Plate-reader exports, with the layout the file stores or layout. analysis: wells (per-well values, blank subtraction, replicate mean/SD/CV, outliers), curve (standard curve, back-calculated concentrations, LLOQ/ULOQ), dose-response (IC50/EC50 per compound with CI and Hill slope), kinetics (Vmax, lag, AUC per well), growth (growth rate, doubling time, lag, logistic fit, and whether each well grew, crashed or regrew, with times), qc (Z′, S/B, S/N, SSMD). An argument that names analyses applies to those only.

One measure over many files as one tidy table, optionally joined to sample sheets or plate maps (the join key is chosen from the data and reported in joins[] with unmatched rows) and summarized by group (by; test against a control). Analyses (peaks, chromatogram, nmr-peaks, ephys-features, spikes, qpcr, gate, assay) take the arguments of their tools as options. Inputs (paths): files, directories, globs or an index query. Returns at most limit rows (page with offset; output writes them all to a file); a failing file is a row with error. openreadout_summarize regroups a table written by an earlier output.

Integrity check: ok plus findings (severity, code, message) for truncation, missing planes or parts, bad blocks; a plate folder reports missing files per well; a file still being written reports acquisition_in_progress.

Chromatograms from mass spectra and detector signals: TIC, BPC, extracted-ion (mz with ppm or da), SRM/MRM transitions, stored chromatograms and UV/DAD/FID/TCD traces (traces). Per chromatogram: apex time and intensity, integral, and thinned arrays. Answers 'when does m/z X elute'.

Compare two files, e.g. a raw file and its export: metadata differences, geometry, channel names, physical sizes, and per-plane hashes or the largest difference within tolerance. identical says whether they hold the same data.

Patch-clamp features: action potentials per sweep, rheobase, f-I slope, input resistance, membrane time constant, capacitance, sag; in voltage clamp, holding current and access resistance.

Convert to an open format, or save a figure, as a new file read back and verified; the source is never touched. format: ome-tiff (images, default; pyramidal when the source is), ome-zarr (multiscale; plates as OME-NGFF HCS), mzml (mass spectra, default), csv (one table or one sweep of a trace, default for tables and traces), parquet or arrow (tables, traces with every sweep, spectra=true for MS points), nwb (electrophysiology), jcamp (NMR, IR/Raman, chromatograms), asm (plate readers), rdml (qPCR), nifti (volumes: CT, MRI). Figures: plot or preview = the arguments of that call, output .png, .jpg, .tiff, .svg or .pdf (scale, dpi for print); the picture comes back too. Sends progress with a progressToken.

Write one attachment a file embeds (a slide label or thumbnail, a preview image, time stamps) to a new file as stored, verified. openreadout_info view=structure lists them.

Flow-cytometry gating from a FlowJo workspace (workspace) or Gating-ML 2.0 file (gatingml): the event count, percentage and medians of every population of the FCS file. Without workspace or gatingml, file is the gating file and the answer describes its samples and gate tree.

Storage health of a share indexed by openreadout_index: truncated or corrupt files, unreadable formats, duplicates (confirmed by content hash unless no_hash), the same experiment stored twice, files at risk, totals and personal-data findings.

Catalog every data set under roots into index_dir (Parquet: one row per data set with format, size, sample, instrument, technique, method, operator, start, dimensions, channels, objective, events, scans, integrity status, personal-data flags). Headers only and resumable: a call stops after max_files/max_seconds with complete=false, and the same call again continues. openreadout_search queries the result. For one folder of files, openreadout_batch with measure info lists what each file is in one call.

What an instrument file or data-set directory holds, from its headers (fast on huge files): format, images[] (sizes, pixel type, µm/px, channels and dyes, objective), tables[], traces[], spectra[] (MS runs), plate, experiment (sample, instrument, method, operator, start) and assurance. view=summary attaches a ~384 px thumbnail of image 0 with full-resolution pixel rulers. ask answers a question in words, naming the fields it used.

Groups files that measured the same sample across instruments and formats (sample id, barcode, plate well + plate, a conversion naming its source, the same acquisition or the same spectra), from headers; every link has its evidence and a confidence (high/medium/low; links below min_confidence are listed in weak_links).

NMR peak list (ppm, height, width, S/N) and integrals of given regions or of every multiplet (auto_integrate), from the vendor's processed spectrum or a spectrum processed from the FID (from=fid: group delay, apodization, zero filling, FT, phase, baseline).

Detect and integrate peaks: chromatograms (detector traces, TIC, XIC, SRM) with retention time, area, height, widths, tailing, plates, resolution, S/N and area % (purity); one peak near rt; a compound list; bands and regions of IR, Raman, UV-Vis and NMR spectra and peaks of sized electropherograms in bp (x_range, integrate). Takes the openreadout_chromatogram arguments to choose the signal.

