CZI multitracksetup to channel name

Hi all, colleagues at CIML are doing multiplexed images with up to 10 different channels, acquired with ZEN -
Keeping track of which channel corresponds to which molecule is essential.

Bioformats and omero are pretty good at importing the metadata, but a key element, the name of each channel, is buried in the Experiment|AcquisitionBlock|MultiTrackSetup|TrackSetup|Name entries of the original metadata.

Does any one know how to have this info as the channel name instead? Ideally at acquisition time in ZEN settings, but I’ll take a post processing solution also!

Thank you for any insight,

Guillaume

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If anyone knows how to make the channel names more useful within Zen, that would be amazing.

Otherwise, there are a few postings about extracting metadata from CZI files you might be able to use for your post-processing, like this one:

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I struggle to understand what then actual problem is …

Does this help?

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My comment specifically was regarding the default names of channels being… well, the detector used. For most biologists and collaborations, those detector names are essentially useless, while the track names could be biologically relevant, and applied at image acquisition time.
image
I realize there are technical reasons that it might be easier to use the detector name/track number, but I suspect the people to whom that information is most useful would also know to look in the Info/metadata for the detector if they needed to know that.

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The second link sure helps, thanks @sebi06 - The problem is that apparently the users are used to put the molecule info in the TrackSetup|Name metadata in Zen (appearing in the original metadata in the blue rectangle on the above image) and not in the channel name. I think with your script I should be able to get that info and put it in the channel name.

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Yes I think you express the issue my collaborators also have

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