Closed Daniel-Mietchen closed 5 years ago
A Fiji (not ImageJ) Script Editor supports multiple languages, including Python 2.7: https://imagej.net/Using_the_Script_Editor
There are ImageJ tutorials involving Jupyter notebooks: https://github.com/imagej/tutorials
For reproducibility and automation, there is the macro recorder that allows to record every single step.
I checked PubMed Central for publications using ImageJ (ideally with published scripts) and looked at a number of them. Also contacted the indicated author of this paper but got an autoresponse that they are out of office over the summer.
Meanwhile, I have the scripts from the above paper, along with a pointer to a thesis at https://refubium.fu-berlin.de/handle/fub188/22959 with further documentation.
https://education.cadre.virginia.edu/#/workshop/1595