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OpenReadout

GenePix Results .gpr

GenePix Pro writes a .gpr results file for each scanned microarray (DNA, protein or antibody arrays). OpenReadout returns the feature table with every column GenePix wrote, plus the scanner, software and scan settings. Derived from public files written by GenePix Pro 3.0.6 and 7.3, with pandas (BSD-3) as the reference reader of the table. Provenance: docs/provenance/genepix-gpr.md. Crate: openreadout-biophys.

format id files reads confidence
genepix-gpr .gpr results of GenePix Pro (microarray scans: DNA, protein, antibody arrays) the feature table (every column GenePix wrote), scanner, software, wavelengths, PMT gain or voltage, laser and scan power, date medium (evidence rubric, docs/assurance.md)

Not read by this reader: array lists (.gal, also ATF: exit 6 with a hint), settings (.gps), the scan images (TIFF: the TIFF reader opens them). No normalization or background correction is applied; values are as GenePix wrote them.

Layout

An Axon Text File: ATF 1.0; the counts of header records and columns; the header records ("Key=value", per-channel records tab-separated); a line of column titles; one line per feature. Header records used: Type (must start GenePix Results), Creator (software and version), Scanner (model and [serial]), DateTime (local), Wavelengths or (GenePix Pro 3) ImageName, PMTGain or PMTVolts, LaserPower, ScanPower, PixelSize, Comment; all records are kept in the vendor tree. The ATF reader (atf) leaves files whose header says Type=GenePix to this reader.

What the reader returns

  • Table 0 features: one row per feature, one column per title in file order (Block, Column, Row, Name, ID, X, Y, Dia., F635 Median, …, Flags). A column whose cells are all numbers, or Error where GenePix could not compute a value, is numeric (Error → NaN); any other column is text (category codes, extra.categories). No unit is attached: the file does not state them. extra.wavelengths_nm lists the channels.
  • Experiment: instrument vendor Molecular Devices (Axon GenePix), model and serial from Scanner, software and version from Creator; method parameters wavelengths and per wavelength pmt_gain_<nm>, pmt_voltage_<nm> (V), laser_power_<nm>, scan_power_<nm>, pixel_size; acquisition started_at (local time) and comment.
  • check: rows with a different number of cells (left out, error finding).

Validation

cargo test -p openreadout-corpus-tests --features corpus (tests/gpr_oracle/mod.rs, oracle/gpr_oracle.py): pandas reads the table (skipping the ATF header by its declared record count): the same row and column counts and titles, every numeric column’s values at 64 rows, the Name column at the same rows; the header’s Creator and Scanner match the experiment model.

Vocabulary (public API of openreadout-biophys, GenePix)

identifier meaning
GprReader reader of GenePix Results .gpr files
GPR_FORMAT_ID genepix-gpr
GprDataset the dataset the reader returns

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