| Name | napari-czitools JSON |
| Version |
0.0.4
JSON |
| download |
| home_page | None |
| Summary | Plugin to read CZI image files and their metadata |
| upload_time | 2025-08-24 12:12:03 |
| maintainer | None |
| docs_url | None |
| author | Sebastian Rhode |
| requires_python | <3.13,>=3.10 |
| license | The MIT License (MIT)
Copyright (c) 2025 Sebastian Rhode
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
|
| keywords |
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| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
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No Travis.
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| coveralls test coverage |
No coveralls.
|
- [napari-czitools](#napari-czitools)
- [Installation](#installation)
- [Supported Operating Systems](#supported-operating-systems)
- [Usage - Core Functionalities](#usage---core-functionalities)
- [Open Complete CZI Files](#open-complete-czi-files)
- [Open CZI Sample Data](#open-czi-sample-data)
- [CellDivision 5D Stack](#celldivision-5d-stack)
- [Neurons 3D Stack](#neurons-3d-stack)
- [AiryScan 3D Stack](#airyscan-3d-stack)
- [Wellplate Data](#wellplate-data)
- [Advanced CZI Reader (CziReadTools) plugin](#advanced-czi-reader-czireadtools-plugin)
- [Current Limitations](#current-limitations)
- [Future plans](#future-plans)
- [Contributing](#contributing)
- [License](#license)
- [Issues](#issues)
- [Disclaimer](#disclaimer)
# napari-czitools
[](https://github.com/sebi06/napari-czitools/raw/main/LICENSE)
[](https://pypi.org/project/napari-czitools)
[](https://python.org)
[](https://github.com/sebi06/napari-czitools/actions)
[](https://codecov.io/gh/sebi06/napari-czitools)
[](https://napari-hub.org/plugins/napari-czitools)
[](https://napari.org/stable/plugins/index.html)
[](https://github.com/copier-org/copier)
Plugin to read CZI image file and metadata
----------------------------------
This [napari] plugin was generated with [copier] using the [napari-plugin-template].
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/napari-plugin-template#getting-started
and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->
## Installation
You can install `napari-czitools` via [pip]:
pip install napari-czitools
To install latest development version :
pip install git+https://github.com/sebi06/napari-czitools.git
## Supported Operating Systems
Currently this only tested on:
- Linux
- Windows
MacOS is not supported yet out of the box yet, but [czitools] uses [pylibCZIrw]. But it should be possible to install it manually: [MaxOS wheels for pylibCZIrw] (read and write CZI files on MacOS).
## Usage - Core Functionalities
The plugin provides a reader for CZI files and allows to load the image data into [napari]. It also reads the metadata from the CZI file and displays it in the metadata panel of [napari].
### Open Complete CZI Files
- Open complete CZI Files and display the metadata in Napari using the [czitools] package
- Open different CZI Image sample data
- if not found locally in current directory `../src/napari_czitools/sample_data` it will be opened from remote repository (might be slow)
### Open CZI Sample Data
#### CellDivision 5D Stack
#### Neurons 3D Stack
#### AiryScan 3D Stack
#### Wellplate Data
### Advanced CZI Reader (CziReadTools) plugin
Select the plugin to show the UI in the right panel of the Napari UI via "Plugins > Advanced CZI Reader (CziReadTools)"
1) Select the CZI file to read its metadata
2) Once the metadata are read the display can be toggled between a **table** and a **tree view**
3) The metadata will update the dimension double-range sliders and enable reading the pixel data
<img src="https://github.com/sebi06/napari-czitools/raw/main/readme_images/reader_adv1.png" alt="Advanced CZI Reader - Plugin" style="width:30%; height:auto;">
1) Metadata will be shown as a **table** or as a **tree view**
2) The **Load Pixel Data** button will be enabled once the metadata is read
3) The **Dimension Sliders** will be enabled and allow to select an range to be read for all available dimensions
<img src="https://github.com/sebi06/napari-czitools/raw/main/readme_images/reader_adv2.png" alt="Advanced CZI Reader - Plugin" style="width:80%; height:auto;">
- The dimensions slider allow to define size of CZI subset to be read
- This allows to read parts of a CZI image dataset
- Important - when reading a subset the metadata will still reflects the size of the complete CZI
- Example for reading a subset
- Timepoints (4-7): 4 slices or T=4
- Channels (0-0): 1 slice or CH=1
- Z-Plane (7-10): 4 slices or Z=4
## Current Limitations
The plugin is still in its very early stage, therefor expect bugs and breaking changes
- reading CZI with multiple scenes only works when the scenes have equal size
- opening the sample CZI files will not display the CZI metadata right now
### Future plans
- allow reading individual scenes when scenes have different sizes
- upgrade [pylibCZIrw] to allow use [bioio-czi] for even better reading
- export of metadata table
Feedback is always welcome!
## Contributing
Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.
## License
Distributed under the terms of the [MIT] license,
"napari-czitools" is free and open source software
## Issues
If you encounter any problems, please [file an issue] along with a detailed description.
# Disclaimer
The software & scripts are free to use for everybody. The author undertakes no warranty concerning the use of this plugins and scripts. Use them on your own risk.
By using this plugin you agree to this disclaimer.
