I did another trial overnight (still running) with 3 images (193 time points, 900mB) and an output in TXT and it seems to have worked for the first time ever…

though if I try and touch the program it will freeze

However, it took a looong time and I have no clue why the 2nd image took so long

Image1:
Active contour: 1h20 (5521 ROI)
spot detector: 8 min (199247 detected scale 1 90%, 109151 filtered >4px)
ROI inclusion analysis: 1h42 min

image 2:
active contour 8h49min (5617 ROI – 5061 filtered)
spot detector 10 min (189 961 ROI detected scale 1 90%, 98529 filtered >4px)
ROI inclusion analysis: 58 min

image 3 is still running active contour….