Big-fish

need a thumbnail
Type
Component
Author
Imbert Arthur
Ouyang Wei
Safieddine Adham
Coleno Emeline
Zimmer Christophe
Bertrand Edouard
Walter Thomas
Mueller Florian
Requires
Python
Execution Platform
Linux
Mac
Windows
Implementation Type
library
Programming Language
Python
Supported image dimension
2D
3D
Interaction Level
Automated
Semi-automated
License/Openness
Free and open source
License
BSD-3 Clause
Description

Big-FISH is a python package for the analysis of smFISH images (2D/3D). It includes various methods to analyze microscopy images, such spot detection and segmentation of cells and nuclei.

has function
Image analysis
Image segmentation
has topic
Microscopy
Fluorescence microscopy
has biological terms
smFish
mRNA
RNAFish
Spatial transcriptomics
Entry Curator
gletort
Post date
08/21/2025 - 13:37
Last modified
08/21/2025 - 14:42
Download Page
Github repository: fish-quant/big-fish
Documentation Link
https://big-fish.readthedocs.io/en/stable/
Reference Publication Link
FISH-quant v2: a scalable and modular tool for smFISH image analysis
Usage Example Link
https://github.com/fish-quant/big-fish-examples/tree/master/notebooks
DOI link
https://doi.org/10.1101/2021.07.20.453024