ImageJ Batch Processing Guide

About this manual

This document provides guidance on using ImageJ to automate the processing of large numbers of image files. It covers single image analysis, the use of plugins, and the Macro Recorder tool for generating scripts.

What's inside

• Introduction
• Single Image Analysis
• Macro Recorder
• Batch Process Command
• Batch Macros
• Process Files in a Directory
• Process Open Images

Frequently asked questions

What programming languages are supported by the Macro Recorder?

The recorder supports ImageJ macro language, JavaScript, and Java.

How does the batch process command handle images that do not have a specified output directory?

If no output directory is specified, the images will not be saved after running the command.

What happens to result windows generated by plugin commands during batch processing?

Any results windows generated by the plugin commands will remain open.