FindEdges module

cellprofiler

#1

I am having an issue with getting IdentifySecondary to properly identify the borders of cells. The FindEdges module, using the Canny edge-finding method, returns a binary image with lots of lines within the cytoplasm of my cells and the outermost line for each cell seems to be a pretty good estimation of the true cell border. I am trying to you the FindEdges module to create an EdgedImage and then use IdentifySecondary on the EdgedImage, but I get an error for the IdentifySecondary module that says, “X must be an arry of double or single numeric values.”


#2

Hi Matt,

FindEdges creates a binary image, which is a logical array. IdentifySecondary is expecting an array of double or single numeric values as an input, so that’s why you are getting the error. Also, you want to think about what IDSecondary is doing- it’s starting at your primary objects and looking around them for a threshold to say, this is where the secondary image ends. Is an edged image really what you want here? Or if you really want these edges as the edges of your cells, do you simply want to identify those as primary objects?

Hope this helps,
Kate