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Krios G4i and K3 with GIF configuration question

Added by Christopher Lilienthal almost 4 years ago

We are bringing a new instrument online and have some questions about the K3 configuration and behavior.

When we configured the K3 PC's instruments.cfg file as shown on this Gatan_K3_installation_and_setup wiki page but the shown K3 configuration for instruments.cfg did not work for our setup. We are running Digital Micrograph 3.32.2403.0.

When we have the following configuration:

[Gatan K3]
class: dmsem.GatanK3
zplane: 50
width: 8184
height: 11520

we receive the following image in the Leginon GUI on the square node:
Please see the attached image file: bad config - square node.png

we also receive the following warning message in the Leginon Client terminal approximately when the bad image is taken:

WARNING: image reshaped (5760L, 4092L)

The way we were able to get Leginon to behave is to change the K3 instruments.cfg file to be the following:

[Gatan K3]
class: dmsem.GatanK3
zplane: 50
width: 11520
height: 8184

Have you heard of anything like this or did I misconfigure something? I can share my config files if that would help.

bad config - square node.png (3.57 MB) bad config - square node.png

Replies (2)

RE: Krios G4i and K3 with GIF configuration question - Added by Anchi Cheng almost 4 years ago

I have not seen G4i with K3 before as a configuration. I have seen in the past K2/K3 camera image presented in many different orientation, though.
This part is messy and almost unique at each site since it is affected by the installation configuration as well as the instrument.

As long as the gain reference get applied correctly, changing width/height in the config is fine. If necessary, change dmsem.cfg FLIP and/or ROTATE so the aligned sum image, i.e., en-a, (representing the orientation of the frames) is the same as the unaligned sum image (i.e., en).

RE: Krios G4i and K3 with GIF configuration question - Added by Christopher Lilienthal almost 4 years ago

Hi Anchi,

I see, thank you for the clarification. With our other K2 cameras we did not encounter this issue in the past but they were not attached to a GIF. We'll verify the reference is applied correctly and if we have more questions or issues we'll let you know.

Thanks again

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