[ome-users] CZI channel description

[Emil Rozbicki]

Hi Forrest,

I have looked into the file you have sent us and it appears that everything is correct.
As given by the ZEN software, the Channel names are: DAPI, Alexa Fluor 488, Alexa Fluor 594 and Alexa Fluor 647.
The values you mentioned are indeed called Channel Description: DAPI1, YFP, ASIC1, Syntaxin1A, and as such are not included in the current OME-XML model.

We have fixed the code (https://github.com/openmicroscopy/bioformats/pull/1213) and values for all the channels will appear in the OriginalMetadata, so instead of:

"Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description: Syntaxin1"

you should get now:

Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #1: DAPI1
Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #2: YFP
Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #3: ASIC1
Experiment|AcquisitionBlock|RegionsSetup|TilesSetup|MultiTrackSetup|Track|Channel|Description #4: Syntaxin1A

I hope that helps you proceed with your analysis workflow.

Regards,
Emil




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