I’m creating a pipeline to process a large number of images for measuring the length of cells in each image and outputting all the data to excel. The pixel scale is stored in the “PhysicalSizeX” and “PhysicalSizeY” OME parameters of each image and I am able to access this in ImageJ and automatically apply it to object measurements. I would like to do the same thing in CellProfiler, but I haven’t been able to access the same metadata parameter. I’m not sure if it is accessible somewhere other than the Metadata input module, but the PhysicalSize parameters are not available there. I would appreciate any advice.
No, unfortunately this cannot be done with CellProfiler in a straightforward way. The Metadata module can grab a few, common metadata from image file headers (SizeC, etc), but not this particular one. Besides modifying the code for Metadata module yourself, our only other suggestion would be to script something external to CellProfiler that would write out the PhysicalSizeX/Y parameters, as well as the filenames associated, to as CSV. You could then use the Metadata module to read in this CSV and re-match it to the files as read in by CellProfiler.
In a perfect world, we would write a metadata viewer that would allow the user to pick and choose the header metadata they want to utilize. But, alas, the world is what it is
Hope that helps,