ImageJ

Owned by Simon Alexander, created
Last updated: Jun 30, 2023
1 min read
1 Overview | 2 Using | 2.1 Working with ‘large’ Images

Overview

Using

Use the module name imagejto discover versions available and to load the application.

Once loaded, using ImageJ from the command line to start the application.

This is a GUI application, and should be run via SouthPass and an interactive desktop session.

Increase the Java related max heap size by calling: ImageJ -Xmx<max mem> -- e.g. if you have an interactive desktop with 16G call: ImageJ -Xmx16g --

Working with ‘large’ Images

There does appear to be some restrictions with the maximum size of images that can be opened and processed.

For example: NegativeArraySizeException: that states “This error usually means that your image planes are larger than the maximum supported size. The original ImageJ only supports image planes with 2 gigapixels (2^31 = 2147483648 pixels; in case of a square image, the maximum allowed is 46340 x 46340 pixels) or less. If your data has extremely large image planes - e.g., 50000 x 50000 pixels - you may need to analyze region by region. One way to do this is using the “Crop on import” feature of the Bio-Formats plugin.“