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.
2 maintainers
Metadata
2 maintainers
Release files for napari-bigfish 0.8
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| napari_bigfish-0.8.tar.gz | 33.2 kB | Without provenance | Details for napari_bigfish-0.8.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| napari_bigfish-0.8-py3-none-any.whl | Python 3 | none | any | Details for napari_bigfish-0.8-py3-none-any.whl |
Total release size: 59.3 kB
Release files / napari_bigfish-0.8.tar.gz
| Download URL | napari_bigfish-0.8.tar.gz |
|---|---|
| Size | 33.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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twine/6.1.0 CPython/3.13.5
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Release files / napari_bigfish-0.8-py3-none-any.whl
| Download URL | napari_bigfish-0.8-py3-none-any.whl |
|---|---|
| Size | 26.1 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.13.5
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Security for napari-bigfish 0.8
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