Note on K2 after GMS Upgraded to 2.2.0.1518 on Jan 18, 2013

Chen Xu

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On K2 computer, Gatan software GMS has been upgraded to version 2.2.0.1518.0 since afternoon of Jan. 18, 2013. I am writing this up for anyone who is interested in the new version together with K2 performance.

You can also get pdf version of this document here.


Table of Contents
1 A few changes according to Gatan
2 Power Spectrum of Images from all Three Modes
3 Data Storage Location
4 Current Issues or Problems

1 A few changes according to Gatan

There are a few changes as they told me over the phone while upgrading was going on. I am not sure if the information I list below is 100% accurate.


2 Power Spectrum of Images from all Three Modes

After freshly preparing gain reference images for the specific 300kV, I collected images from all three modes. For counted and Super-res modes, the dose rate on physical chip is about 10 electron/pixel/second. And for Linear mode, it is about 600 electron/pixel/second.

Above is the Power Spectrum from a Linear mode image at dose rate of 600e/pixel/second. The lines can still be seen.

The above is one from Counted Mode. There is a small, but sharp line in the middle. Other than that, the background is flat.

The above is the one from Super-res image. It is almost perfect. This is significantly better than from the old version.


3 Data Storage Location

For normal single shot images, there are a few options.

On Fileserver.

K2 movie data, speed is a big concern.

For dose-fractionation (movie) series data collection, there are even more options. Beside the above two disk devices being avalible to be mounted on K2 Win7 computer, there are three disks locally on K2 computer, D:\Data, X:\ and Y:\. However, currently, dose-fractionation data collection from SerialEM requires faster disks than USB2.0. Small series might OK, large series will cause "timeout" error for SerialEM. The final summed image frame from the stack returning to SerialEM seems a lot slower than with a SATA controller. Except the timeout error, the movie stack is written diectly to the disk drive from K2 computer, which doesn't cause any problem though. In other word, even if you don't care about not being fast, the timeout error related to slow disk drive will pulse and pop up an error message window on SerialEM. Obviously, this will interrupt the automation of data collection.

Therefore, if you collect multiple movie stack files using SerialEM, you are better off using /data500 network drive or one of the local disks on K2. Preferably, D:\Data should be used, as X:\ and Y:\ are used for K2 temporary intermediate files. And if they are full, K2 camera will not behave.


4 Current Issues or Problems