napari-trackastra

A napari plugin for cell tracking with trackastra.

Installation

1. Please install napari as outlined here.

2. After that, install the latest version of this plugin from PyPI with:

   pip install napari-trackastra
   

Notes:

• For tracking with an integer linear program (ILP, which is optional), follow the installation instructions of the main trackastra package.
• On Windows currently only supported for Python 3.10.

Usage

• trackastra expects a timeseries of raw images and corresponding segmentations masks as input.
• We provide some demo data at File > Open Sample > trackastra.
• Tracked cells can be directly saved in
  • Cell Tracking Challenge format (CTC)
  • Graph Exchange File Format (GEFF)
• Results can be drag-and-dropped back into napari for inspection.