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OME model (specification, code generator, implementation)
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No "Plane" elements in Artificial Datasets metadata #73

Open gajomi opened 6 years ago

gajomi commented 6 years ago

The docs at https://docs.openmicroscopy.org/ome-model/5.6.1/ome-tiff/data.html#d-datasets state that Each plane is labeled according to its dimensional position for easy testing, but it seems that there are no plane elements in the metadata for the 5D artificial datasets. There is plane-like cross section information keyed by the "IFD" attribute:

         <TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1">
            <UUID FileName="multi-channel-time-series.ome.tif">
               urn:uuid:8bce8751-8546-4a77-9d60-2f7c391e2d16
            </UUID>
         </TiffData>
         <TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1">
            <UUID FileName="multi-channel-time-series.ome.tif">
               urn:uuid:8bce8751-8546-4a77-9d60-2f7c391e2d16
            </UUID>

but no plane elements themselves. It might be nice to have such data to test plane related metadata access.

dgault commented 6 years ago

Hi @gajomi, thank you for bringing this to our attention. Indeed it seems that none of the sample files listed on that page contain Plane elements. There may also be some confusion with the terminology used here. The sample files contain a TiffData element for each plane, which is used to locate the position of the pixel data within the Tiff file. The actual Plane element within OME-XML is used to store physical position information for the microscope stage and timing and should look as below:

<Plane DeltaT="7860.281704545454" DeltaTUnit="s" PositionX="-8982.25" PositionXUnit="µm" PositionY="3502.25" PositionYUnit="µm" PositionZ="1194.93" PositionZUnit="µm" TheC="0" TheT="0" TheZ="0"/>

The documentation could probably do a better job of explaining what is meant by plane and position in this case. Also I can see that it would be useful to include samples with an example of this Plane element.