In version 1 there was a way to set the pixel size in microns. I have searched the 2.0 manual + application windows and have yet to find the same feature. Am I missing something?
I have a pipeline established to identify/count total number of surface brain mets (GFP positive), measure the object size and shape, and output that information image and object information into an excel spreadsheet. As per the microscope metadata .XML file and my micrometer, 1 pixel is 10.1um for my 10X 8bit .Tif images.
The end result I am looking to yield is the surface area of each individual tumor and then the total surface area for all tumors in one image.
If there is no way to set the default pixel size, could I use the CalculateMath module to do the conversion and output that in my excel file?
I have attached my pipeline and 2 example images. I think at this point I have the thresholding about as good as I can get–although I am just learning to use CellProfiler (I used to work with the Broads Screen Group using MetaXpress and running the high content screening microscopes).
Thanks in advance!
SurfaceMets2.cp (5.3 KB)