so this acknowledged as a problem in CP?
i have a similar situation, though nothing is wrong with the metadata. i've created a single large OME-TIFF per stage position in order to improve network performance (rather than using thousands of smaller files)
the tif stores a time lapse movie with 4 channels and >2000 time points. it also uses IFD references to previous planes because all channels are not present at every time point - in this example, channel 0 has a real file (IFD 1) whereas channel 1 refers to IFD 0, which is a blank pane:
<TiffData FirstC="0" FirstT="1" FirstZ="1" IFD="1">
<TiffData FirstC="1" FirstT="1" FirstZ="1" IFD="0">
it opens fine in FIJI and Omero, and the XML validates using OME command line tools, but in CP, extracting metadata from this single tif only finds channel 0.
not sure why this should work in FIJI and not CP unless there is an issue with the version of bioformats itself. i'm using the latest stable versions of each.
do you suggest that i create one OME-TIFF per channel instead, which means i'll use a companion OME-XML file?
also, complicating the effort to track down version info is the following bug: when i select Help->About..., i get an exception:
Traceback (most recent call last):
File "cellprofiler\gui\cpframe.pyc", line 996, in __on_help_about
File "wx\_controls.pyc", line 997, in __init__
File "encodings\cp1252.pyc", line 15, in decode
UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 865: character maps to <undefined>
then when i click "Send report...", i get "Filed to upload, server reported code 405"