I have split my image into the 3 channels each representing a different dye. I have segmented each image and I now want to 1) Identify each of the segmented regions and 2) Detect the level of dye based on itensity measurements in each segment 3) Use the dye intensity measurements-so that the 2 dyes which have a higher overall intensity over a 3rd dye will be assigned a color to identify the dye combination in the merged imaged to represent of segmented regions with different dual combinations of dye based on the knowledge that each regions can only have 2 dyes.

I am limited to the number of images so have added the segmented blue channel and an unsegmented green channel as examples. channelgreen


  • $\begingroup$ What I see here are two images with white blobs that consist of many smaller blobs. I would surely help you if you can explain a bit more detailed what you already tried, what a "segmented region" in your case is. Just remember that people need to understand what you are seeking and not all have experience with biological microscopy images (if your images are those). $\endgroup$ – halirutan Mar 6 '17 at 10:26
  • $\begingroup$ To add to halirutan's comment: if you could explain what you want the output to be, it would make it easier to help. For example, for these images, what should the answer be (approximately)? For example, I do not know what you mean when you refer to "dyes". Do you mean color channels in the image? Or something else? $\endgroup$ – bill s Mar 6 '17 at 14:22
  • $\begingroup$ Thanks @halirutan for the comments. Grayscale images of cells- top image is a image for cells in 1 channel (unsegmented),the lower image is for another channel after it has been segmented outside Mathematica. The dyes are fluorophores,total of 3 used. I know that each region can have only 2 fluoros. I need a way of being able to find out which 2 fluoros are within each segment so that I can assign a pseudocolor to the segment in the merged image which would be 1 out of a total of 3 different pseudocolors. e.g.Segment has AB combo based on A and B with higher intensity values than C $\endgroup$ – doro_t Mar 6 '17 at 21:07
  • $\begingroup$ Thank you @bill s for comment. I have added a comment above. I would like to 1)identify the segments by number in each a channel- could use a mask of the merged image with the identified segments to map back onto each channel 2)get the fluoro intensity values for each numbered segment. Each segment should only have a max of 2 fluoros-channel A & B have higher intensity values above 70% over C.Then in the end I can assign yellow to all segments in the merged mage which have A & B fluoros or blue to segments which have B & C fluoros. Im ok with a longer method of doing this as id like to learn $\endgroup$ – doro_t Mar 7 '17 at 10:05
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    $\begingroup$ @doro_t Would you mind joining the Mathematica Chat and pinging me with a message starting with @halirutan? It's still not entirely clear what you want, but I'm sure we can solve this. $\endgroup$ – halirutan Mar 11 '17 at 15:44

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