A finished figure from lab files in one call, as image content plus what was drawn (series, data read, ranges, units, marked peaks). Name data by file and selector, never by pasting numbers: traces and sweeps, chromatograms (TIC, XIC) and the spectrum at an rt or the TIC apex, plate wells by range or layout group (curves per well, or mean ± spread per group), FCS dot plots coloured by gate population and histograms, f–I curves, dose-response and standard-curve fits, a table file's columns (openreadout_batch output); small inline values are allowed. Several files overlay; facet=series gives small multiples, facet=plate plate positions; panels side by side; annotate with bands, lines, labelled points, arrows. Draws only; openreadout_export saves the figure.

A picture of the data as image content plus what was drawn: an image plane (default channel 0, middle z), a composite, a max projection (mip=z), a region (only the tiles needed are read), a trace or spectrum plot (largest peaks labelled; marks=spikes marks action potentials; x_range zooms), a Sanger chromatogram with base calls and quality or a sized electropherogram with the ladder, a plate heat map or, for kinetic reads, per-well growth curves coloured by layout group, or a flow-cytometry density plot. Image pictures carry rulers in full-resolution pixels and a µm scale bar, so a region read off the rulers zooms in. annotations draw your own labelled points, boxes, outlines, arrows, lines and bands in the picture's coordinates, to show the user what you found. Draws only; openreadout_export saves the picture.

Real-time PCR (RDML, .eds, .rex, ...): one record per well and target with sample, task, Cq and Tm; compute_cq recomputes Cq, ddcq gives 2^-ΔΔCq fold changes, standard_curve fits efficiency per target.

A privacy-reviewed diagnostic bundle for a file that is refused, fails or is not validated, for a new-variant issue: no data values, free text only with include_text, and the issue_url to file it at. Nothing is sent; the user files it.

The scans of a mass-spectrometry run, without decoding peaks: scan number, MS level, retention time, polarity, precursor m/z and charge, isolation window, activation, collision energy, filter, stored TIC; filtered and paged, and every match counted (matched, ms_level_counts). IR, Raman, UV-Vis and NMR spectra are traces: openreadout_trace.

Query an index from openreadout_index: 'format=nd2 objective=60x', 'channel~CD4', 'events>100000', 'rate>=20kHz', 'acquired<2015', 'status=truncated|corrupt'. Returns {total, returned, results[]}: total counts every match, results is capped by limit (default 50); fields=['all'] returns every column.

One mass spectrum, picked by retention time (rt, minutes: the scan nearest it), scan number or zero-based spectrum index: metadata, peaks[] (the most intense, with charge from the isotope spacing and neutral mass) and mz[]/intensity[].

Extracellular spike detection per channel: band-pass, threshold at K x MAD noise, spike counts, rates and times.

Pixel statistics per channel and image: count, min, max, mean, std, percentiles p1–p99, zero and saturated fractions (at the detector's 2^bits−1 when recorded), histogram; RGB images also per component. per=plane adds every plane; per=well or field gives rows per well of a screening plate. mip='z' measures the maximum-intensity projection; whole slides: a coarser level and/or a region. Measurements on one plane: line (intensity profile, FWHM), polygon (statistics inside), objects (count nuclei, cells or spots; preview marks=objects shows them), lanes (gel and blot lanes, band volumes and sizes; preview marks=lanes).

Group statistics of a table written by an earlier openreadout_batch output (or any CSV, TSV, JSON Lines, JSON or Parquet table): n, mean, sd, sem, median, min, max and CV % per group of by, optionally averaging replicates first and testing every group against a control.

Rows of a table {columns, labels, rows, total_rows, truncated}: FCS events ($PnN columns), plate reads (well, row, col, read, wavelength_nm, time_s, value), event, spike or peak tables (including the vendor's own integration results). Values are raw; FCS can be compensated, transformed and given 0/1 population columns from a workspace or Gating-ML file. filter with count=true counts the events meeting conditions.

One window of one sweep of a sampled signal or 1-D spectrum in physical units: electrophysiology sweeps, chromatography detector traces, ÄKTA curves, ITC thermograms, SPR sensorgrams, NMR FIDs and spectra (process=true turns an FID into a spectrum), IR/Raman/UV-Vis/CD spectra (each spectrum of a map is a sweep), qPCR curves, EPR, XRD, electrochemistry, thermal analysis. Per channel: min, max, mean, std and argmax_axis_value (the maximum's position on the axis: retention time, ppm, cm⁻¹, °2θ) over the window, plus the first max_samples values.

Follow directories an instrument writes to: each call looks once and returns events since cursor (dataset_new, plane_new, scan_new, frame_new, dataset_complete, dataset_stalled, qc with qc=true: saturation, focus drift, dropped frames, TIC drop, error). Poll with the returned cursor; files are never locked.