napari-imagej
latest

Contents:

  • Installation
  • Initialization
  • Basic Usage
  • Configuration
  • Troubleshooting
  • Use Cases
    • Tracking HeLa cell nuclei with TrackMate
    • Viewing TrackMate Data in the napari Viewer
    • Using BoneJ2
    • 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
  • 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
Previous Next

© Copyright 2023, ImageJ2 developers. Revision e2bfdebf.

Built with Sphinx using a theme provided by Read the Docs.
Read the Docs v: latest
Versions
latest
stable
0.1.0
Downloads
On Read the Docs
Project Home
Builds