I’m trying to perform a simple cell count of stained tissue sections of the brain. I have stained for Fos in the green (FITC) channel and DAPI (cell nuclei) in blue. The pipeline I have constructed is very close to achieving the desired values for the Fos positive cells (which would be a subset of DAPI positive cells). However, not all the Fos positive cells are being counted correctly, while there are some cells that being counted as doublets (as seen in the ‘OverlayOutlines’ module).
The biggest hurdle currently is deciding the ‘Minimum Value’ for either the ‘MeanIntensity’ or ‘IntegratedIntensity’ filters in the ‘FilterObjects’ module. For the ‘MeanIntensity’ parameter, would this value then be the mean intensity of both DAPI AND Fos? Or just the mean intensity of Fos? And similarly for ‘IntegratedIntensity’, would the minimum value be the integrated intensity for DAPI and Fos or just Fos?
Thanks in advance!