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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]];

enter image description here

The result of the segmentation img2 = segmentImage[img]//Colorize is shown below:

enter image description here

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?

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  • $\begingroup$ Also if i do Dilation after applying segmentImage to close the cells then it considers all the cells as a single unit. Nothing i have tried so far seems to be working $\endgroup$
    – Ali Hashmi
    May 21, 2017 at 19:39
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    $\begingroup$ Dilation seems to work for me. (seg2 = Dilation[segmentImage[img], 2]) // Colorize $\endgroup$
    – Simon Woods
    May 21, 2017 at 20:03
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    $\begingroup$ Related: (128596) (you own question; merely linked for organizational purposes) $\endgroup$
    – Mr.Wizard
    May 21, 2017 at 20:07
  • $\begingroup$ @SimonWoods i noticed that when i apply ComponentMeasurements on seg2 (that you mentioned in your comment) it works, however, when i apply it on the image i.e. from Colorize I do not get the count. Do you have any idea why? $\endgroup$
    – Ali Hashmi
    May 21, 2017 at 20:12
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    $\begingroup$ It's simply that ComponentMeasurements requires a label matrix as input, not the color image that Colorize produces. $\endgroup$
    – Simon Woods
    May 22, 2017 at 21:38

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