Problems with opening well info from .czi-files



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?


example images 1_2 and (2.5 MB)
subpopulations_ring_2channels.cppipe (16.2 KB)


Hi Ninar,

(I revisit your issue of “not recognizing well ID”)

It may be better for you to create a .csv file, where you specify the “Well” column (among other crucial columns ImageNumber, Channels etc…) and then use the module LoadData for it.

Hope that helps.


You could also create a CSV just with the ‘Series’ to ‘Well’ mapping (one column with a heading of ‘Series’ that has values of 0,1,2,3,etc, and a column with a heading of ‘Well’ that has values of B02,B02,B03,B03, etc- this should be easy to do with Excel’s fill-in and find-and-replace tools or with a more sophisticated scripting language) and use Metadata’s ‘Import from file’ function to map that information onto the information already existing in the czi header.