Image analysis of tumor nodules in mice CT scans

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.

Installation

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-omero

or from the repository:

pip install git+https://github.com/EPFL-Center-for-Imaging/depalma-napari-omero.git

or 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 .

Usage

From the command-line, start Napari with the depalma-napari-omero plugin:

napari -w depalma-napari-omero

License

This project is licensed under the AGPL-3 license.

This project depends on the ultralytics package which is licensed under AGPL-3.

Related projects

• Mouse Tumor Net | Detect tumor nodules in mice CT scans.
• Mouse Lungs Seg | Detect the lungs cavity in mice CT scans.
• Mouse Tumor Track | Track tumor nodules in mice CT scans.
• JupyterHub (De Palma) | A tailored JupyterHub deployment.