napari blob detection

Detects blobs in images

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

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 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.