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ImageJ2 Python Scripts

    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