IdentifySecondaryObject based on primary object from different RGB channel

#1

Hi, I have DAPI images and after identifying nuclei as primary objects (blue channel) I am trying to identify gene stains (from red and green channels) as secondary objects, based on the primary nuclei
(I am having trouble with “cathching” the secondary objects and instead just end up with the same primary objects).

How would be best to do so?
Thanks
Shimmy

#2

Hi Shimmy,

You’ll likely get better help if you provide more details (like images) :slight_smile:
Start here for hints: BEFORE POSTING - Please read this

#3

Hi,
Attached are the images where you can see :

  1. Separating original colour image to separate grayscale channels.
  2. Identified primary nuclei objects in blue channel.
  3. Identified primary objects in red channel.
  4. Attempting to identify object in red channel as secondary in relation to blue channel’s nuclei - unsuccessfully.
  5. Attempting to use “RelateObjects” instead of IdentifySecondaryObjects in order to find which objects on red channel fall within the area of the nuclei objects from blue channel (which is my objective). It is not clear to me if it based the result on both objects correctly or if this is weak result.

Any suggestions on how to do this better?
Thanks,
Shimmy

RGB primaryBlue primaryRed secondaryRedPrimaryBlue relateBlueRed

#4

Hi Shimmyb

It would be a lot easier to figure it out if you could give a representative image and your pipeline.

Just by looking I would say that you are not thresholding correctly. Is this OTSU? Have you adjusted the OTSU setting? Are you able to define the cell bodies? Are you segmenting the cell bodies that touch?

Best
Lee