BigFISH smFISH Analysis
A napari-plugin providing an alternative GUI for Big-FISH. Big-FISH is a python package for the analysis of smFISH images.
napari-bigfish
A napari-plugin providing an alternative GUI for Big-FISH. Big-FISH is a python package for the analysis of smFISH images.
The plugin provides a graphical user interface for some of the functionality in Big-FISH. Currently implemented are:
- Gaussian-background subtraction
- FISH-spot detection with
- Elimination of duplicates
- Auto-detection of threshold
- Dense-region decomposition
The plugin further implements by itself:
- Counting of spots per cell, inside and outside of the nucleus
- Batch processing on a list of images
You can find the user and the api-documentation of napari-bigfish here.
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
Installation
You can install napari-bigfish via pip:
pip install napari-bigfish
Contributing
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
License
Distributed under the terms of the MIT license, "napari-bigfish" is free and open source software
Issues
If you encounter any problems, please [file an issue] along with a detailed description.
Version:
- 0.8
Last updated:
- 2025-07-23
First released:
- 2023-04-07
License:
- MIT
Supported data:
- Information not submitted
Plugin type:
Open extension:
Save extension:
Operating system:
- Information not submitted
Requirements:
- numpy
- magicgui
- qtpy
- pyperclip
- big-fish
- scikit-image
- tox; extra == "testing"
- pytest; extra == "testing"
- pytest-cov; extra == "testing"
- pytest-qt; extra == "testing"
- napari; extra == "testing"
- pyqt5; extra == "testing"