Use cases

Below we document use cases for the napari-imagej plugin.

• Tracking HeLa cell nuclei with TrackMate
  • TrackMate Setup
  • Preparing the Data
  • Running TrackMate
  • Processing tracks with napari-stracking
• Viewing TrackMate Data in the napari Viewer
  • TrackMate XML
  • Obtaining sample data
  • Opening the data
• Puncta Segmentation with SciJava Scripts (headless)
  • Configuration
  • The Code
  • Installing the script
  • Running the script
• Image Processing with ImageJ Ops (headless)
  • Ops, explained
  • A simple gaussian Blur