napari-mousetumorpy 0.0.1

No project description provided

🐭 napari-mousetumorpy

A Napari plugin for mousetumorpy: a toolbox to segment and track murine lung tumor nodules in mice CT scans.

Installation

Install napari-mousetumorpy with pip:

pip install napari-mousetumorpy

or clone the project and install the development version:

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

Usage

Start napari from the terminal:

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.