also asked on Community: http://community.wolfram.com/groups/-/m/t/1100430
I have the following image that i segment into respective cells using the function below:
segmentImage[binarizedMask_?ImageQ] :=
Module[{seg, areas, indexMaxarea, maxArea},
seg = MorphologicalComponents@*ColorNegate@Dilation[binarizedMask, 1];
areas = ComponentMeasurements[seg, "Area"];
{indexMaxarea, maxArea} = First@MaximalBy[areas, Last] /. Rule -> List;
If[maxArea > 20000, ArrayComponents[seg, Length@areas, indexMaxarea -> 0], seg]];
The result of the segmentation img2 = segmentImage[img]//Colorize is shown below:
The problem that I am facing is that the boundaries between the cells are completely lost. I cannot recover any information of the neighbours or the neighbourcount:
ComponentMeasurements[img2,"NeighborCount"]
(* {1 -> 0, 2 -> 0, 3 -> 0, 4 -> 0, 5 -> 0, 6 -> 0, 7 -> 0, 8 -> 0,
9 -> 0, 10 -> 0, 11 -> 0, 12 -> 0, 13 -> 0, 14 -> 0, 15 -> 0,
16 -> 0, 17 -> 0, 18 -> 0, 19 -> 0, 20 -> 0, 21 -> 0, 22 -> 0,
23 -> 0, 24 -> 0, 25 -> 0, 26 -> 0, 27 -> 0, 28 -> 0, 29 -> 0,
30 -> 0, 31 -> 0, 32 -> 0, 33 -> 0} *)
This should not be the case since in the original image the cells are sharing boundaries. Is there a way to recover the neighbours or better way to do segmentation so that I do not lose boundaries between the cells?
Dilationafter applyingsegmentImageto close the cells then it considers all the cells as a single unit. Nothing i have tried so far seems to be working – Ali Hashmi May 21 '17 at 19:39(seg2 = Dilation[segmentImage[img], 2]) // Colorize– Simon Woods May 21 '17 at 20:03ComponentMeasurementsonseg2(that you mentioned in your comment) it works, however, when i apply it on the image i.e. fromColorizeI do not get the count. Do you have any idea why? – Ali Hashmi May 21 '17 at 20:12ComponentMeasurementsbehaves differently in the prior comment – Ali Hashmi May 21 '17 at 20:14ComponentMeasurementsrequires a label matrix as input, not the color image thatColorizeproduces. – Simon Woods May 22 '17 at 21:38MorphologicalComponents[image, 0]and this it's useless to differentiate colors. – Batracos Jun 05 '17 at 07:56