Batch Processing

Revision as of 12:54, 11 September 2014 by Rueden (talk | contribs) (Overview)


A fundamental benefit to creating scripts and macros in ImageJ is the ability to reuse their functionality on more than one image. Although this can be done manually, there are multiple ways to easily automate this batch processing.

General workflow

  1. Create a basic macro which operates on the active image.
  2. Apply your macro to a group of images.
    • These images do not need to be open in ImageJ already—they will be read in as part of the batch process.
    • See below for details.

Easy option

The fastest way to start batch conversion is via the Process > Batch > Macro... command. This will open a dialog (below) that will allow you to specify an input and output directory. You can select an output file format, and then use the Add Macro Code drop-down to generate a macro with the desired functionality.


Flexible option

Open the script editor, select Templates > IJ1 Macro > Process Folder. This will generate the following boilerplate:

Process folder ij1.png

Lines 26 and 27 can now be edited, replaced with the functional macro code you would like to apply to all images of a given type in a folder. Furthermore you can now modify the batch processing logic itself, for example if you need to customize what (if any) output information is saved.