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 .
napari.2022-03-30.19-56-36.mp4
An experimental tracking widget that will track your blobs in 2DT and 3DT images is also available:
napari.2022-04-02.16-10-02.mp4
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.