Metadata-Version: 2.4
Name: napari-mousetumorpy
Version: 0.0.2
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: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: tifffile
Requires-Dist: napari[all]
Requires-Dist: napari-toolkit
Requires-Dist: imaging-server-kit>=0.1.3
Requires-Dist: mousetumorpy>=0.0.2
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`. Several tools are available:

- `Mousetumorpy`: The main image processing functions from the `mousetumorpy` package. Three workflows are available under *Algorithms*:
  - `Lungs segmentation`: Segments the lungs and crops a CT scan around them.
  - `Tumor segmentation`: Segments tumor nodules in a CT scan image (cropped around the lungs).
  - `Tumor tracking`: Tracks tumor nodules in a 4D (TZYX) tumor segmentation masks series.
- `Color picker`: Allows to display a segmentation in a chosen color.
- `Manual cropping`: Allows to crop CT scans manually by setting limits in the X, Y and Z directions.
- `Convert to tracks`: Displays tracks from a segmentation (Labels) layer, based on the label values.
- `Data table`: Displays tumor labels and corresponding volumes in a table. Allows to follow tumors across scans when the time slider is moved.
- `Remove objects`: Allows to remove individual tumors.

## Sample image

We provide a sample image under `File > Open Sample > Mouse lung CT scan` to test the package's functionality.
