🐭 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. 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.