Dear CellProfiler Community

I’d first like to thank the CellProfiler developer team for this great tool and your support on this board. I’m new to CellProfiler and I’m trying to use it besides Matlab to analyze movies from in vivo two-photon calcium imaging. I’m currently implementing Cellprofiler 2.0 to find regions of interest in these movies (@1.48fps, ~1400 frames per stack, currently >250 stacks and increasing), because finding them by hand takes weeks, obviously. I made huge progress in identifying and segmenting the signals, the only problem is the tracking. As I understood it, the implemented tracker just tracks signals from frame to frame and not through a whole stack. So if a signal disappears for a few frames, it is considered a new signal when it reappears. I understand that this tracker wasn’t designed for this purpose, thats why I wrote my own in Matlab. So far so good .

But for further analysis in Matlab, I need to get the regions of interest as polygons. Is there a way to get the polygon vertices for each object? Or could you imagine a way to convert an outline image into polygons and their vertices?

Thank you very much for your answer!

Kim

PS: Maybe I need to state, that in the end I’d like to measure intensities, etc. from those ROIs over the whole imaging period.