small-fish-gui

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 or virtual environnement to install small fish.

conda create -n small_fish python=3.8
activate small_fish

Then download the small_fish package :

pip install small_fish

(Recommended) Results visualisation is achieved through Napari which you can install with :

pip install napari[all]

Run Small fish

First activate your python environnement :

activate small_fish

Then launch Small fish :

python -m small_fish

Developpement

Optional features to include in future versions :

• batch processing
• time stack (which would include cell tracking)
• 3D segmentation