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fiji-scripts

This repository contains various image processing and image analysis scripts written in languages supported by Fiji (e.g. Groovy, Python (Jython), ImageJ Macro, etc...).

How to run a script in Fiji

To run a script in Fiji, open the script editor with the [ hotkey or New > Script... from the menu. Copy or open a script in the script editor and then click Run to execute the script.

script editor

Notes

  • Scripts starting with the ijo prefix utilize ImageJ Ops to perform the image processing.
    • ImageJ Ops ships with Fiji, no additional installation is required.
  • Scripts starting with the sjo prefix utilize SciJava Ops to perform t he image processing.
    • SciJava Ops must be installed first before using scripts that use the OpEnvironment.
    • See these instructions on how to install SciJava Ops.