napari-imagej
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
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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 Setup
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