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Dear all,
I’m trying to extract individual images for cell tracking from a .czi file acquired with Zen Blue (Zeiss). In order to image several positions at the time and use different acquisition regimes, I had to create serveral "blocks" which were looped over time. This resulted in a .czi file with 504 timepoints, 2 scenes each, and 504 blocks which means one block equals one timepoint. Now, I would like to save all images of the same position in one folder, nicely named, so that cell profiler or other analytic software can take over.
But how to get these individual files? I can create Image subsets by applying the "processing" function in Zen for the different channels which works fine. But when I try to export the pictures as tiff file I get much more pictures than I originally imaged. This is due to the fact that the program is generating pictures of every possible combination: Block*Timepoint*Scene*Channel. Subsequently the export function leads to the creation of millions of empty pictures.
I have the same problem when I try to open the .czi file with Fiji via the LOCI plugin. Even though the file is only ~ 1GB Fiji runs out of Memory.
Is there any way to export only the pictures that were really made? Has anybody experiences with writing an appropriate marco? Can anyone assist me creating one?
Thanks for you reply! Best,
Richard
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