[3dem] parameters for K2 super-resolution

Fislage, Marcus mf2944 at cumc.columbia.edu
Wed Sep 20 08:50:33 PDT 2017

Hi Garry,

when we used super resolution we use the same dose settings and frame times (8 e-/px/s, 30-40 frames) as we do using normal counting mode. This is done because the dose rate is measured per physical pixel. In super resolution you will measure (2 e-/superresolution pixel/s, which corresponds to 8e-/physical pixel/s)


Marcus Fislage, PhD

Howard Hughes Medical Institute (HHMI)
Columbia University
Department of Biochemistry and Biophysics
Lab of Joachim Frank
New York, NY

email address: mf2944 at cumc.columbia.edu
Phone: 212.305.9524
Fax: 212.305.9500

From: 3dem <3dem-bounces at ncmir.ucsd.edu> on behalf of Garry P Morgan <Garry.Morgan at Colorado.EDU>
Sent: Wednesday, September 20, 2017 11:22:53 AM
To: 3dem at ncmir.ucsd.edu
Subject: [3dem] parameters for K2 super-resolution


we’ve been collection SPA images with a K2 Summit on a Tecnai F30; so far we have only used counting mode at a nominal magnification of 31,000x.  we’d like to try using super-resolution at a lower mag (i.e., nominal mag of 20,000x) to get a wider field of view with a roughly equivalent pixel size.  i’m wondering if anyone is doing this as a standard for their SPA data acquisition? and if so, how are you setting up your acquisition parameters? i.e., frame time and number of frames.  because the dose is so much lower at the lower mag, it takes a significantly longer total acquisition time (20-30 seconds) to achieve our desired sample dose. in order to keep the number of frames in the movie stack to ~40 (so that the movie stack file size isn’t too large), we would need to increase the frame exposure time to between 0.5 and 1.0 sec. however, i’m worried this longer frame time would incorporate too much drift and essentially nullify the whole point of using the K2 and drift correction. i would appreciate any thoughts and advice on this.

one more question…Gatan recommends a dose rate no more than 10e-/ubpxel/sec going to the K2 while in counting mode. i  believe we were told the dose rate should be 2.5e-/ubpixel/sec for super-resolution mode.  can anyone tell me if this is true, or is the dose rate of 10e-/ubpixel/sec in regular counting mode actually the same as 2.5e- dose rate in super-res mode because of the 0.5x binning?  in other words, can i use the same beam intensity for for unbinned counting mode and super-res mode?


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