Napari interface for the De Palma lab.
Project description
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.
Project details
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