Leginon image orientation on Krios and Arctica using K2 Summit
Added by Christopher Lilienthal over 8 years ago
Hello,
We are trying to determine whether we need to change an image's orientation in DM to work with Leginon and the explanation for this is not overly helpful:
From http://emg.nysbc.org/projects/leginon/wiki/Gatan_K2_installation_and_setup :
to make the images acquired from the camera to have the standard Leginon orientation, the camera configuration in Digital Micrograph will need a rotation and flip (270 degree rotation and a flip around the vertical axis on our camera) on typical FEI F20 but maybe not so post-GIF or on Krios. Therefore, the height is longer than width in the configuration below
We have a Krios and an Arctica with K2 Summit detectors, how are we to determine whether an image needs rotation or flipping? Why would we need to be concerned about this?
Thanks
Replies (2)
RE: Leginon image orientation on Krios and Arctica using K2 Summit - Added by Anchi Cheng over 8 years ago
The best way to determine the rotation flip is to make image you acquired from Digital Micrograph in the same orientation as what you see on the Flu Cam on the scope. Once the flip and rotation is determined there, set dmsem.cfg accordingly. Then it should appear in Leginon in the same way.
RE: Leginon image orientation on Krios and Arctica using K2 Summit - Added by Christopher Lilienthal over 8 years ago
Great thank you Anchi.