Hello all. I am looking for some pipeline optimisation suggestions that will allow me to count and associate nuclei and foci in mouse retina immunostaining images.
The attached pipeline initially splits the input image into two channels to give me dapi raw and Casz1 raw images. Then I use the dapi raw image to define an ROI that will be used for downstream analysis. What I want to do then is:
- Count the number of dapi nuclei within the ROI,
- Count the number of Casz1 foci within the ROI,
- Associate the number of dapi nuclei that contain Casz1 foci.
Basically I am having problems identifying the foci. I have changed several parameters in the ‘Identify Primary Objects’ module but I am still stuck with the same problems. I have attached my pipeline and a sample image if someone wants to try and help me out.
There is probably a simple solution for this but it currently escapes me!
Many thanks for any help,
Casz1Pipeline.cppipe (25.9 KB)