Adding angle information into ome-xml/ome-tiff

Hi,

I am trying to add appropriate metadata for X-ray tomography to tiff files but the ordering is XYTZC (or some other order of those axes). Given that the tilt happens over time, T seems like the most appropriate third axis out of the available options. I would like to link T to tilt angle in some way, if possible, or have some way to specify the start, end, and step.

I’ve been going over the schema but the only angle I can find a reference to is “UnitsAngle” (but I can’t see where that’s used). Would anyone be able to help, please? The tilt angle is obviously a fairly important bit of metadata for a tilt-series!

Thanks,
Tom

Hi @fish,

there has been similar discussion on the now retired ome-devel mailing list - see https://lists.openmicroscopy.org.uk/pipermail/ome-devel/2017-January/003863.html and probably a few other

Shortly, although you are correct that tilt acquisitions are happening over time, this is also true for plane acquisitions at different channels and depths. The Plane.DeltaT attribute is meant to capture the timestamp associated with each plane. In terms of the traditional OME 5D dimensions, I would think Z would be most suitable axis for what you describe as it is used for spatially coupled acquisitions while time and channel are different concept.

One way to specify the metadata would be to use map annotations to capture the tilt start, step and end values. As mentioned in the ome-devel thread above, the best option for representing this type of imaging data using the current OME schema might be to use the Modulo extension for storing for representing the tilt dimension and the associated metadata. A few examples are available in the public samples. The SPIM one is probably the one most relevant to your use case.

Best,
Sebastien

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Hi Tom,
The OME team can probably answer this in much greater detail and with much more authority but let me try to point you in the right direction. As you noticed the base OME model is limited to the 5 canonical dimensions XYZCT. A work-around to add and define additional dimensions such as the Angle dimension you want to save is provided by the interim 6D, 7D, and 8D storage extension: https://docs.openmicroscopy.org/ome-model/6.0.0/developers/6d-7d-and-8d-storage.html

Also note that a number of teams around the globe are working towards a next-generation file format (search for NGFF in this forum) and we are all making sure a better solution will exist in the future.

Cheers,
Damir

PS. And I see Sebastien just chimed in as I had hoped.

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Hi @dsudar and @s.besson,

Thank you both for responding, the Modulo extension is exactly what I needed. Also, I was going back and forth on Z vs T, so it’s good to have a second opinion on that, thanks.

I’m currently working on extending the work from Python Bioformats’s omexml.py to include more of the schema, so I should be able to contribute some of this back at some point :slight_smile:

Thanks again,
Tom

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