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

CHANGELOG

v6.1.0 (2026-07-01)

Feature

feat: add subblock header enumeration (#121) (6feeaff)

Fix

fix: pre-populate eigen for CI (#126) (3fd66f6)

v6.0.1 (2026-03-12)

Fix

fix: add defensive template change and only render subject lines for changelog (#120) (1c0e27e)

v6.0.0 (2026-03-10)

Breaking

feat: Pass through reader options related to coordinates (#118) (3bfafd4)

Deps

deps: bump actions/github-script from 7 to 8 (#105) (9ecb0e7)
deps: bump github/codeql-action from 3 to 4 (#106) (c5c648b)
deps: bump actions/upload-pages-artifact from 3 to 4 (#107) (3bc2a20)
deps: bump actions/upload-artifact from 4 to 5 (#108) (8989aff)
deps: Bump actions/download-artifact from 5.0.0 to 6.0.0 in /.github/workflows (#66) (dbb0bfc)
deps: bump codecov/codecov-action from 4 to 5 (#69) (43ce3d7)
deps: bump actions/download-artifact from 4.1.0 to 5.0.0 (#91) (cb807c4)
deps: bump actions/checkout from 3 to 5 (#92) (dce8aa3)
deps: bump amannn/action-semantic-pull-request from 5 to 6 (#103) (74535f7)
deps: bump fsfe/reuse-action from 1 to 6 (#100) (c71a865)
deps: update pybind to latest 2.x version (2.13.6) (#101) (0ac54dc)

Documentation

docs: Update README and CONTRIBUTING (#65) (fc52575)

Feature

feat: add editing in-place for metadata (#114) (959a898)
feat: More complete type hints for open_czi and create_czi (#73) (992f92a)

v5.1.1 (2025-10-22)

Fix

fix(setup): correct setup.py configuration (#102) (552a47d)

v5.1.0 (2025-10-21)

Chore

chore: Wheels for MacOS and ARM Linux (#85) (c8fd2ff)
chore: Upgrade from windows-2019 to windows-2022 (#84) (0dabe3a)

Feature

feat: add "mask support" for reading & composition (#96) (cc17eb3)

v5.0.0 (2025-04-11)

Breaking

feat: Support python upto 3.13 (#64) (c2f7cb3)

Chore

chore: Move deploy job from reusable workflow to caller workflow (#71) (805ce42)

Deps

deps: Batch-bump pages-related actions (#3) (844d89c)

v4.1.3 (2024-08-26)

Fix

fix: Channel ID and Name in display settings metadata (#37) (04316fe)

v4.1.2 (2024-08-06)

Chore

chore: remove temporary debugging logic to push to PyPI (#30) (3b2ea06)

Fix

fix: consider only dimensions with size >1 for plane-coordinate (#28) (264fcb4)

v4.1.1 (2024-07-26)

Chore

chore: Add codeowners (#27) (dc1717b)

Deps

deps: bump codecov/codecov-action from 3 to 4 (#2) (dab7b18)

Refactor

refactor: Megalinter and infrastructure (#19) (2e60a2b)

