Hi Tom,

To the best of my understanding, ChimeraX displays images and associated segmentations in physical space not image space. However, segmentations are performed in image space. EMDB-SFF uses the first transform in the transforms_list field (with id=0) as the image-to-physical transform. (https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html#segmentation_transform_list)

I've tested with two files having the same segmentation but different values for transform 0 and they render the same.

Could you please implement this feature in ChimeraX?

Kind regards,