Batch Processing


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/script which operates on the active image or on a single file.
  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.

Option 1 - Process  ▶ Batch  ▶ Macro...

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.


Option 2 - Script Template

Open the script editor, select Templates  ▶ ImageJ 1.x  ▶ Batch  ▶ Process Folder (IJ1 Macro). 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.

Option 3 - Batch Processing with Script Parameters

See also