[ome-devel] CZI white balance / offset

[Sebastien Besson (Staff)]

Hi Manuel,

On 17 Jul 2017, at 15:32, Manuel Stritt <manuel.stritt at idorsia.com<mailto:manuel.stritt at idorsia.com>> wrote:

Dear all,

I've been informed by the vendor that in BF images the white point (the gray values to be skipped for visualization) is stored by the machine and
it should be possible to read it via the CZIReader.
(Not sure if 'white balance' is the correct wording here.)

So far I did not find a specific meta data for that. Do you know anything about this value and can tell me how to read it out?

Looking at a couple of example CZI files, I would think the following key/value pairs in the original
metadata table populate at the reader initialisation would contain the information you need:

$ ~/bftools-5.5.3/showinf -nopix 2015_08_21__16_09__0954.czi  | grep WhiteBalance
Experiment|AcquisitionBlock|AcquisitionModeSetup|Camera|WhiteBalance #1: 0.40944686621105,0.50887655000016,1
Experiment|AcquisitionBlock|AcquisitionModeSetup|Camera|WhiteBalanceOffset #1: 0
Experiment|AcquisitionBlock|AcquisitionModeSetup|Camera|WhiteBalanceOffset|Status #1: Valid
Experiment|AcquisitionBlock|AcquisitionModeSetup|Camera|WhiteBalance|Status #1: Valid
HardwareSetting|ParameterCollection|WhiteBalance #1: 0.55201666149549,1,0.79661143765063
HardwareSetting|ParameterCollection|WhiteBalance #2: 0.40944686621105,0.50887655000016,1
HardwareSetting|ParameterCollection|WhiteBalance.Default #1: 1.01,0.8,0.5
HardwareSetting|ParameterCollection|WhiteBalance.Default #2: 1,1,1
…

Or maybe even more in general - is there a white balance meta data field even for other formats?

It is certainly possible other formats store the same information. Note however that
this information will be available via the Original Metadata and not the OME metadata.
This means that both the existence and the nomenclature will be vendor specific with no
cross-format naming consistency [1].

Best,
Sebastien

[1] https://www.openmicroscopy.org/site/support/bio-formats5.5/about/index.html#bio-formats-metadata-processing

Thanks for your help!

Regards,
Manuel





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