Unknown

Metadata

Release files for pylibCZIrw 6.1.0

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for pylibCZIrw 6.1.0
File	Size	Uploaded
pylibczirw-6.1.0.tar.gz	6.1 MB	Jul 6, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for pylibCZIrw 6.1.0
File	Interpreter	ABI	Platform	Reset
pylibczirw-6.1.0-cp313-cp313-win_amd64.whl 1.4 MB Jul 6, 2026	CPython 3.13	CPython 3.13	Windows x86-64	Details
pylibczirw-6.1.0-cp313-cp313-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 4.4 MB Jul 6, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.17+ x86-64	Details
pylibczirw-6.1.0-cp313-cp313-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 4.6 MB Jul 6, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.17+ ARM64	Details
pylibczirw-6.1.0-cp313-cp313-macosx_11_0_arm64.whl 1.1 MB Jul 6, 2026	CPython 3.13	CPython 3.13	macOS 11.0+ ARM64	Details
pylibczirw-6.1.0-cp312-cp312-win_amd64.whl 1.4 MB Jul 6, 2026	CPython 3.12	CPython 3.12	Windows x86-64	Details
pylibczirw-6.1.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 4.4 MB Jul 6, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.17+ x86-64	Details
pylibczirw-6.1.0-cp312-cp312-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 4.6 MB Jul 6, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.17+ ARM64	Details
pylibczirw-6.1.0-cp312-cp312-macosx_11_0_arm64.whl 1.1 MB Jul 6, 2026	CPython 3.12	CPython 3.12	macOS 11.0+ ARM64	Details
pylibczirw-6.1.0-cp311-cp311-win_amd64.whl 1.4 MB Jul 6, 2026	CPython 3.11	CPython 3.11	Windows x86-64	Details
pylibczirw-6.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 4.4 MB Jul 6, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.17+ x86-64	Details
pylibczirw-6.1.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 4.6 MB Jul 6, 2026	CPython 3.11	CPython 3.11	Linux glibc 2.17+ ARM64	Details
pylibczirw-6.1.0-cp311-cp311-macosx_11_0_arm64.whl 1.1 MB Jul 6, 2026	CPython 3.11	CPython 3.11	macOS 11.0+ ARM64	Details
pylibczirw-6.1.0-cp310-cp310-win_amd64.whl 1.4 MB Jul 6, 2026	CPython 3.10	CPython 3.10	Windows x86-64	Details
pylibczirw-6.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 4.4 MB Jul 6, 2026	CPython 3.10	CPython 3.10	Linux glibc 2.17+ x86-64	Details
pylibczirw-6.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 4.6 MB Jul 6, 2026	CPython 3.10	CPython 3.10	Linux glibc 2.17+ ARM64	Details
pylibczirw-6.1.0-cp310-cp310-macosx_11_0_arm64.whl 1.1 MB Jul 6, 2026	CPython 3.10	CPython 3.10	macOS 11.0+ ARM64	Details
pylibczirw-6.1.0-cp39-cp39-win_amd64.whl 1.4 MB Jul 6, 2026	CPython 3.9	CPython 3.9	Windows x86-64	Details
pylibczirw-6.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl 4.4 MB Jul 6, 2026	CPython 3.9	CPython 3.9	Linux glibc 2.17+ x86-64	Details
pylibczirw-6.1.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl 4.6 MB Jul 6, 2026	CPython 3.9	CPython 3.9	Linux glibc 2.17+ ARM64	Details
pylibczirw-6.1.0-cp39-cp39-macosx_11_0_arm64.whl 1.1 MB Jul 6, 2026	CPython 3.9	CPython 3.9	macOS 11.0+ ARM64	Details

Total release size: 63.3 MB

Release files / pylibczirw-6.1.0.tar.gz

Download URL	pylibczirw-6.1.0.tar.gz
Size	6.1 MB
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Publishing platform: GitHub Actions
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Release files / pylibczirw-6.1.0-cp312-cp312-win_amd64.whl

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Tags	CPython 3.12 Linux glibc 2.17+ ARM64
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Size	1.1 MB
Tags	CPython 3.12 macOS 11.0+ ARM64
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Release files / pylibczirw-6.1.0-cp311-cp311-win_amd64.whl

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Size	1.4 MB
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Uploaded using Trusted Publishing? What is trusted publishing?	Yes
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Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp311-cp311-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp311-cp311-macosx_11_0_arm64.whl

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Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp310-cp310-win_amd64.whl

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

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Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Artifact

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Release files / pylibczirw-6.1.0-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

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Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp310-cp310-macosx_11_0_arm64.whl

Download URL	pylibczirw-6.1.0-cp310-cp310-macosx_11_0_arm64.whl
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Upload date	Jul 6, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp39-cp39-win_amd64.whl

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Upload date	Jul 6, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Download URL	pylibczirw-6.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
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Upload date	Jul 6, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Artifact

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Release files / pylibczirw-6.1.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl

Download URL	pylibczirw-6.1.0-cp39-cp39-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
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Upload date	Jul 6, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

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Release files / pylibczirw-6.1.0-cp39-cp39-macosx_11_0_arm64.whl

Download URL	pylibczirw-6.1.0-cp39-cp39-macosx_11_0_arm64.whl
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Upload date	Jul 6, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/6.1.0 CPython/3.13.12`

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Publishing platform: GitHub Actions
Publishing repository: github.com/ZEISS/pylibczirw
Publishing commit: github.com/ZEISS/pylibczirw/tree/3fd66f681d82f5781e404fa56d783e5b8b74684f

Workflow

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Artifact

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