EMDB-SFF segmentation file: application of transform 0 for image-to-physical projection
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#... <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html#...>) 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, -- Paul K. Korir, PhD 3D Visualisation Lead CS3DB EMBL-EBI
Hi Tom/ChimeraX admin, Just to clarify: what are the units of physical space in ChimeraX: Å or nm? Kind regards, Paul K. Korir, PhD 3D Visualisation Lead CS3DB EMBL-EBI On 30/01/2023 08:51, Paul Korir wrote:
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#... <https://emdb-empiar.github.io/EMDB-SFF/v0.8.0.dev1/segmentation_da_xsd.html#...>)
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,
-- Paul K. Korir, PhD 3D Visualisation Lead CS3DB EMBL-EBI
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Paul Korir