Hello ImageJ team,
I am currently working on some fly wing imaging problems and was wondering if you could run a macros that I have created from terminal. I have created a macros which would automate all of the steps in Fiji, but now I need a wrapper that will initiate 1) Fiji 2) image that I am trying to process 3) run the macros that I wrote on the image 4) save outputs in a specific folder.
I have been looking into jython and trying to connect different tools in ImageJ/Fiji to tools in Jython, but I am running into some rode blocks.
If anyone have ideas of how I could initialize fiji in terminal that would be great.
This is the code that I have currently:
os.system("open -a fiji") os.system("open -a fiji $Image_file")
os.system("open -a fiji $image_file $macros > $results_save_path $processed_image_save_path")
Thanks to everyone in advance for all of the help.