R packages follow the command names. Python has File.scans() and openreadout.summarize(), and R has openreadout_scans(), openreadout_spectrum() and openreadout_summarize().