Q: OME-TIFF, Image type, sample range, reference frame units

I’m not sure this is the correct place to post but I have a few questions about the XML image description embedded in OME-TIFF files. In particular I’m looking at the sub-resolution images on the OME-TIFF sample data page.

One of the images, LuCa-7color_Scan1.ome.tiff, has 4 images, a primary image, thumbnail, overview and label. Is there a way for a reader to know which type of image each is? I’m assuming that the Image tag’s Name attribute is arbitrary.

On floating point TIFF images, such as BGal_000438_frames.ome.tiff, knowing range of the input data is particularly important. TIFF has SMinSampleValue and SMaxSampleValue tags but they aren’t always present. A reader could scan the input sample data to determine this range but for large images (such as those commonly seen in Whole Slide Imaging), this is impractical to do interactively. Is there a way to determine this from an OME-TIFF file?

The image Leica-2.ome.tiff has 4 images for regions on the slide (plus a macro image). Each of the 4 images has a Plane tag specifying positions in “reference frame” units. Does this mean that the position values are in the same units as the containing Pixels tag (µm in this case) or that the units of the value cannot be determined from the contents of the OME-TIFF file alone? This comes up when you want to be able to render a scene with all 4 regions correctly positioned relative to one another.

– Grant

For reference

OME-TIFF sample data / Sub-resolutions
https://docs.openmicroscopy.org/ome-model/6.0.1/ome-tiff/data.html#sub-resolutions

1 Like

Hi @gboyle, for the sample fileset you mentioned the thumbnail and overview image are treated by the reader the same as any other image series. The image name may be of help but shouldn’t be relied upon as it will often be dependent on the original underlying format. To formally identify an image as a thumbnail you can still use the TIFF tag NEW_SUBFILE_TYPE (254) = 1 (https://www.awaresystems.be/imaging/tiff/tifftags/newsubfiletype.html).

Similarly for the range of data, this would be handled the same as for a standard TIFF tags rather than in the OME-XML.

Reference frame is an abstract unit and is not convertible to any other length unit without a scaling factor. Its use should be limited to uncalibrated stage positions, and converted to an appropriate length unit using a calibrated scaling factor.

Some useful docs links that may be useful on OME-XML:
OME-TIFF Spec
Model Overview
Full schema