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OpenReadout

stats

stats computes pixel statistics per plane, channel and image (min, max, mean, standard deviation, percentiles, histogram, zero and saturated fractions), or per well of a screening plate.

openreadout stats [OPTIONS] [FILE]...

Flags

  • --json: print the JSON wrapper instead of text.
  • --image N: only this image.
  • --select SEL: plane selection such as c=0, z=2-5, t=0,3. Repeatable. The per-image aggregate covers exactly the selected planes.
  • --level N: pyramid level, 0 = full resolution. Default 0.
  • --region X,Y,W,H: only this rectangle of each plane, in the pixels of --level.
  • --bins N: histogram bins, 0 = none, at most 65536. Default 64.
  • --scale linear|log: histogram bin spacing. Default linear.
  • --no-planes: leave out the per-plane entries.
  • --mip z|t: take the maximum-intensity projection first, then the statistics of the projections.
  • --per channel|image|plane|well|field: what one row is. well gives one row per well and channel of a plate over its fields; field one row per well, field and channel. Default channel.
  • --well WELL: with --per well or --per field, only this well (C05). Repeatable.

stats takes the flags in Several inputs and the batch table flags.

Examples

Terminal window
$ openreadout stats doctor.tif --bins 0
doctor.tif (tiff)
                            min   max     mean      std     p1      p50       p99   zero  saturated
image 0 (2 planes, uint16)    0  1127  563.500  501.363  2.550  563.500  1124.450  0.39%          0
  c=0                         0  1127  563.500  501.363  2.550  563.500  1124.450  0.39%          0
…
Terminal window
openreadout stats stack.nd2 --mip z --select c=1 --json      # the z-MIP of channel 1
openreadout stats slide.svs --level 2 --region 0,0,2048,2048

What the numbers mean

  • Statistics cover finite samples; NaN and infinities are counted in non_finite. std is the population standard deviation.
  • Percentiles use NumPy’s default linear interpolation. They are exact for 8- and 16-bit data (exact: true).
  • RGB planes are summarized over all samples, and per colour component under components[].
  • saturated_fraction counts samples at the detector’s maximum. When the file records how many bits the detector fills (for example 12-bit data in uint16), the maximum is 2^bits − 1; otherwise it is the pixel type’s maximum. saturation_basis says which.
  • Files without images exit 6 with a hint towards trace.

High-content screening plates

A plate (Harmony, ImageXpress, CellVoyager, OME-Zarr HCS) is one data set whose images are its fields of view. --per well gives one tidy row per well and channel, merged across fields. Planes the instrument never acquired are left out; planes whose files are missing are skipped and counted in planes_missing.

Terminal window
openreadout stats MeasurementData.mlf --per well --select c=0 --csv > hoechst_by_well.csv
openreadout stats plate/ --per field --well C05 --json

Plate layouts, replicate averaging and group tests are covered in Plate analysis and Batch tables.

JSON

stats, stats --per well, batch table.

Run openreadout stats --help for the full help of your installed version.