https://github.com/imcf/python-imcflibs
🐍 ☕ 🔩 🔧 🪛 A collection of commonly used Python helper functions.
https://github.com/imcf/python-imcflibs
Last synced: 2 months ago
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🐍 ☕ 🔩 🔧 🪛 A collection of commonly used Python helper functions.
- Host: GitHub
- URL: https://github.com/imcf/python-imcflibs
- Owner: imcf
- License: gpl-3.0
- Created: 2018-11-09T16:50:38.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2025-04-15T14:21:03.000Z (3 months ago)
- Last Synced: 2025-04-15T15:32:19.365Z (3 months ago)
- Language: Python
- Homepage: https://imcf.one/apidocs/imcflibs/
- Size: 701 KB
- Stars: 0
- Watchers: 6
- Forks: 3
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.txt
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README
# IMCFlibs 🐍 ☕ 🔩 🔧 🪛
[](https://github.com/imcf/python-imcflibs/actions/workflows/lint.yml)
[](https://github.com/imcf/python-imcflibs/actions/workflows/pytest-python2.yml)
[](https://github.com/imcf/python-imcflibs/actions/workflows/pytest-poetry.yml)
[](https://codecov.io/github/imcf/python-imcflibs)
[][build]
[][doi]
This package contains a diverse collection of Python functions dealing with
paths, I/O (file handles, ...), strings etc. and tons of [Fiji][fiji] /
[ImageJ2][imagej] convenience wrappers to simplify scripting and reduce
cross-script redundanciees.
Initially this has been a multi-purpose package where a substantial part had
been useful in **CPython** as well. However, since the latest Jython
release is still based on Python 2.7 (see the [Jython 3 roadmap][jython3] for
more info), *imcflibs* is now basically limited to the **Fiji / ImageJ2
ecosystem**.
Releases are made through Maven and published to the [SciJava Maven
repository][sj_maven]. The easiest way to use the lib is by adding the **`IMCF
Uni Basel`** [update site][imcf_updsite] to your ImageJ installation.
The [`pip install`able package][pypi] is probably only useful for two cases:
running `pytest` (where applicable) and rendering [HTML-based API docs][apidocs]
using [`pdoc`][pdoc]. Let us know in case you're having another use case 🎪 for
it.
Developed and provided by the [Imaging Core Facility (IMCF)][imcf] of the
Biozentrum, University of Basel, Switzerland.
## Example usage
### Shading correction / projection
Apply a shading correction model and create a maximum-intensity projection:
```Python
from imcflibs.imagej.shading import correct_and_project
model = "/path/to/shading_model.tif"
raw_image = "/path/to/raw_data/image.ome.tif"
out_path = "/path/to/processed_data/"
correct_and_project(raw_image, out_path, model, "Maximum", ".ics")
```
### Split TIFFs by channels and slices
* See the [Split_TIFFs_By_Channels_And_Slices.py][script_split] script.
### Use status and progress bar updates
* See the [FluoView_OIF_OIB_OIR_Simple_Stitcher.py][script_fvstitch] script.
[imcf]: https://www.biozentrum.unibas.ch/imcf
[imagej]: https://imagej.net
[fiji]: https://fiji.sc
[jython3]: https://www.jython.org/jython-3-roadmap
[sj_maven]: https://maven.scijava.org/#nexus-search;gav~ch.unibas.biozentrum.imcf~~~~
[imcf_updsite]: https://imagej.net/list-of-update-sites/
[script_split]: https://github.com/imcf/imcf-fiji-scripts/blob/master/src/main/resources/scripts/Plugins/IMCF_Utilities/Convert/Split_TIFFs_By_Channels_And_Slices.py
[script_fvstitch]: https://github.com/imcf/imcf-fiji-scripts/blob/master/src/main/resources/scripts/Plugins/IMCF_Utilities/Stitching_Registration/FluoView_OIF_OIB_OIR_Simple_Stitcher.py
[doi]: https://zenodo.org/badge/latestdoi/156891364
[build]: https://github.com/imcf/python-imcflibs/actions/workflows/build.yml
[apidocs]: https://imcf.one/apidocs/imcflibs/imcflibs.html
[pdoc]: https://pdoc.dev/
[pypi]: https://pypi.org/project/imcflibs/