A napari-plugin providing an alternative GUI for Big-FISH. Big-FISH is a python package for the analysis of smFISH images.
Project description
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.
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