Closed chrisvanrun closed 6 months ago
Having read the OME-TIFF documentation a bit more it seems like the physical properties are optional in the XML schema, albeit it is sometimes used as (in the lightmycells challenge):
<Pixels ID="Pixels:0" DimensionOrder="XYZCT" Type="uint16" SignificantBits="12" Interleaved="false" BigEndian="false"
SizeX="1024"
SizeY="1024"
SizeZ="1"
SizeC="1"
SizeT="1"
PhysicalSizeX="0.103580094900373"
PhysicalSizeXUnit="µm"
PhysicalSizeY="0.103580094900373"
PhysicalSizeYUnit="µm"
PhysicalSizeZ="0.47"
PhysicalSizeZUnit="µm"
/>
Moreover, the schema contains the following description:
All of the values in the Pixels object when present should match the same value stored in any associated TIFF format (e.g. SizeX should be the same). Where there is a mismatch our readers will take the value from the TIFF structure as overriding the value in the OME-XML. This is simply a pragmatic decision as it increases the likelihood of reading data from a slightly incorrect file.
As such, the physical properties should really be encoded in the correct tiff tags.
There is a certain irony that the example files from https://docs.openmicroscopy.org/ome-model/5.6.3/ome-tiff/# have incorrect TIFF tags set.
It seems like OME-TIFF format, which contains an OME-XML (https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47) metadata model in the ImageDescription are seemingly not parsed by panimg.
This metadata also contains physical dimensions (e.g. pixel size in micrometres). The 'regular' tags for this (i.e.
XResolution
/YResolution
andResolutionUnit
) are either set to 0 or to "NONE".The latter is a problem because panimg explicitly tries to read these to report on this metadata.