I am finally getting around to polay with StarDist in ernest and have hit a snag in batch processing in Fiji with it.
The data is 3 channel time series of celltrack/PI/AnnexinV for looking at appoptosis. We have a Fiji macro that has served us well over the years but StarDist is much faster and more robust at pulling out the nuclei.
I am hitting a few issues when trying to batch process it however.
I am using Stardist with default settings and if i run without activating batch mode it all works fine with Label image output or ROI manager output.
Once in batch mode i have the following issues
- If output is set to Label Image, no Label Images are created. Cant then use them to make masks
- If output is set to ROI Manager a blank window titled ROI Manager is created after each run of StarDist by the macro and the created rois can’t be used to generate masks as the ROI list isn’t addressed properly, i assume due to the extra roi windows.
- If i run the first stack through without batchmode enabled and then turn it on at teh end of the first loop it works fine with the ROI manager with no extra windows.
Any ideas on what coudl be going on? I have my code working now with the last point on the issues but it woudl be nice to have it truly headless.
If batchmode isn;t enabled, everything