I have written a bunch of macros at this point for image analysis and know a few languages but I am by no means a programmer.
I have this macro I wrote that batch processes a bunch of images and utilizes StarDist to phenotype cells within an image based on an intensity threshold in individual ROIs. I have been recommended to adapt this macro to a CLIJ based process to try to make it faster, and not require babysitting, as right now we have to hit “Ok” every time the StarDist window appears. From what I’m reading on the CLIJ page I’m guessing I would have to adapt the macro into a Java plugin? I don’t know if it makes a difference but my images need to be imported through BioFormats.
Is this the platform I should even be using?
How? Java? Python? (It’s been a hot minute since I’ve used either language)
Can StarDist be used as a CLIJ plugin?