I have problems with opening .czi multi-position files properly. I take images of multiple positions in each well of 384 plate with 2 or more channels. I’m able to open the files but well numbers cannot be recognized from metadata. Instead, all positions are seen as individual series.
I uploaded examples of my pipeline and TIFF with metadata .xml file. Czi -file is too large to be sent, and therefore I added printscreen how czi-file is detected by CellProfiler. Series 0-1 (or s1 and s2 in TIFFs) are separate positions imaged at well B2 and series 2-3 (or s3 and s4 in TIFFs) are at B3 well. Channels are shown correctly. Any suggestions how wells could be read from metadata?