ImageJ Macro is a small piece of code written in the hybrid ImageJ/Java language in order to automatize image processing. Image J can be downloaded for free here. FiJi, another distribution of ImageJ, can be downloaded here.

To run a macro, download the .ijm file and drag and drop in ImageJ. It should open a new window, then just push the 'Run' button. Another possibility is to create a new blank macro and copy-paste the macro code in there.

If you want to learn more about macro and coding in general, this introduction is perfect. And the ImageJ built-in macro function documentation is indispensable!

Recursive Manual Crop

Here is a simple but user-friendly and useful macro for all my microscopist friends out there.

This macro process in a recursive manner all tif images to allow manual cropping of the cell of interest then split the channel and save them in a split folder. Still rely on YOU to select and crop the cell, but avoid a lot of clicking and fiddling with the menus. Speed up your work by 5!

Also, have a version for time-series!

lif to tif

I am more a user of tif file and tends to avoid proprietary extension. Even if I love Leica, their files can be dozens, sometimes hundreds of Giga for my time series. Time series that I need to check one by one before doing further analysis by Python. Hence this macro converts all images in multiple tif, based on how you parameters your lif save file.

ImageJ macro workshop

I animate a small workshop on how to make a macro on ImageJ, and more importantly for a lot of people, on how to make it work on all images in a folder, with the recursive option.

All the documentation and test images are on my GitHub:

https://github.com/leclercsimon74/ImageJ-Macro-Workshop-Level-1