Algae real time cell counts

[Paris Morgan]

Hello,

I'm currently working on getting my AxioCam HRc to do real time cell counting. I have Micro Manager set up and can do the particle / cell finding, but right now the lines in the picture are messing me up. I've tried to set ROI's for the lines and do everything but that, but the ROI line tool is too narrow to exclude the edge detection. Any suggestions? Or maybe is there a protocol that does this already? 

tl;dr: I need to count cells and the lines are messing with the detection. =)

Any help greatly appreciated!!

Thanks,

Paris

[Stephane]

Hello,

Line ROI cannot do that as there are only intersection tool for intensity profile analysis.
What you can do however is to filter your spot result depending certain criterion.
I used spot detection with scale 3 and sensitivity set to 80 with ROI export enable on your image.
From the ROI, i filtered all ROI with a size (interior column) < 20 or > 40 pixels.
Already doing that you can discard a lot of false positive. Then i used 'sphericity' and 'homogeneity' criterion to discard almost all remaining wrong detection by removing all ROI with (sphericity < 80 and homogeneity > 0.20).
You can do that kind of filtering afterward, when you exported the results in excel file.

Best,

- Stephane