epicure 1.6.1

Napari plugin to manually correct epithelia segmentation in movies

EpiCure

Napari plugin to ease manual correction of epithelia segmentation in movies.

To analyse individual cell trajectory from epithelia movies marked for cell-cell junctions, a very precise segmentation and tracking is required. Several tools such as TissuAnalyzer, Epyseg, CellPose or Dist2Net perform very good segmentation (~5% of errors). However, this still implies a high amount of cells to correct manually.

EpiCure allows to decrease the burden of this task. Several features are proposed to ease the manual correction of the segmented movies, such as error detection, numerous shortcuts for editing the segmentation, option for tracking, display and measure/export options. EpiCure detect segmentation errors by taking advantage of temporal information. When a correction is done at a given frame, EpiCure relink the track to adjust for the changes.

See the full documentation here

Installation

Install plugin

To install EpiCure on a fresh python virtual environment, type inside the environement:

pip install epicure

Then launch Napari, and the plugin should be visible in the Plugins list.

If you already have an environment with Napari installed, you can also install it directly in Napari>Plugins>Install/Uninstall plugins

Install code

To have the code to be able to modify it, clone this repository. You can use pip install -e . so that everytime you update the code, the plugin will be updated.

Dependencies

The input files of EpiCure can be already tracked or not. Tracking options are proposed in EpiCure:

• Laptrack centroids
• Laptrack overlaps

Usage

Refer to the documentation for documentation of the different steps possible in the pipeline.

References

If you use EpiCure, thank you for citing our work:

EpiCure is not published yet, you can cite it using Zenodo for now: https://doi.org/10.5281/zenodo.13952184

Dataset

The dataset presented in our main EpiCure publication is available on zenodo: 10.5281/zenodo.20607705.

Contributing and Feedback

EpiCure is mainly developed in CNRS UMR3738, in the Developmental and Stem Cell Biology Department of Institut Pasteur. If you have a question on using EpiCure or ask to add a feature, either file an issue or write in the imagesc forum.

Any contribution is most welcome. Do not hesitate to contact us beforehand through filing an issue (choose "Other questions/comments" type). To suggest the addition of a new feature, you can also contact us by filing an issue choosing the "Feature request" option.

If you encounter a code related issue using EpiCure, please file an issue in this repository.

To facilitate contributions, we added a pixi file in the repository. Developers can run:

• pixi run build to install locally the plugin and test it manually
• pixi run test to run locally the tests from the src/tests directory
• pixi run build-doc to locally build the documentation pages. The documentation will be build in the site folder in the repository. The file site\index.html can be open in a browser to see the generated documentation.

The code API can be found here in the online documentation. Examples of using EpiCure without opening the interface can be found in the test files and the repository notebooks.