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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.“