napari-imagej
0.1.0

Contents:

  • Installation
  • Initialization
  • Configuration
  • Troubleshooting
  • Use cases
    • Tracking HeLa cell nuclei with TrackMate
    • Viewing TrackMate Data in the napari Viewer
    • Puncta Segmentation with SciJava Scripts (headless)
    • Image Processing with ImageJ Ops (headless)
  • Developer’s Guide
  • napari-imagej Architecture
  • Benchmarking
napari-imagej
  • Use cases
  • Edit on GitHub

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
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