I’m trying to do something pretty straightforward but I don’t know what the right tool is.
I have combined in situ and IHC of the spinal cord. I used 4 colors. I now want to determine the co-expression of these different markers.
DAPI = Blue
White = Gene 1
Red = Gene 2
Green = GFP transgene
I want to quantitate the co-occurrence of these signals, so for example (GFP+/Gene1+/Gene2-) etc in an efficient manner. I’ve used Photoshop in the past and used the selection too. But I know ImageJ must have a good way to do this.
I think it is best that I define the ROIs (what is a cell?) but then I pretty much want a way for ImageJ to look at all those ROIs and determine which of the colors co-occur in that ROI, so that I get a count of all the different possibilities. This is such a standard thing, but I’m trying to avoid doing it by hand/eye. When I have just two colors,I use photoshop, but there must be a better way.
Here’s an example of what I’m looking at.