Improving segmentation

Hi,
I’m trying to improve my pipeline which I’ve tried to tailor to segmenting root cells. However, I’m having trouble improving the segmentation, particularly with respect to erosion/dilation of cells to rejoin those which have been erroneously split and separate those which have been merged. Please note that I am intending to mask the vasculature (the centre of the root, which as you can see is terribly segmented) due to poor staining.

Any advice would be greatly appreciated,

Regards,
Rosalind
ongoing2.cp (8.22 KB)

Hi Rosalind,

I took a look and think you were on the right track. I’ve put together a pipeline which should get you closer. I basically used the illumination correction modules to remove the background staining (rather than EnhanceOrSupress). I tried using EnhanceOrSupress on the result of the illumination correction, but interestingly, it made matters worse so I removed it.

Regards,
-Mark
2013_04_19.cp (7.91 KB)

1 Like

Hi Mark,

Thanks a lot, you’re pipeline really helped. Would it be appropriate for me, as the primary objects identified aren’t in contact with each other, to use identifysecondary objects to identify ‘whole’ cells?

Regards,
Rosalind

Yes, definitely. You could either use Distance-N to expand the cells by however many pixels you think would be adequate to get them to touch, or use Propagation, and then adjust the thresholding settings accordingly.
-Mark