We provide a unified user interface in Napari to detect, track, visualize, annotate, and measure the size evolution of lung tumor nodules in mice CT scans. The datasets and experiment metadata are automatically downloaded and parsed from OMERO.
This project is part of a collaboration between the EPFL Center for Imaging and the De Palma Lab.
As a standalone app
Download and run the latest installer from the Releases page.
In Python
We recommend performing the installation in a clean Python environment. Install our package from PyPi:
pip install depalma-napari-omeroor from the repository:
pip install git+https://github.com/EPFL-Center-for-Imaging/depalma-napari-omero.gitor clone the repository and install with:
git clone git+https://github.com/EPFL-Center-for-Imaging/depalma-napari-omero.git
cd depalma-napari-omero
pip install -e .In Napari
From the command-line, start Napari with the depalma-napari-omero plugin:
napari -w depalma-napari-omero
As a CLI
In interactive mode:
dno interactive
To run all workflows on a given project ID:
dno run <project_id> --lungs-model v1 --tumor-model oct24
This project is licensed under the AGPL-3 license.
This project depends on the ultralytics package which is licensed under AGPL-3.
This project uses the PyApp software for creating a runtime installer.