Storing / Retrieving Min/Max Pixel Intensity Values in OME-XML

Hi Folks!

New here. We’ve recently implemented read support for multi-channel multi-z data in OME-TIF in our software.

In working our way through the OME-XML schema documentation

(https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome.html)

we’ve identified the Pixels/@SignificantBits attribute that helps sort out when you’ve got say a 10bit camera storing 10bit data in a 16 bit container.

What we’re wondering is if folks have any agreed upon strategy for storing specific min / max pixel intensity values themselves in the OME-XML. There doesn’t seem to be a parameter for this?

Currently, we just process the data and determine the min / max we need for say a particular channel or particular Z plane. It would be nice to follow an agreed convention for storing / retrieving that data so as to avoid reprocessing the data every time it’s loaded.

Thank for your thoughts! Happy to clarify anything if I’ve been unclear.

Best Regards,
Nathanael Reveal
BIOQUANT Image Analysis Corporation

You are correct that there is no official place within OME-XML for such values. One option would be to use the TIFF IFD tags Tag SMinSampleValue and SMaxSampleValue. These values will be parsed and added to the global metadata. Alternatively annotations could be used to store additional metadata that is not defined in OME-XML

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Hi David!

Thanks for the quick feedback. We’ll have a look at TIFFTAG_SMINSAMPLEVALUE and TIFFTAG_SMAXSAMPLEVALUE and update this topic accordingly.

If anyone has used Structured Annotations in OME-XML to store this type of data, we’d be happy to hear about it and see if we couldn’t “follow along” rather than create our own redundant wheel.

Best,
Nat