'Custom Macros' ImageJ/Fiji Plugin - A Long Overdue Introduction

Hello everyone! In 2019, our lab released a plugin suite called “Custom Macros - Lab Image Analysis/Processing Plugin for ImageJ.” This was accompanied by a publication in the Journal of Neuroscience Methods describing the software. I have been meaning to introduce our plugin here on image.sc ever since.

In short, Custom Macros is a large collection of ‘interconnected’ ImageJ/Fiji macros/functions for facilitating straightforward and systematic image analysis workflows, especially in medium-to-large scale projects, including area measurement experiments, object counts, pre-processing, batch tasks, masking, etc. A major goal is enabling automated record keeping of all image and numerical data generated during each analysis run for later review - ultimately to facilitate reproducible science. There is a login system (for generating dedicated user folder/directory hierarchies and config files), an automated unit-calibration system, numerous handy keyboard and interface button shortcuts, and a detailed built-in help system. Macros, either in sets or in different files, utilize calls to a dedicated function library file. Everything is GPL3 licensed.

You can find the install files for Custom Macros, along with documentation and tutorial videos below:

Documentation direct link.

I’ve held back on posting because I anticipated setting up a git or other distributed version control site,thought doing so may be a good/necessary step prior to introducing our plugin. The thing is, Custom Macros includes its own simple decentralized versioning system that automatically timestamps and saves changes (convenient for backup and diff), and is suited for use over cloud storage. There is also a ‘development’ module that allows for quick IDE testing of macro code in clipboard text (with access to the plugin’s built in function library). Ultimately, I find these more convenient to use so I just upload current releases on the ijmacros.com site - this of course may change with additional developers. Installation preserves older versions in a backup folder allowing for rollback if issue are encountered. There is a ‘recent changes’ dialog popup upon login detailing newest version details.

The Custom Macros plugin is probably one of the most extensive uses of the ImageJ macro language and library in a unified project with thousands of lines of codes. It even has its own ‘drag-and-drop’ plugin system. :grinning: Since 2019, a lot of new functionality has been added, as well. I am trying my best keeping up code annotation…

My thanks to the developers of ImageJ/Fiji and especially to those maintaining and expanding the macro language and built-in function library!

Also, I decided to post this in the main forum, but please advise if there is a better sub-forum.

Anyway, please tell me what you think. I look forward to being being an active participant on image.sc. :slightly_smiling_face:

Best regards,
Miky Timothy
Brooklyn College, New York


Mmmmm! So much this. Sounds interesting.

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