I’m looking for advice/help with modifying the ‘imagej_roi_converter’ plugin provided by Cellpose to use it for batch processing. (I’ve scoured the forum for help but haven’t found anything similar``)
Right now when you open the plugin, it requires an open image and asks for input in the form of a .txt file containing coordinates to outlines of segmented features. These are then listen in ROI manager. My data requires me to measure area of the outlines and save the list as txt file. Because of multiple inputs that have to be done manually as well as saving the measurements it is not possible to run via the ‘batch’ command in processing menu.
This is the list of actions I have to take for each image before I can run the script again for another one.
open("C:/Users/annac/Desktop/Experiment 50.1_sub/WR_sub/WR1-substack-0009.tif"); selectWindow("WR1-substack-0009.tif"); run("imagej roi converter"); roiManager("Measure"); saveAs("Results", "C:/Users/annac/Desktop/Experiment 50.1_sub/WR_sub/WR1-substack-0009_cp_measurement.csv"); roiManager("Delete"); close();
I was wondering if there is a way to make this run automatically for each folder? The files have sequential names: for example the name of the image is WR1-substack-0001.tif and the name of the outline file would be WR1-substack-0001_cp_outlines.txt. And I would like the output file of measured area to be WR1-substack-0001_cp_measurement.csv.
I’d be grateful for any help with this!
(Also I’m a complete newbie so I apologise if this is a trivial issue).