bioio-openreadout

A bioio reader plugin that reads microscopy files with OpenReadout's Rust readers. It is licensed MIT OR Apache-2.0 and depends on no GPL plugin, vendor SDK or Java. Wheels need no compiler. Each plane is one dask chunk and is decoded only when a computation needs it.

pip install bioio bioio-openreadout

from bioio import BioImage
import bioio_openreadout

img = BioImage("run42.czi", reader=bioio_openreadout.Reader)
img.scenes  # ('P2', 'P3', 'P1') — one per CZI scene / ND2 position / LIF series
img.dims  # <Dimensions [T: 1, C: 3, Z: 5, Y: 325, X: 475]>
img.channel_names  # ['EGFP', 'TaRFP', 'Bright']
img.physical_pixel_sizes  # PhysicalPixelSizes(Z=1.0, Y=1.083, X=1.083)  (µm)
img.set_scene(1)
zyx = img.get_image_dask_data("ZYX", T=0, C=1).compute()  # decodes 5 planes, not the file
img.ome_metadata  # ome_types.OME built from the normalized metadata

BioImage(path) without reader= also works for .czi, .nd2, .lif, .vsi, .svs, .ndpi, .qptiff, .ims, .oir, .oib, .oif and .zvi: the plugin registers these extensions through the bioio.readers entry point. Other formats OpenReadout reads, such as OME-TIFF or OME-Zarr, open with reader=bioio_openreadout.Reader. When another plugin for the same extension is installed (for example bioio-nd2), bioio's own ordering decides which is tried first; pass reader= to choose.

What you get

Mosaics are returned stitched (no M dimension); pyramidal files at full resolution only. Remote (fsspec) paths are not supported: the file must be local.

Tests

pip install -e 'python/bioio-openreadout[test]'
OPENREADOUT_CORPUS_DIR=corpus/files pytest python/bioio-openreadout/tests

The tests compare img.data against bioio-nd2, czifile and liffile (all BSD) on files from the public test corpus and skip when those files or readers are absent.

Guide: https://openreadout.github.io/openreadout/guides/python.html. Part of OpenReadout. Licensed MIT OR Apache-2.0. OpenReadout is not affiliated with any instrument vendor.