napari-blob-detection 0.0.2
Detects blobs in images
License: BSD-3-Clause
Requires Python: >=3.8

# napari-blob-detection

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Detects blobs in images

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This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.

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This plugin consists of two widgets:

1. Detects blobs on images
2. Convert points layer to labels layer

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### Detects blobs on images

This widget uses [scikit-image's blob detection algorithms](https://scikit-image.org/docs/stable/auto_examples/features_detection/plot_blob.html) to detect bright blobs on dark backgrounds.

Parameters

- method: Laplacian of Gaussian (most accurate) or Difference of Gaussian (faster approximation) 
- image: Image layer for blob detection. Can be a 2D, 3D, or higher dimensionality image.
- dimensionality: users can specify if the image is 2D(+t) or 3D(+t).
- min sigma: the smallest blob size to detect
- max sigma: the largest blob size to detect
- threshold: the lower the threshold, the more low intensity blobs are detected. 

Output

Blobs are represented by the Points layer.
The size of each blob is proportional to `Points.feature['sigma']`,
which signifies the scale at which the feature point was found.

### Convert points layer to labels layer

This widget takes a points layer and converts it into a labels layer, with the image dimension matching the selected image layer.
By converting points to labels, users can leverage feature extraction functions that are available to labels to the detected points.

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## Installation

You can install `napari-blob-detection` via [pip]:

    pip install napari-blob-detection



To install latest development version :

    pip install git+https://github.com/andy-sweet/napari-blob-detection.git


## 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 [BSD-3] license,
"napari-blob-detection" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin

[file an issue]: https://github.com/andy-sweet/napari-blob-detection/issues

[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/