Leginon

h1. K2 Summit introduction

The main use of K2 Summit is in Counted or Super-resolution mode in combination with dose fractionation (frame saving).  The counting detection is achieved by very fast internal frame rate and hardware image processing that locates the the single incident electron event in that low dose image, and the addition of these electron counts at given pixel over the output frame time.

h2. Gain/Dark Correction Handling

K2 Summit in counted/super-resolution mode has two layers of gain reference correction, known as hardware (HW) correction and software correction.

Hardware dark correction is essential for electron counting, without it, its processor can not find individual electrons.

Hardware gain correction is a rough gain correction.  It is only done to make sure the data from different ADC boards are reasonably normalized before counting.

After these hardware correction and counting, the images are integers, representing the number of counts received at each pixel.  We call this type of data "raw".

Software dark correction for counted/super-resolution mode is fake.  The image taken in dark condition is set to 0 internally and output as such if a dark exposure is requested externally by SerialEM and Leginon.

Software gain reference taken in DM is equivalent to the bright image taken in Leginon.  The software gain correction, as well as Leginon's correction use this image of the blank area to normalize the more subtle differences from pixel to pixel.

After this level of gain normalization, the image data type is float.

Since Leginon duplicates the DM software gain normalization, we decided to receive images from DM  without software gain normalization.   This is set in the code, and means gain correction is still needed in Leginon.

# The hardware correction has been applied in DM before counting.  Therefore, the "raw" image Leginon get are integers and roughly gain corrected.

# The dark image in Leginon should always be 0.  Therefore, acquiring dark image only need to be done once per camera configuration.  There is also no need to average several images in the making.

# The bright image acquired in Correction node should be taken at the dose rate to be used.  It should also be taken so that accumulated exposure time is at least 100 second (DM reference accumulates 500 seconds of exposure by taking 50 of 10 second exposure).  If you don't want to wait this long, a reasonably good reference can normally be obtained with averaging 20 of 5 second exposure.  Alternatively, take a single very long exposure (100 s).

The bright image will display variation in sensitivity of the pixels.  There is likely a general gradient across the detector known as growth zone like this attached image:

!K2brght.png!

h2. Recommended dose rate and exposure time for different K2 modes

This recommendation is based on our experience.

As a general rule, the dose rate corresponds to the value used during DM gain reference acquisition.  You can put down the small viewing screen once the intensity is adjusted at the beginning of DM procedure to get the values.  You will notice that Linear mode calibration uses much higher beam intensity than the calibration for counted/super-resolution modes.  For our Tecnai F20 at 200 kV, the former reading of exposure time by the small viewing screen is 0.25 s while the value for latter is 1.6 s.  You should use similar intensity during Leginon calibration and data collection.

At 1.2 A/pixel, we use the following for final exposure that has binning of 1:

|mode|small viewing screen exp time (s)|detector dose rate (e/physical pixel)|acquisition exposure time for ~ 20 e/A^2 specimen dose with 1.2 A/pixel pixel size (s)|

|Linear|0.25|64|0.5|

|Counted/Super-resolution*|1.6|10|5.0|

*Most literature recommend at even lower dose in the range of 6-8 e/s/pixel.  This is just a number we have had success with.

h2. Preset Recommendation

See [[Pre-MSI_Set-up#Preset-Design-Example-for-small-pixel-Gatan-K2-camera-alone]] specific for K2 camera using counted/super-resolution mode.