openreadout (Python)
Read raw lab-instrument files from Python without vendor software, Java or a C toolchain. The package wraps OpenReadout's Rust readers. It returns the same JSON as the openreadout command-line tool, and NumPy, dask or xarray arrays for pixels. The formats it reads are listed at https://openreadout.github.io/openreadout/formats.html.
pip install openreadout # needs only NumPy
pip install 'openreadout[xarray]' # adds dask and xarray for lazy, labelled arrays
One abi3 wheel per platform covers CPython 3.10 and newer on Linux (manylinux and musllinux, x86_64 and aarch64), macOS (x86_64 and arm64) and Windows (x64).
import openreadout
meta = openreadout.info("run42.czi") # header-only summary, a dict
meta["images"][0]["size_c"], meta["images"][0]["physical_size"]
with openreadout.File("run42.czi") as f:
plane = f.read_plane(image=0, c=1, z=4) # np.ndarray (Y, X), or (Y, X, 3) for RGB
stack = f.read_image(0) # np.ndarray (T, C, Z, Y, X[, S])
lazy = f.to_dask(0) # dask array, one chunk per plane, read on demand
xarr = f.to_xarray(0) # labelled: channel names, µm and s coordinates
f.check()["ok"] # integrity report
f.export("run42.ome.tiff") # verified OME-TIFF; the source is never modified
Tables, traces and spectra (flow cytometry, electrophysiology, chromatography, mass spectrometry) are read with File.read_table, File.read_trace and File.read_spectrum, and convert to Arrow or pandas with File.to_arrow and File.to_pandas.
Arrays use the dimension order TCZYX, with S added for interleaved RGB. File objects are thread-safe and picklable, so lazy arrays work with dask's threaded, multiprocessing and distributed schedulers.
Every error is an openreadout.OpenReadoutError and also the closest built-in exception (for example FileNotFoundError or ValueError). It carries the command-line tool's code, exit_code and a hint.
bioio-openreadout plugs these readers into bioio.BioImage, and napari-openreadout into napari.
Guide and full API: https://openreadout.github.io/openreadout/guides/python.html. Source: https://github.com/openreadout/openreadout. Licensed MIT OR Apache-2.0. OpenReadout is not affiliated with any instrument vendor.
1 maintainer
Metadata
1 maintainer
Release files for openreadout 0.3.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| openreadout-0.3.0.tar.gz | 3.4 MB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| openreadout-0.3.0-cp310-abi3-win_amd64.whl | CPython 3.10 | abi3 | Windows x86-64 | Details |
| openreadout-0.3.0-cp310-abi3-musllinux_1_2_x86_64.whl | CPython 3.10 | abi3 | Linux musl 1.2+ x86-64 | Details |
| openreadout-0.3.0-cp310-abi3-musllinux_1_2_aarch64.whl | CPython 3.10 | abi3 | Linux musl 1.2+ ARM64 | Details |
| openreadout-0.3.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ x86-64 | Details |
| openreadout-0.3.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl | CPython 3.10 | abi3 | Linux glibc 2.17+ ARM64 | Details |
| openreadout-0.3.0-cp310-abi3-macosx_11_0_arm64.whl | CPython 3.10 | abi3 | macOS 11.0+ ARM64 | Details |
| openreadout-0.3.0-cp310-abi3-macosx_10_12_x86_64.whl | CPython 3.10 | abi3 | macOS 10.12+ x86-64 | Details |
Total release size: 130.8 MB
Release files / openreadout-0.3.0.tar.gz
| Download URL | openreadout-0.3.0.tar.gz |
|---|---|
| Size | 3.4 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
c558799d402332189fabe26ec04d4a9f524b7381a7c98a71f738bf2f8e144146
|
|
BLAKE2b-256 checksum How to use checksums |
b9bc1549486e0cd49cb05b1021b243267b5beab0a6bbb48a1f1c20d85f916edf
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency logRelease files / openreadout-0.3.0-cp310-abi3-win_amd64.whl
