Metadata-Version: 2.4
Name: fishfeats
Version: 1.1.19.post1.dev0
Summary: Napari plugin for RNA-Fish+cells analysis pipeline
Author: Gaëlle Letort
License-Expression: BSD-3-Clause
Project-URL: Bug Tracker, https://github.com/gletort/FishFeats/issues
Project-URL: Documentation, https://gletort.github.io/FishFeats/
Project-URL: Source Code, https://github.com/gletort/FishFeats
Project-URL: User Support, https://github.com/gletort/FishFeats/issues
Classifier: Framework :: napari
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: napari<0.6.3
Requires-Dist: numpy
Requires-Dist: imaris_ims_file_reader
Requires-Dist: czifile
Requires-Dist: tifffile
Requires-Dist: munkres
Requires-Dist: matplotlib
Requires-Dist: scikit-image
Requires-Dist: opencv_python_headless
Requires-Dist: lxml
Requires-Dist: packaging
Provides-Extra: full
Requires-Dist: big-fish>=0.6.2; extra == "full"
Requires-Dist: epyseg; extra == "full"
Requires-Dist: cellpose[distributed]; extra == "full"
Requires-Dist: stardist; extra == "full"
Dynamic: license-file

# Fish&Feats ![snap](./docs/imgs/snap.png)

[![License BSD-3](https://img.shields.io/pypi/l/fishfeats.svg?color=green)](https://github.com/gletort/FishFeats/-/blob/main/LICENSE)
[![Python Version](https://img.shields.io/pypi/pyversions/fishfeats.svg?color=green)](https://python.org)

[Napari](https://napari.org/stable/) plugin to quantify 3D cells in a tissue and their smRNA-Fish or other RNA contents.

[main.webm](https://github.com/user-attachments/assets/7eda5fa8-3241-4af8-b392-bc3e64aa31b9)


FishFeats offers several flexible options to analyse 3D cells and RNA counts, from segmentation of apical cells and nuclei to hierarchical clustering of cells based on their RNA contents. 
Installation/Usage... are all described in the [documentation](https://gletort.github.io/FishFeats/).

![main interface](./docs/imgs/Main_snapshot.png)

# Installation

Soon available as a pip module.

# Usage

You can launch `fishfeats` in Napari by going to `Plugins>fishfeats>Start`.
It will open a file dialog box asking you to select the image that you want to analyze. 
Refer to the [documentation](https://gletort.github.io/FishFeats/) for presentation of the different steps possible in the pipeline.


# License

Fishfeats is distributed freely under the BSD-3 license.


[napari]: https://github.com/napari/napari
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
