[ome-users] metadata bug in czi files?

[Teresa VazMartins (JIC)]

Dear OME,

I think that I have found an issue with the parsing/generation of meta data from czi files.

The bug is:

- when we have several channels (yellow, cyan...) that we image simultaneously, bioformats metadata assumes that we read them sequentially, if the image is a Zeiss czi file.

This would be a problem if we want to make ratios between channels, for instance. It totally changes the resolution.

The attached files are from the same image capture.
The ``showinf`` command gives the correct output for the lsm file, but not for the czi file.


N108541:bftools vazmart$ ./showinf /Users/vazmart/Documents/images/metadatatest/testeseq/1minute30asecinterval2cycles807ms.czi -nopix -omexml | grep -i DeltaT
         <Plane DeltaT="729.0428883030303" DeltaTUnit="s" PositionX="0" PositionXUnit="reference frame" PositionY="0" PositionYUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
         <Plane DeltaT="758.9996632121212" DeltaTUnit="s" PositionX="0" PositionXUnit="reference frame" PositionY="0" PositionYUnit="reference frame" TheC="1" TheT="0" TheZ="0"/>
N108541:bftools vazmart$ ./showinf /Users/vazmart/Documents/images/metadatatest/testeseq/1minute30asecinterval2cycles807ms.lsm -nopix -omexml | grep -i DeltaT
         <Plane DeltaT="0.0" DeltaTUnit="s" PositionX="47.2" PositionXUnit="reference frame" PositionY="147.4" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="0" TheT="0" TheZ="0"/>
         <Plane DeltaT="0.0" DeltaTUnit="s" PositionX="47.2" PositionXUnit="reference frame" PositionY="147.4" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="1" TheT="0" TheZ="0"/>
         <Plane DeltaT="0.0" DeltaTUnit="s" PositionX="47.2" PositionXUnit="reference frame" PositionY="147.4" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="2" TheT="0" TheZ="0"/>
         <Plane DeltaT="29.956774909090882" DeltaTUnit="s" PositionX="47.2" PositionXUnit="reference frame" PositionY="147.4" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="0" TheT="1" TheZ="0"/>
         <Plane DeltaT="29.956774909090882" DeltaTUnit="s" PositionX="47.2" PositionXUnit="reference frame" PositionY="147.4" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="1" TheT="1" TheZ="0"/>
         <Plane DeltaT="29.956774909090882" DeltaTUnit="s" PositionX="47.2" PositionXUnit="reference frame" PositionY="147.4" PositionYUnit="reference frame" PositionZ="0.0" PositionZUnit="reference frame" TheC="2" TheT="1" TheZ="0"/>
N108541:bftools vazmart$ ./showinf -version
Version: 5.1.10
VCS revision: 3125500841deff07687b25eb3f430dca62dee648
Build date: 6 May 2016
N108541:bftools vazmart$

Kind regards,

Teresa
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