# napari-blob-detection
[](https://github.com/andy-sweet/napari-blob-detection/raw/main/LICENSE)
[](https://pypi.org/project/napari-blob-detection)
[](https://python.org)
[](https://github.com/andy-sweet/napari-blob-detection/actions)
[](https://codecov.io/gh/andy-sweet/napari-blob-detection)
[](https://napari-hub.org/plugins/napari-blob-detection)
Detects blobs in images
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started
and review the napari docs for plugin developers:
https://napari.org/plugins/stable/index.html
-->
This plugin consists of two widgets:
1. Detects blobs on images
2. Convert points layer to labels layer
----------------------------------
### 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.
----------------------------------
## 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/
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"description": "# napari-blob-detection\n\n[](https://github.com/andy-sweet/napari-blob-detection/raw/main/LICENSE)\n[](https://pypi.org/project/napari-blob-detection)\n[](https://python.org)\n[](https://github.com/andy-sweet/napari-blob-detection/actions)\n[](https://codecov.io/gh/andy-sweet/napari-blob-detection)\n[](https://napari-hub.org/plugins/napari-blob-detection)\n\nDetects blobs in images\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/plugins/stable/index.html\n-->\n\nThis plugin consists of two widgets:\n\n1. Detects blobs on images\n2. Convert points layer to labels layer\n\n----------------------------------\n\n### Detects blobs on images\n\nThis 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.\n\nParameters\n\n- method: Laplacian of Gaussian (most accurate) or Difference of Gaussian (faster approximation) \n- image: Image layer for blob detection. Can be a 2D, 3D, or higher dimensionality image.\n- dimensionality: users can specify if the image is 2D(+t) or 3D(+t).\n- min sigma: the smallest blob size to detect\n- max sigma: the largest blob size to detect\n- threshold: the lower the threshold, the more low intensity blobs are detected. \n\nOutput\n\nBlobs are represented by the Points layer.\nThe size of each blob is proportional to `Points.feature['sigma']`,\nwhich signifies the scale at which the feature point was found.\n\n### Convert points layer to labels layer\n\nThis widget takes a points layer and converts it into a labels layer, with the image dimension matching the selected image layer.\nBy converting points to labels, users can leverage feature extraction functions that are available to labels to the detected points.\n\n----------------------------------\n\n## Installation\n\nYou can install `napari-blob-detection` via [pip]:\n\n pip install napari-blob-detection\n\n\n\nTo install latest development version :\n\n pip install git+https://github.com/andy-sweet/napari-blob-detection.git\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-blob-detection\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/andy-sweet/napari-blob-detection/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n\n",
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