Question: How can I fix misaligned fiducials?
Answer: Space Ranger automatically identifies and aligns to the fiducial frame of brightfield H&E images when the hourglass-shaped fiducial is in the upper left-hand corner of the image.
When the hourglass is not the upper left-hand corner of the image there are three approaches to fixing it.
1. Rotate the image in to the proper orientation and run Space Ranger again
2. Add the
--reorient-images flag to your Space Ranger command and rerun. Space ranger will attempt to reorient (rotate and/or mirror) the image to match the fiducial frame.
3. Use the manual alignment feature in Loupe Browser. Please note that manual alignment is required for immunofluorescent image input.