| Download URL | openreadout-0.3.0-cp310-abi3-win_amd64.whl |
|---|---|
| Size | 19.8 MB |
| Tags | CPython 3.10 Windows x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
806794b122ee8f600b7795ec70bd2ba3fcf319527d1e9fc0c35427ba8bfcb79e
|
|
BLAKE2b-256 checksum How to use checksums |
9a01781c6b8d6ab438fcd7f620c052fdc5166a4da5da9aa3df51091bb2fe0c64
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency logRelease files / openreadout-0.3.0-cp310-abi3-musllinux_1_2_x86_64.whl
| Download URL | openreadout-0.3.0-cp310-abi3-musllinux_1_2_x86_64.whl |
|---|---|
| Size | 19.1 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
d8db7fbb25ded964870f2d4f28a07215ee97816c7aa52fcef05e278492a370a3
|
|
BLAKE2b-256 checksum How to use checksums |
9b468003d8599e0a9bcd38b3147ff0b15f44512ae40f774af0e758d82b5beb79
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency logRelease files / openreadout-0.3.0-cp310-abi3-musllinux_1_2_aarch64.whl
| Download URL | openreadout-0.3.0-cp310-abi3-musllinux_1_2_aarch64.whl |
|---|---|
| Size | 17.4 MB |
| Tags | CPython 3.10 Linux musl 1.2+ ARM64 abi3 |
|
SHA-256 checksum How to use checksums |
01291dbf32a632b4b0394a80c438710c58b22a94c9b49a3ab936d6920b3767e3
|
|
BLAKE2b-256 checksum How to use checksums |
a61832dbce1cab42e9a9396b5ec7d889de79665d11e9635d95cdf6b96bb2a27c
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency logRelease files / openreadout-0.3.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | openreadout-0.3.0-cp310-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 18.9 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 abi3 |
|
SHA-256 checksum How to use checksums |
f0580452d1c9a3adf529c97242820385fb8cbcae6b6633d6e56d5f1420619604
|
|
BLAKE2b-256 checksum How to use checksums |
a401f9e913fba3c5a9a123d840838d5256cdf188612f1b3e319579d98a21c072
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency logRelease files / openreadout-0.3.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
| Download URL | openreadout-0.3.0-cp310-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl |
|---|---|
| Size | 17.2 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ ARM64 abi3 |
|
SHA-256 checksum How to use checksums |
8d816307a760fa7ffbfa0fa4ee0c05133ce75ef2a44f02d4fc70fefcd64d5568
|
|
BLAKE2b-256 checksum How to use checksums |
cb8fd4c35f9a8e2c3b73036a1684ada36055f4c30964708fd91807a0b67993d1
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency logRelease files / openreadout-0.3.0-cp310-abi3-macosx_11_0_arm64.whl
| Download URL | openreadout-0.3.0-cp310-abi3-macosx_11_0_arm64.whl |
|---|---|
| Size | 16.8 MB |
| Tags | CPython 3.10 abi3 macOS 11.0+ ARM64 |
|
SHA-256 checksum How to use checksums |
1c1e3d36d82bcaaa5c32c17ac84effeb0ef66c114f4ef5242679bcbe6194d8d1
|
|
BLAKE2b-256 checksum How to use checksums |
e0ed252d6b36a3a2133fbb8a7f725972381f440d4466f529427be1ecf0353a83
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency logRelease files / openreadout-0.3.0-cp310-abi3-macosx_10_12_x86_64.whl
| Download URL | openreadout-0.3.0-cp310-abi3-macosx_10_12_x86_64.whl |
|---|---|
| Size | 18.2 MB |
| Tags | CPython 3.10 abi3 macOS 10.12+ x86-64 |
|
SHA-256 checksum How to use checksums |
b196d4bf5bbae7350ddcd602013c9ca90e7922ff064175aea17055b5a6bfeabb
|
|
BLAKE2b-256 checksum How to use checksums |
bacb004c64f2df0ba97628a8893d5dfe8d3f90766bccd8e5b99137110090b8d8
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
Yes |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
PyPI Publish Attestation
PyPI verified that this artifact, at this checksum, originated from the publisher listed below.
Signed by GitHub Actions, verified by PyPI on Oct 13, 2026.
Transparency log
