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Performance of Gatan K2 Summit in "movie mode"
Added by Mario Borgnia over 10 years ago
Hi,
We are now set up and collecting data using Leginon in our Krios equipped with a post-GIF Gatan K2 summit.
Images are collected using DM 2.3 and the corresponding 64 bit SerialEM plugin.
Now, we notice that it takes over 2 minutes for DM to process the image stack and a few seconds for it to write the result to disk. We are collecting 38 frames. Is this performance what others are typically finding or is our system particularly slow?
Thanks
Mario
Replies (4)
RE: Performance of Gatan K2 Summit in "movie mode" - Added by Anchi Cheng over 10 years ago
You didn't say if it is letting DM to do alignment (when you activate align option in Leginon) or not. We typically are at 5 second exposure and 200 ms frame. The 25 frame movie takes about 30 sec to write. If we turn on alignment, so that it is processed by DM, it is about 2 min, too.
RE: Performance of Gatan K2 Summit in "movie mode" - Added by Mario Borgnia over 10 years ago
Hmm, I did not specify everything. I don't have alignment checked, but, I am using super-resolution.
RE: Performance of Gatan K2 Summit in "movie mode" - Added by Mario Borgnia over 10 years ago
When I take a picture in manual mode with frames in super-resolution mode, the system exposes and then a small window in DM shows "processing stack" followed by a % of completion. That process takes a couple of minutes and seems to be a rate limiting step in automated data collection.
Are the numbers you refer in counting or super-resolution mode?
RE: Performance of Gatan K2 Summit in "movie mode" - Added by Anchi Cheng over 10 years ago
It was counted. In super-resolution our timing is similar to yours. (1 min and 40 s for 16 frames).