We have some macros for ImageJ/FIJI for making figures and blind analysis which could be useful to others.
I made an ImageJ Update Site so that the latest versions can be pushed out to the people in the lab, but this also gives the opportunity to share our code with the world. Feel free to add the quantixed ImageJ update site to your ImageJ or FIJI installation. Details of how to do that are here.
The code is maintained in this GitHub repo, which has a walkthrough for figure-making in the README. So, if you’d like to make figures the quantixed way, adding ROIs and zooms, then feel free to give this code a try. Please raise any issues there or get in touch some other way.
Disclaimer: this code is under development. I offer no guarantees to its usefulness. I am not responsible for data loss or injury that may result from its use!
Update @ 10:35 2016-12-20 I should point out that other projects already exist to make figures (MagicMontage, FigureJ, ScientiFig). These projects are fine but they didn’t do what I wanted, so I made my own.