I noticed that the Plane PositionY for all BioFormats formats we produce in our lab, except Metamorph, is inverted from the local positive Y direction in the image planes themselves. In other words, if you use the Plane PositionX/PositionY to place the image planes in space (like the ImageJ BioFormats importer “stitch tiles” option) then the image tiles are all obviously upside down. I haven’t done a systematic study of public example files from other formats.
I can’t find any statement in the OME data model docs or BioFormats code about this issue. I know that there are at least these two conventions on where the origin for a raster image should be (top left or bottom left), so it would be very helpful if BioFormats could address this to aid in writing tools to perform image stitching. Is this something that would be considered? One non-breaking solution would be a new property on Plane to indicate which convention is used and a new ReaderWrapper that uses that information to normalize the Plane orientation.