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

• Jython Scripting
• Jython Examples