Metadata-Version: 2.4
Name: napari-mousetumorpy
Version: 0.0.1
Author-email: EPFL Center for Imaging <imaging@epfl.ch>
License: Copyright (c) 2024, EPFL
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Project-URL: homepage, https://github.com/mousetumorpy/napari-mousetumorpy
Project-URL: repository, https://github.com/mousetumorpy/napari-mousetumorpy
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: napari[all]
Requires-Dist: opencv-contrib-python-headless
Requires-Dist: mousetumorpy
Dynamic: license-file

![EPFL Center for Imaging logo](https://imaging.epfl.ch/resources/logo-for-gitlab.svg)
# 🐭 napari-mousetumorpy

A Napari plugin for [mousetumorpy](https://github.com/EPFL-Center-for-Imaging/mousetumorpy.git): a toolbox to segment and track murine lung tumor nodules in mice CT scans.

## Installation

Install `napari-mousetumorpy` with `pip`:

```sh
pip install napari-mousetumorpy
```

or clone the project and install the development version:

```sh
git clone https://github.com/EPFL-Center-for-Imaging/napari-mousetumorpy.git
cd napari-mousetumorpy
pip install -e .
```

## Usage

Start napari from the terminal:

```sh
napari
```

You can find the plugin functions under `Plugins > Mousetumorpy`:

- `ROI and Lungs detection`: Segments the lungs and crops a CT scan around them.
- `Tumor segmentation`: Segments tumor nodules in a CT scan image (cropped around the lungs).
- `Track tumors`: Tracks tumor nodules in a 4D (TZYX) tumor segmentation masks series.

## Sample image

We provide a sample image under `File > Open Sample > Mouse lung CT scan` to test the package's functionality for lungs segmentation, cropping, and tumor segmentation.
