Thank you all for the quick reply @chalkie666, @etarena!!
I wasn’t in the lab today, but tomorrow I will be and I’ll re-post my question publicly on the main forum with my code samples.
As for now, I’ll answer your, @chalkie666, questions (w/o the codes though):
I was tasked to do an automation of colocalization calculations on several TIFF files located in the same directory.
In order to do so, I thought about either writing a Java code and/or an ImageJ’s macro script.
I have struggled to run the colocalization’s “run” method both on the macro code and the Java code.
My main problem was not knowing which input arguments I should pass to the “run” method. After seeing several examples, I have realized what I should do with the macro, and it worked.
However, I still have a problem with the Java code.
Later on I save the results of the colocalization calculation in an excel file.
While the macro script currently works, I still prefer working with the Java code. The main reason is that I’ll have to do String parsing of the TIFF files’ titles (the images’ names). Also, it is easier to write to an excel file with Java than with ImageJ’s macros.
I saw that someone wrote an excel macro for ImageJ but it doesn’t work on my macro.
I will add my codes tomorrow as I don’t have them with me currently.