Metadata-Version: 2.1
Name: fishfeats
Version: 1.2.6
Summary: Napari plugin for RNA-Fish+cells analysis pipeline
Author: Gaëlle Letort
License: BSD 3-Clause License
        
        Copyright (c) 2023, Gaëlle  LETORT
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
        
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: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pyqt6<6.10; python_version < "3.11"
Requires-Dist: epyseg; python_version < "3.11"
Requires-Dist: tensorflow<2.15; python_version < "3.11"
Requires-Dist: tensorflow; python_version >= "3.11"
Requires-Dist: big-fish>=0.6.2
Requires-Dist: napari<0.6.3; python_version < "3.11"
Requires-Dist: napari; python_version >= "3.11"
Requires-Dist: numpy<=1.26; python_version < "3.11"
Requires-Dist: numpy; python_version >= "3.11"
Requires-Dist: pyqt5
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
Requires-Dist: cellpose[distributed]
Requires-Dist: stardist

# 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)
[![PyPI](https://img.shields.io/pypi/v/fishfeats.svg?color=green)](https://pypi.org/project/fishfeats)
[![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

Please refer to our [documentation page](https://gletort.github.io/FishFeats/Installation/) for more details on the installation.

`FishFeats` is distributed as a pip module on pypi.
It can be installed by typing in a python virtual environement:
```
pip install fishfeats
``` 

Some options of `Fishfeats` rely on dependencies that are not required by default, so to not force a lot of dependencies installation.
If you want to do directly the installation with **all dependencies**, type:
``` 
pip install `fishfeats[full]`
```

## 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.


## Test dataset

You can find in this zenodo repository [https://zenodo.org/records/17048217](https://zenodo.org/records/17048217) freely available images that can be used to test our pipeline.
All the steps are fully documented in the online [documentation](https://gletort.github.io/FishFeats/) and can be performed with one of these test images.

Example of analysis you can do with `FishFeats` are detailled step-by-step [here](https://gletort.github.io/FishFeats/Step-by-step/) and can be followed with the test image.

## 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/
