Napari DeepFinder
A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
A napari plugin for the DeepFinder library which includes display, annotation, target generation, segmentation and clustering functionalities. An orthoslice view has been added for an easier visualisation and annotation process.
The documentation for users is available here.
[!WARNING]
An upstream bug in
napariversions ≥ 0.5.0 causes the menu bar to break when closing the Orthoslice view.See this issue for more details: https://github.com/napari/napari/issues/7588.
As a temporary workaround, you can use napari v0.4.19, which is not affected by this bug.
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
Installation
You can install napari-deepfinder via pip:
pip install napari-deepfinder
To install latest development version :
pip install git+https://github.com/deep-finder/napari-deepfinder.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 GNU GPL v3.0 license, "napari-deepfinder" is free and open source software
Issues
If you encounter any problems, please file an issue along with a detailed description.
Version:
- 0.0.2
Last updated:
- 2025-04-04
First released:
- 2022-07-25
License:
- GPL-3.0-only
Supported data:
- Information not submitted
Operating system:
- Information not submitted
Requirements:
- cryoet-deepfinder
- numpy
- magicgui
- qtpy
- napari
- scikit-image
- typing
- pandas
- lxml[html_clean]
- pillow
- h5py
- mrcfile
- scipy
- tox; extra == "testing"
- pytest; extra == "testing"
- pytest-cov; extra == "testing"
- pytest-qt; extra == "testing"