pylibCZIrw 5.1.1

A python wrapper around the libCZI C++ library with reading and writing functionality.

pylibCZIrw - Python wrapper for libCZI

This project provides a simple and easy-to-use Python wrapper for libCZI - a cross-platform C++ library intended for providing read and write access to CZI image documents.

Important Remarks

• At the moment, pylibCZIrw completely abstracts away the subblock concept, both in the reading and in the writing APIs.
• The core concept of pylibCZIrw is focussing on reading and writing 2D image planes by specifying the dimension indices and its location in order to only read or write what is really needed.
• It allows reading data via http/https-protocol enabling cloud storage scenarios.

Example Usage

from pylibCZIrw import czi as pyczi

filepath = "myimagefile.czi"

# open the CZI document to read the
with pyczi.open_czi(filepath) as czidoc:
    # get the image dimensions as a dictionary, where the key identifies the dimension
    total_bounding_box = czidoc.total_bounding_box

    # get the total bounding box for all scenes
    total_bounding_rectangle = czidoc.total_bounding_rectangle

    # get the bounding boxes for each individual scene
    scenes_bounding_rectangle = czidoc.scenes_bounding_rectangle

    # read a 2D image plane and optionally specify planes, zoom levels and ROIs
    image2d = czidoc.read(plane={"T": 1, "Z": 2, "C": 0}, zoom=1.0, roi=(0, 0, 50, 100))

The detailed usage can be inferred from the sample notebooks.

For more detailed information (on the latest version) refer to https://zeiss.github.io/pylibczirw/.

Installation

In case there is no wheel available for your system configuration, you can:

• try to install from the provided source distribution
  For Windows:
  • try to keep paths short on systems with maximum path lengths
  • make Win10 accept file paths over 260 characters
• reach out to the maintainers of this project to add more wheels

Disclaimer

The library and the notebook are free to use for everybody. Carl Zeiss Microscopy GmbH undertakes no warranty concerning the use of those tools. Use them at your own risk.

By using any of those examples you agree to this disclaimer.

Version: 2023.11.20

Copyright (c) 2023 Carl Zeiss AG, Germany. All Rights Reserved.

CHANGELOG

v5.1.1 (2025-10-23)

Fix

• fix(setup): correct setup.py configuration (#102)

• mention MacOS as operating system (552a47d)

v5.1.0 (2025-10-21)

Chore

• chore: Wheels for MacOS and ARM Linux (#85)

• I followed the How to structure your PR.

Fixes #57 Fixes #82 Fixes https://github.com/bioio-devs/bioio-czi/issues/51

Context

pylibrczirw does not provide wheels for MacOS or ARM Linux. In some installation contexts, build dependencies like cmake are unavailable, which makes pylibczirw unusable. Specifically, this is an issue downstream for bioio-czi.

Changes

Added 3 new build artifacts: x86-64 MacOS, ARM64 MacOS, and ARM64 Linux, with MacOS-specific build logic in setup.py.

Testing

I only tested the ARM64 MacOS wheel, since that's the hardware I have. I was able to install the wheel and import pylibCZIrw.

Review notes

I strongly recommend also merging my PR #84 so that CI continues to work past the end of the month.

---

Co-authored-by: Sebastian Rhode <[e-mail]> Co-authored-by: PintoCraig <[e-mail]> (c8fd2ff)

• chore: Upgrade from windows-2019 to windows-2022 (#84)

Context

The windows-2019 action runner image will be fully unsupported by 2025-06-30. https://github.com/actions/runner-images/issues/12045

Changes

Replace all instances of windows-2019 with the oldest supported windows runner, windows-2022. windows-2025 is also available; I have no preference. Dropped support for python 3.8 as not default supported by windows-2022 pip version

• I followed the How to structure your PR.

