Detects blobs in images
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
This plugin consists of two widgets:
- Detects blobs on images (a.k.a. spot detection)
- Convert points layer to labels layer
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.
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.
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
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.
Distributed under the terms of the BSD-3 license, "napari-blob-detection" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.