Version: 2025.08.20
[napari]: https://github.com/napari/napari
[copier]: https://copier.readthedocs.io/en/stable/
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[napari-plugin-template]: https://github.com/napari/napari-plugin-template
[file an issue]: https://github.com/sebi06/napari-czitools/issues
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[czitools]: https://pypi.org/project/czitools/
[pylibCZIrw]: https://pypi.org/project/pylibCZIrw/
[MaxOS wheels for pylibCZIrw]: https://pypi.scm.io/#/package/pylibczirw
[bioio-czi]: https://pypi.org/project/bioio-czi/
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"description": "- [napari-czitools](#napari-czitools)\n - [Installation](#installation)\n - [Supported Operating Systems](#supported-operating-systems)\n - [Usage - Core Functionalities](#usage---core-functionalities)\n - [Open Complete CZI Files](#open-complete-czi-files)\n - [Open CZI Sample Data](#open-czi-sample-data)\n - [CellDivision 5D Stack](#celldivision-5d-stack)\n - [Neurons 3D Stack](#neurons-3d-stack)\n - [AiryScan 3D Stack](#airyscan-3d-stack)\n - [Wellplate Data](#wellplate-data)\n - [Advanced CZI Reader (CziReadTools) plugin](#advanced-czi-reader-czireadtools-plugin)\n - [Current Limitations](#current-limitations)\n - [Future plans](#future-plans)\n - [Contributing](#contributing)\n - [License](#license)\n - [Issues](#issues)\n- [Disclaimer](#disclaimer)\n\n# napari-czitools\n\n[](https://github.com/sebi06/napari-czitools/raw/main/LICENSE)\n[](https://pypi.org/project/napari-czitools)\n[](https://python.org)\n[](https://github.com/sebi06/napari-czitools/actions)\n[](https://codecov.io/gh/sebi06/napari-czitools)\n[](https://napari-hub.org/plugins/napari-czitools)\n[](https://napari.org/stable/plugins/index.html)\n[](https://github.com/copier-org/copier)\n\nPlugin to read CZI image file and metadata\n\n----------------------------------\n\nThis [napari] plugin was generated with [copier] using the [napari-plugin-template].\n\n\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/napari-plugin-template#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Installation\n\nYou can install `napari-czitools` via [pip]:\n\n pip install napari-czitools\n\nTo install latest development version :\n\n pip install git+https://github.com/sebi06/napari-czitools.git\n\n## Supported Operating Systems\n\nCurrently this only tested on:\n\n- Linux\n- Windows\n\nMacOS is not supported yet out of the box yet, but [czitools] uses [pylibCZIrw]. But it should be possible to install it manually: [MaxOS wheels for pylibCZIrw] (read and write CZI files on MacOS).\n\n## Usage - Core Functionalities\n\nThe plugin provides a reader for CZI files and allows to load the image data into [napari]. It also reads the metadata from the CZI file and displays it in the metadata panel of [napari].\n\n### Open Complete CZI Files\n\n- Open complete CZI Files and display the metadata in Napari using the [czitools] package\n\n\n\n- Open different CZI Image sample data\n- if not found locally in current directory `../src/napari_czitools/sample_data` it will be opened from remote repository (might be slow)\n\n\n\n### Open CZI Sample Data\n\n#### CellDivision 5D Stack\n\n\n\n#### Neurons 3D Stack\n\n\n\n#### AiryScan 3D Stack\n\n\n\n#### Wellplate Data\n\n\n\n### Advanced CZI Reader (CziReadTools) plugin\n\nSelect the plugin to show the UI in the right panel of the Napari UI via \"Plugins > Advanced CZI Reader (CziReadTools)\"\n\n1) Select the CZI file to read its metadata\n2) Once the metadata are read the display can be toggled between a **table** and a **tree view**\n3) The metadata will update the dimension double-range sliders and enable reading the pixel data\n\n<img src=\"https://github.com/sebi06/napari-czitools/raw/main/readme_images/reader_adv1.png\" alt=\"Advanced CZI Reader - Plugin\" style=\"width:30%; height:auto;\">\n\n1) Metadata will be shown as a **table** or as a **tree view**\n2) The **Load Pixel Data** button will be enabled once the metadata is read\n3) The **Dimension Sliders** will be enabled and allow to select an range to be read for all available dimensions\n\n<img src=\"https://github.com/sebi06/napari-czitools/raw/main/readme_images/reader_adv2.png\" alt=\"Advanced CZI Reader - Plugin\" style=\"width:80%; height:auto;\">\n\n- The dimensions slider allow to define size of CZI subset to be read\n- This allows to read parts of a CZI image dataset\n- Important - when reading a subset the metadata will still reflects the size of the complete CZI\n\n\n\n- Example for reading a subset\n - Timepoints (4-7): 4 slices or T=4\n - Channels (0-0): 1 slice or CH=1\n - Z-Plane (7-10): 4 slices or Z=4\n\n\n\n## Current Limitations\n\nThe plugin is still in its very early stage, therefor expect bugs and breaking changes\n\n- reading CZI with multiple scenes only works when the scenes have equal size\n- opening the sample CZI files will not display the CZI metadata right now\n\n### Future plans\n\n- allow reading individual scenes when scenes have different sizes\n- upgrade [pylibCZIrw] to allow use [bioio-czi] for even better reading\n- export of metadata table\n\nFeedback is always welcome!\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [MIT] license,\n\"napari-czitools\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n# Disclaimer\n\nThe software & scripts are free to use for everybody. The author undertakes no warranty concerning the use of this plugins and scripts. 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