The core of any batch-processing code consists of the following:

• Input directory
• Output directory – I believe in most cases it is better to save the output in a separate directory, especially when working with more complex tasks. The example below, however, does not include an output directory.
• Loop {} – indicates repetitive actions
• File opening
• Manipulations
• File saving

This macro will process all the images in the selected source directory. It opens each image, converts it to 8-bit, applies “Smooth” and “Find Edges” filters, saves the processed image as TIFF with the prefix “processed_”, and closes the image. You can modify the steps according to your needs.

// Batch Processing Macro for ImageJ

dir = getDirectory("Choose Source Directory ");
list = getFileList(dir);

for (i=0; i<list.length; i++) {
opening
  path = dir + list[i];
  open(path);
//Manipulation
  run("8-bit");
  run("Smooth");
  run("Find Edges");
// saving
  saveAs("Tiff", dir + "processed_" + list[i]);
  close();
}

To run a macro in ImageJ, follow these steps:

1. Open ImageJ.
2. Click the “Plugins” menu, then select “New” and then “Macro”. This will open the macro editor.
3. Copy and paste the macro code into the editor window.
4. Save the macro using the “File” menu and give it a descriptive name, such as “BatchProcessing.ijm”.
5. Close the macro editor.
6. Navigate to the “Plugins” menu, then select “Macros” and then “Run”. This will open the window where you need to find the directory and select in it the name of the macro you just saved. Choose Open.
7. The macro will run and process the images according to the steps defined in the code.

Note: You may need to modify the macro code to fit your specific needs and input the image

Where can this be applied?

You can automate any Image J task that requires repetitive button pressing. I’ve used it to merge two different fluorescence channels for all images. Additionally, I used it to add scale bars to pictures as well as extract coordinates for wound healing analysis.

If I have no experience in coding, what should I do?

Four options are available in this case:

• To begin with, I strongly believe you should learn how to do it. The more you understand the basics of any coding language, the more you’ll understand how computers work. Furthermore, if you explain your needs clearly to the computer, it will solve your problem more effectively. Using documentation as your vocabulary source and adapting codes posted in forums will enable you to solve your problems.
• To create your final puzzle, you can use the macro recorder in Image J to record your steps.
• The codes can be borrowed from other forum members, such as the one here for Image J.
• In addition, ChatGPT, which everyone is talking about nowadays, can help you generate code templates faster without no knowledge of coding. Based on my request, ChatGPT generated the code above. Check it out. It is completely free. You can get started right away by registering here.