Introduction
This page is a primer of ImageJ2 only Python scripts. It means that the examples included here avoid IJ1 as much as possible, unless it’s really necessary.
Note that all the scripts of this page are links from https://github.com/imagej/imagej-scripting/tree/master/src/main/resources/script_templates/ImageJ2.
Scripts
Stack Projection
Projection.py
Apply Threshold
Apply_Threshold.py
Apply_Threshold_Fast.py
Crop an image
Crop.py
Rotate all the frames of a stack
Rotate_Stack.py
Subtract a stack to its first image
Subtract_First_Image_Stack.py
Apply DOG Filter
Apply_DOG_Filtering.py
Apply a mask
Apply_Mask.py
Retrieve objects/particles from a mask
Particles_From_Mask.py
Manual Simple Registration on Stack
Manual_Registration.py
Resources