Metadata-Version: 2.3
Name: small_fish_gui
Version: 1.2.0
Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
Project-URL: Homepage, https://github.com/2Echoes/small_fish
Project-URL: Issues, https://github.com/2Echoes/small_fish/issues
Author-email: Slimani Floric <floric.slimani@live.com>
License-File: LICENSE
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.8
Requires-Dist: big-fish==0.6.2
Requires-Dist: cellpose==3.0.7
Requires-Dist: czifile==2019.7.2
Requires-Dist: imageio==2.34.0
Requires-Dist: napari-console==0.0.9
Requires-Dist: napari-plugin-engine==0.2.0
Requires-Dist: napari-plugin-manager==0.1.0a2
Requires-Dist: napari-svg==0.1.10
Requires-Dist: napari==0.4.19.post1
Requires-Dist: numpy==1.24.4
Requires-Dist: openpyxl==3.1.2
Requires-Dist: pandas==1.5.3
Requires-Dist: pyarrow==11.0.0
Requires-Dist: pysimplegui==4.60.5
Requires-Dist: scikit-image==0.19.1
Requires-Dist: scikit-learn==1.3.2
Requires-Dist: scipy==1.9.1
Description-Content-Type: text/markdown

# Small Fish
**Small Fish** is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.

Cell segmentation is peformed using *cellpose* (published work) : https://github.com/MouseLand/cellpose

Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish

Time stacks are not yet supported.

## Installation

It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.

```bash
conda create -n small_fish python=3.8
activate small_fish
```
Then download the small_fish package : 
```bash
pip install small_fish
```
<b> (Recommended) </b> Results visualisation is achieved through *Napari* which you can install with :

```bash
pip install napari[all]
```

## Run Small fish

First activate your python environnement : 
```bash
activate small_fish
```
Then launch Small fish : 
```bash
python -m small_fish
```
## Developpement

Optional features to include in future versions : 
- batch processing
- time stack (which would include cell tracking)
- 3D segmentation