---

Co-authored-by: PintoCraig <[e-mail]> Co-authored-by: PintoCraig <[e-mail]> (0dabe3a)

Feature

• feat: add "mask support" for reading & composition (#96)

This PR is updating libCZI to latest version, which includes support for "mask" (c.f. https://github.com/ZEISS/libczi/pull/153). The new functionality of "mask-aware tile-composition" is made available to pylibczirw by introducing a ReaderOptions object which optionally can be passed to open_czi. Mask-aware composition is therefore an opt-in function at this point (motivation is to limit risk and ensure backwards compatibility). (cc17eb3)

v5.0.0 (2025-04-11)

Breaking

• feat: Support python upto 3.13 (#64)

BREAKING CHANGE: We no longer support python 3.7 as it is not supported by packaging

[x] I followed the How to structure your PR. [ ] Based on Commit Parsing: In case a new major release will be created (because the body or footer begins with 'BREAKING CHANGE:'), I created a new Jupyter notebook with a matching version. [x] Based on Commit Parsing: In case a new minor/patch release will be created (because PR title begins with 'feat'/('fix' or 'perf')), I optionally created a new Jupyter notebook with a matching version. [ ] In case of API changes, I updated API.md.

Summary of the change(s) and which issue(s) is/are fixed
Added support for python upto 3.13 Relevant motivation and context
Seems to work ootb, and new windows images have default higher version of python than 3.11 Dependencies required for this change
None (c2f7cb3)

Chore

• chore: Move deploy job from reusable workflow to caller workflow (#71)

[x] I followed the How to structure your PR. [ ] Based on Commit Parsing: In case a new major release will be created (because the body or footer begins with 'BREAKING CHANGE:'), I created a new Jupyter notebook with a matching version. [ ] Based on Commit Parsing: In case a new minor/patch release will be created (because PR title begins with 'feat'/('fix' or 'perf')), I optionally created a new Jupyter notebook with a matching version. [ ] In case of API changes, I updated API.md.

Fixes #70 (805ce42)

Deps

• deps: Batch-bump pages-related actions (#3)

