I recently ran into lots of trouble extracting metadata from CZI files. I have multiple images created on the same date, by the same system. CellProfiler seems to be unable to extract the metadata from most of them, although when analyzing them using Fiji, all the metadata seems to be available.
Attached to this post you will find a screenshot from Fiji (showing the metadata), one from the Images module and one from the Metadata module as well as an archive containing the two files used to demonstrate the issue.
I am using CellProfiler 3.1.8 on Windows 10.
czi_metadata.zip (17.4 MB)