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A napari plugin for blob detection. For more information on how to use the plugin on your own data please refer to the docs.

• blob_detection: Implements a user interface to use scikit-image blob detection algorithms (https://scikit-image.org/docs/dev/auto_examples/features_detection/plot_blob.html).
• filter_widget: Widget to filter the detected blobs by a blob feature value (or a combination of feature values).
• selection_widget: Widget to manually annotate a subset of detected blobs as foreground vs. background blobs. The widget can then use the annotated blobs to train a support vector machine to classify the remaining blobs in the image.
• tracking_widget: EXPERIMENTAL: tracking of the detected blobs in 2DT and 3DT images .

An experimental tracking widget that will track your blobs in 2DT and 3DT images is also available:

It's best to create a new python environment to try the plugin:

conda create -n napari-blob-detection python=3.9

Activate the environment:

conda activate napari-blob-detection

You will need to install napari and JupyterLab or Jupyter Notebook (if you want to test the examples)

pip install napari[all]
pip install jupyterlab

You can then install napari-blob-detection via pip:

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

To try the example jupyter notebooks do the following:

git clone https://github.com/adrtsc/napari-blob-detection
cd napari-blob-detection/examples/

Start JupyterLab

jupyter lab 

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

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.