[ome-users] metadata bug in czi files?

[Melissa Linkert]

Hi Teresa,

> 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.
>

Thank you very much for the detailed bug report - I can confirm that
the current behavior is incorrect.  We are currently reviewing a fix
here:

https://github.com/openmicroscopy/bioformats/pull/2441

for inclusion in the next release of Bio-Formats.

Regards,
-Melissa

On Fri, May 27, 2016 at 8:55 AM, Teresa VazMartins (JIC)
<Teresa.VazMartins at jic.ac.uk> wrote:
> 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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