Bumps actions/deploy-pages from 1 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/deploy-pages/releases&#34;&gt;actions/deploy-pages&#39;s releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <h1>Changelog</h1> <ul> <li>Deploy pages using artifact IDs <a href="https://github.com/konradpabjan&#34;&gt;&lt;code&gt;@​konradpabjan&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/251&#34;&gt;#251&lt;/a&gt;)&lt;/li> <li>This version requires the permission <code>actions: read</code> in the workflows which use it.</li> </ul> <hr /> <p>ℹ️ This version of <code>actions/deploy-pages</code> is <strong>ONLY</strong> compatible with artifacts uploaded by either:</p> <ul> <li><a href="https://github.com/actions/upload-pages-artifact/releases/tag/v3.0.0&#34;&gt;&lt;code&gt;actions/upload-pages-artifact@v3&lt;/code&gt;&lt;/a> or newer</li> <li><a href="https://github.com/actions/upload-artifact/releases/tag/v4.0.0&#34;&gt;&lt;code&gt;actions/upload-artifact@v4&lt;/code&gt;&lt;/a> or newer.</li> </ul> <p>See details of <a href="https://github.com/actions/deploy-pages/compare/v3.0.1...v4.0.0&#34;&gt;all code changes</a> since previous release.</p> <p>:warning: For use with products other than GitHub.com, such as GitHub Enterprise Server, please consult the <a href="https://github.com/actions/deploy-pages/#compatibilty&#34;&gt;compatibility table</a>.</p> <h2>v3.0.1</h2> <h1>Changelog</h1> <ul> <li>Bump eslint from 8.54.0 to 8.55.0 <a href="https://github.com/dependabot&#34;&gt;&lt;code&gt;@​dependabot&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/266&#34;&gt;#266&lt;/a&gt;)&lt;/li> <li>Bump nock from 13.3.8 to 13.4.0 <a href="https://github.com/dependabot&#34;&gt;&lt;code&gt;@​dependabot&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/267&#34;&gt;#267&lt;/a&gt;)&lt;/li> <li>Bump eslint-config-prettier from 9.0.0 to 9.1.0 <a href="https://github.com/dependabot&#34;&gt;&lt;code&gt;@​dependabot&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/268&#34;&gt;#268&lt;/a&gt;)&lt;/li> <li>Bump <code>@​actions/core</code> from 1.10.0 to 1.10.1 <a href="https://github.com/dependabot&#34;&gt;&lt;code&gt;@​dependabot&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/269&#34;&gt;#269&lt;/a&gt;)&lt;/li> <li>Bump <code>@​actions/github</code> from 5.1.1 to 6.0.0 <a href="https://github.com/dependabot&#34;&gt;&lt;code&gt;@​dependabot&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/261&#34;&gt;#261&lt;/a&gt;)&lt;/li> <li>Update compatibility table for v3 <a href="https://github.com/JamesMGreene&#34;&gt;&lt;code&gt;@​JamesMGreene&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/270&#34;&gt;#270&lt;/a&gt;)&lt;/li> </ul> <h2>🧰 Maintenance</h2> <ul> <li>chore/docs: update version, fix typos <a href="https://github.com/kbdharun&#34;&gt;&lt;code&gt;@​kbdharun&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/272&#34;&gt;#272&lt;/a&gt;)&lt;/li> </ul> <hr /> <p>See details of <a href="https://github.com/actions/deploy-pages/compare/v3.0.0...v3.0.1&#34;&gt;all code changes</a> since previous release.</p> <p>:warning: For use with products other than GitHub.com, such as GitHub Enterprise Server, please consult the <a href="https://github.com/actions/deploy-pages/#compatibilty&#34;&gt;compatibility table</a>.</p> <h2>v3.0.0</h2> <h1>Changelog</h1> <ul> <li>Update action to node20 <a href="https://github.com/takost&#34;&gt;&lt;code&gt;@​takost&lt;/code&gt;&lt;/a> (<a href="https://redirect.github.com/actions/deploy-pages/issues/256&#34;&gt;#256&lt;/a&gt;)&lt;/li> </ul> <hr /> <p>See details of <a href="https://github.com/actions/deploy-pages/compare/v2.0.5...v3.0.0&#34;&gt;all code changes</a> since previous release.</p> <p>:warning: For use with products other than GitHub.com, such as GitHub Enterprise Server, please consult the <a href="https://github.com/actions/deploy-pages/#compatibilty&#34;&gt;compatibility table</a>.</p> <h2>v2.0.5</h2> <h1>Changelog</h1> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/deploy-pages/commit/d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e&#34;&gt;&lt;code&gt;d6db901&lt;/code&gt;&lt;/a> Merge pull request <a href="https://redirect.github.com/actions/deploy-pages/issues/324&#34;&gt;#324&lt;/a> from actions/error-message-request-id</li> <li><a href="https://github.com/actions/deploy-pages/commit/055f4259a5b2e76fa0789ad7922a992670f3f6b7&#34;&gt;&lt;code&gt;055f425&lt;/code&gt;&lt;/a> compile changes</li> <li><a href="https://github.com/actions/deploy-pages/commit/5ab929b0772a9c574971c2357565e79163c9088f&#34;&gt;&lt;code&gt;5ab929b&lt;/code&gt;&lt;/a> Include request id in the error message of an error response</li> <li><a href="https://github.com/actions/deploy-pages/commit/3ff795bc32f6f1ceb4dd02ca0c135001516c35ba&#34;&gt;&lt;code&gt;3ff795b&lt;/code&gt;&lt;/a> Merge pull request <a href="https://redirect.github.com/actions/deploy-pages/issues/318&#34;&gt;#318&lt;/a> from actions/dependabot/npm_and_yarn/non-breaking-cha...</li> <li><a href="https://github.com/actions/deploy-pages/commit/f5a2f0d405b68f09cea281329308ca2cd64c1264&#34;&gt;&lt;code&gt;f5a2f0d&lt;/code&gt;&lt;/a> Update distributables after Dependabot 🤖</li> <li><a href="https://github.com/actions/deploy-pages/commit/1364cde56e32972e043d974794ed0a0e449616cf&#34;&gt;&lt;code&gt;1364cde&lt;/code&gt;&lt;/a> Bump the non-breaking-changes group with 2 updates</li> <li><a href="https://github.com/actions/deploy-pages/commit/2ed07f748804ece802939c5fa8753c2858c4dc4d&#34;&gt;&lt;code&gt;2ed07f7&lt;/code&gt;&lt;/a> Merge pull request <a href="https://redirect.github.com/actions/deploy-pages/issues/316&#34;&gt;#316&lt;/a> from actions/dependabot/npm_and_yarn/non-breaking-cha...</li> <li><a href="https://github.com/actions/deploy-pages/commit/d5a892b11c1e1a34d36b6c8dd3b79f53e904086d&#34;&gt;&lt;code&gt;d5a892b&lt;/code&gt;&lt;/a> Bump the non-breaking-changes group with 1 update</li> <li><a href="https://github.com/actions/deploy-pages/commit/05977f58bc03458243006330b90b3352b6ceead6&#34;&gt;&lt;code&gt;05977f5&lt;/code&gt;&lt;/a> Merge pull request <a href="https://redirect.github.com/actions/deploy-pages/issues/314&#34;&gt;#314&lt;/a> from actions/dependabot/npm_and_yarn/non-breaking-cha...</li> <li><a href="https://github.com/actions/deploy-pages/commit/9414024cfce3ef0ceee3850d28ee5290f189d0d8&#34;&gt;&lt;code&gt;9414024&lt;/code&gt;&lt;/a> Update distributables after Dependabot 🤖</li> <li>Additional commits viewable in <a href="https://github.com/actions/deploy-pages/compare/v1...v4&#34;&gt;compare view</a></li> </ul> </details> <br />

