Extract metadata from CZI file


I am very new to the Cell Profiler World and I believe it is a great resource. I have this problem which I don’t know how to solve: I can extract metadata from this czi file WT_161101_s3_w3_-Scene-01.zip (6.7 MB)
but not from this one
WT_161114_s1_w3_-Scene-01.zip (6.9 MB)
and it gives me this message:

Traceback (most recent call last):
File “cellprofiler\gui\moduleview.pyc”, line 1134, in callback
File “cellprofiler\gui\moduleview.pyc”, line 2064, in __on_do_something
File “cellprofiler\settings.pyc”, line 1934, in on_event_fired
File “cellprofiler\modules\metadata.pyc”, line 483, in
File “cellprofiler\modules\metadata.pyc”, line 863, in do_update_metadata
File “bioformats\formatreader.pyc”, line 985, in get_omexml_metadata
File “javabridge\jutil.pyc”, line 369, in run_script
JavaException: null

Do you have any suggestions how I can solve this? I am using version 2.2.0 on Windows 10.

Thanks, Karen


I think something in your second image is corrupted- when I try to open it up in ImageJ, I get an error in the metadata reader as well. Try re-exporting it from your microscope. Sorry!


I directly extract metadata from image file header for czi files (acquired from LSM 780 microscope).


Hi, thanks for your answers, I was impressed by your quick reply, Beth!
The metadata problem only occurs for files recorded with the Positions module from Zeiss. The way it worked was to open the czi files, save as lsm file and then as a czi file again. Funny, but at least I got this solved