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
• Using BoneJ2
  • napari Setup
  • BoneJ2 Setup
  • Preparing and Opening the Data
    • Opening Data in napari
    • Processing Data in napari with nsbatwm
    • Processing Data in napari with BoneJ2 and napari-imagej
    • The final measurements
• 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