The stitched volumes for SmartSPIM as displayed in neuroglancer have the same axes as the SmartSPIM instrument itself, which seems to have axes increasing in the right, anterior, and inferior directions, which is a left-handed coordinate system. This is a confusing coordinate system to present data, as most imaging software uses a right-handed coordinate system that is either right, anterior, superior (RAS) or left, posterior, superior (LPS). I think that neuroglancer should use a right-handed coordinate system, and between the two common ones I find RAS more intuitive.
Additionally, it would be nice if the volumes were oriented in a standard way in neuroglancer, especially if they are acquired in a standard direction. I think the field standards are for sagittal slices to have superior up, and coronal slices to have superior up. It seems like other software (e.g. slicer) defaults to this display in something close to third angle projection, though slicer breaks third angle to have horizontal slices have anterior up (maybe more common in the field?).
If brains are not imaged in a standard direction it would be nice to account for that before data presentation in neuroglancer.
Picture of default view of neuroglancer and SmartSPIM volumes, note each slice is in a non-standard direction:
Picture of default view of slicer showing a MRI volume, note each slice is in the standard direction, though this causes it to not be a normal orthographic view:
The stitched volumes for SmartSPIM as displayed in neuroglancer have the same axes as the SmartSPIM instrument itself, which seems to have axes increasing in the right, anterior, and inferior directions, which is a left-handed coordinate system. This is a confusing coordinate system to present data, as most imaging software uses a right-handed coordinate system that is either right, anterior, superior (RAS) or left, posterior, superior (LPS). I think that neuroglancer should use a right-handed coordinate system, and between the two common ones I find RAS more intuitive.
Additionally, it would be nice if the volumes were oriented in a standard way in neuroglancer, especially if they are acquired in a standard direction. I think the field standards are for sagittal slices to have superior up, and coronal slices to have superior up. It seems like other software (e.g. slicer) defaults to this display in something close to third angle projection, though slicer breaks third angle to have horizontal slices have anterior up (maybe more common in the field?).
If brains are not imaged in a standard direction it would be nice to account for that before data presentation in neuroglancer.
Picture of default view of neuroglancer and SmartSPIM volumes, note each slice is in a non-standard direction:
Picture of default view of slicer showing a MRI volume, note each slice is in the standard direction, though this causes it to not be a normal orthographic view: