depalma-napari-omero 0.3.0

Napari interface for the De Palma lab.

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

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

License

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.

Related projects

• Mousetumorpy
• Napari-mousetumorpy