This project has been archived by its maintainers, and is no longer receiving any updates.
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
1 maintainer
Metadata
1 maintainer
Release files for depalma-napari-omero 0.4.8
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| depalma_napari_omero-0.4.8.tar.gz | 566.5 kB | Without provenance | Details for depalma_napari_omero-0.4.8.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| depalma_napari_omero-0.4.8-py3-none-any.whl | Python 3 | none | any | Details for depalma_napari_omero-0.4.8-py3-none-any.whl |
Total release size: 622.2 kB
Release files / depalma_napari_omero-0.4.8.tar.gz
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Release files / depalma_napari_omero-0.4.8-py3-none-any.whl
| Download URL | depalma_napari_omero-0.4.8-py3-none-any.whl |
|---|---|
| Size | 55.6 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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No |
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twine/6.2.0 CPython/3.10.20
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