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Signed-off-by: dependabot[bot] <[e-mail]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Felix Scheffler <[e-mail]> (844d89c)

v4.1.3 (2024-08-26)

Fix

• fix: Channel ID and Name in display settings metadata (#37)

This PR inlcudes the latest version ov libczirw to fix #13 Fixes #13 (04316fe)

v4.1.2 (2024-08-06)

Chore

• chore: remove temporary debugging logic to push to PyPI (#30)

[x] I followed the How to structure your PR. [ ] Based on Commit Parsing: In case a new major release will be created (because the body or footer begins with 'BREAKING CHANGE:'), I created a new Jupyter notebook with a matching version. [ ] Based on Commit Parsing: In case a new minor/patch release will be created (because PR title begins with 'feat'/('fix' or 'perf')), I optionally created a new Jupyter notebook with a matching version. [ ] In case of API changes, I updated API.md.

Remove debugging code for temporaily pushing to testpypi until infrastructure properly set up. (3b2ea06)

Fix

• fix: consider only dimensions with size >1 for plane-coordinate (#28)

[x] I followed the How to structure your PR. [ ] Based on Commit Parsing: In case a new major release will be created (because the body or footer begins with 'BREAKING CHANGE:'), I created a new Jupyter notebook with a matching version. [ ] Based on Commit Parsing: In case a new minor/patch release will be created (because PR title begins with 'feat'/('fix' or 'perf')), I optionally created a new Jupyter notebook with a matching version. [ ] In case of API changes, I updated API.md.

Re-write of #16 due to changes in infrastructure.

Fixes #10

---

Co-authored-by: Soyer, Sebastian <[e-mail]> Co-authored-by: soyers <[e-mail]> (264fcb4)

v4.1.1 (2024-07-26)

Chore

• chore: Add codeowners (#27)

Add CODEOWNERS file (dc1717b)

Deps

• deps: bump codecov/codecov-action from 3 to 4 (#2)

Bumps codecov/codecov-action from 3 to 4.

Signed-off-by: dependabot[bot] <[e-mail]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Felix Scheffler <[e-mail]> (dab7b18)

Refactor

• refactor: Megalinter and infrastructure (#19)

[x] I followed the How to structure your PR. [ ] Based on Commit Parsing: In case a new major release will be created (because the body or footer begins with 'BREAKING CHANGE:'), I created a new Jupyter notebook with a matching version. [ ] Based on Commit Parsing: In case a new minor/patch release will be created (because PR title begins with 'feat'/('fix' or 'perf')), I optionally created a new Jupyter notebook with a matching version. [ ] In case of API changes, I updated API.md.

Infrastructure related changes, linting (2e60a2b)

Unknown