I have a question regarding large multichannel “whole slide” pathology images. I am working with virtual slide images acquired on the Zeiss AxioScan system (*.czi files). There are 4-5 color channels in each image and (in one case) multiple z-planes.
As far as I understand it right now, in order to do analyses in Cellprofiler on these images, I have to export parts of these huge images as tiles and then import the tiles into Cellprofiler. I managed to do that. However, since I want to carry out further “downstream” data analyses with FCS Express, I need to rename the images according to a specific naming scheme (giving row and column numbers). Doing this manually is really not feasible with the number of images I have to analyze. The Zeiss Software (ZEN blue) seemingly does not offer the possbility to apply a custom naming scheme to the tiles, even though I can tell the software exactly how many rows and colums I want. Still, ZEN blue merely assigns continuous numbers to the tiles.
Is there any way to make Cellprofiler open the *.czi images directly, generate its own tiles and carry out the analysis in a way that is compatible with further analysis in FCS Express?
Any suggestions would be greatly appreciated!