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OpenReadout

Bio-Rad Image Lab .scn

Bio-Rad Image Lab (desktop, and Image Lab Touch on ChemiDoc and Gel Doc imagers) saves gel and blot scans as .scn files. OpenReadout returns the 16-bit image of each scan with its pixel size, imager, exposure, filters, user, dates and audit log.

Derived from public files of many depositors (Image Lab 3.0.1 to 6.1.0), with Bio-Formats 8.5.0 run as a black box for ground truth. Provenance: docs/provenance/biorad-scn.md. Crate: openreadout-gel.

format id files reads confidence
biorad-scn .scn written by Bio-Rad Image Lab (desktop and the imagers’ Image Lab Touch) the 16-bit image of each scan, pixel size, imager, application, exposure, filters, user, dates, audit log high (evidence rubric, docs/assurance.md)

Leica SCN whole-slide files share the extension; they are TIFF and the TIFF reader takes them.

Layout

A MIME document (RFC 2046): header lines MIME-Version: 1.0 (Generated by Image Lab <version>), Content-Type: multipart/mixed; boundary="<b>", Content-Description: Image Lab Image File, a blank line, then parts separated by --<b> lines. Image Lab writes a delimiter after every part and no --<b>-- closing marker: a multipart ends where the enclosing multipart’s delimiter (or the end of the file) follows its last delimiter. Leaf parts carry Content-Length; the reader uses it to skip binary bodies (a body may contain anything) and never loads an image to parse the file.

Parts seen, in order:

part (Content-Description) type holds
ItemHeaderTag text/xml authoring application and version, item name, scan id, description, user, channel count, display settings (per scan transform low/high fraction, gamma, invert)
ScanImageTag<n> multipart one scan: ImageData and ImageHeader
ImageData application/octet-stream width × height little-endian unsigned 16-bit samples, row-major from the top left (8-bit when the length is width × height)
ImageHeader text/xml name, creation_date (Unix time), endian, size_pix, org_size_pix (size before cropping), size_mm (known true/false), scanner (data_ceiling, max_value), image/@zero_is, scan_attributes and extended_scan_attributes (name/value/type triples), units, history, scaler
ItemProtocolSettingsTag text/xml imager type, exposure settings, band-detection and molecular-weight settings, the audit log ListLogEntries/LogEntry (Timestamp, FullName, User, Type, Data)

An XML part starts <!DOCTYPE XML>. Any other part is listed by info --view structure and, when XML, kept in the vendor tree. No file seen stores lane or band analysis.

What the reader returns

  • Images: one per ScanImageTag holding ImageData + ImageHeader; uint16 (or uint8), one channel, one plane. A scan whose data length is neither width × height × 2 nor × 1, or whose byte order is not little, is refused (the file still opens; check reports it).
  • Pixel size (µm): size_mm × 1000 / size_pix when size_mm/@known is true; none when it is false (an imported TIFF gets an 88.9 mm, 300-dpi default that is not a measurement; Bio-Formats uses it, we do not).
  • Channel: name = the Application attribute (Chemiluminescence, Chemi, Chemi+Marker, Colorimetric, Coomassie Blue, Ethidium Bromide, IRDye 800CW, …; signal when absent), exposure_ms from Exposure Time (sec), and emission_nm/emission_range_nm from an emission filter written <centre>/<width> Filter (835/50 Filter → 835 nm, 810-860 nm).
  • Image extra: zero_is and display_inverted (true when zero_is is white: Image Lab shows the image dark-on-light; values are as stored, higher = more signal), size_mm, original_size_px (before cropping), data_ceiling, max_value, excitation_source, emission_filter, creation_date, history, gel_scaling (mode, real_scale of a Molecular Dynamics .gel import: the stored values are the square-root-encoded counts and are not linearized), scan_attributes (every attribute as the file names it).
  • Table 0 log (when the file has an audit log): time (s, Unix time), user and entry as category codes (the full name, or the user id; the logged action: rotation, crop, “saved as”).
  • Experiment: instrument vendor Bio-Rad, model (the Imager attribute without ™), serial number, software Image Lab and its version (FileAuthoringInfo/version); sample.name = the item name; acquisition.started_at = Image Date, operator = the item’s user, comment = its description; method parameters exposure_time (s), application, excitation_source, emission_filter, binning; the measurement names western blot (OBI:0000854) for chemiluminescence and IRDye applications and gel electrophoresis (CHMO:0001021) for stains and gel dyes, nothing otherwise.

Validation

cargo test -p openreadout-corpus-tests --features corpus compares every development file with Bio-Formats 8.5.0 (oracle/gen.py biorad_scn): image size, pixel type, physical size (where Image Lab marks it known) and the plane, bit for bit (xxh3-128): 14 of 14 match. One further depositor’s file is held out.

Vocabulary (public API of openreadout-gel)

identifier meaning
ImageLabReader reader of Bio-Rad Image Lab .scn files
IMAGE_LAB_FORMAT_ID biorad-scn
ScnDataset the dataset the reader returns

How this reader was derived, file by file: provenance log.