Leginon

h1. Using Gatan K2 Summit in Counting mode in Leginon

If you want to use DM's dose fractionation, activate the "save frames" check box in the particular preset camera configuration.  You can also use DM's frame alignment algorithm by activating "align frames" check box, but the latter is not recommended since the alignment in DM will delay the return of the image to Leginon and therefore affects throughput greatly.

h2. Preset Recommendation

See [[Pre-MSI_Set-up#Preset-Design-Example-for-small-pixel-Gatan K2 camera alone]]

h2. Calibrations

Most calibration and operation are similar to that of a typical digital camera.

Leginon treats linear/counted/super-resolution modes of K2 Summit as three cameras.  Therefore, they each need its own calibrations.

A python script is available to make the copying of the calibrations easier.  See message#1498.  You may need to modify it for different modes you are copying calibrations to.

h2. Gain/Dark Correction Handling

Leginon receives images from DM  without software gain correction.  This means:

h2. Counted/Super-Resolution

# In linear mode, the dark image will have a large mean and the value changes with exposure time.  Ideally, the dark images should therefore be taken at the same exposure time as the later images to be corrected.

# In counted/super-resolution modes, the hardware correction has been applied, the "raw" image Leginon get are integers, and the dark image should always be 0.

# The bright image is for correcting variation in sensor response.  This should be taken at long exposure

Because of its small size, we have a modified [[MSI_Quick-start_for_DD_only|Quick-start procedure]] we use regularly at NRAMM FEI F20.

We have also a script for transferring the frame images from the Gatan computer to Leginon's session image path using rsync.  See [[DDD_raw_frame_file_transfer]].  This will remove also the transferred files on Gatan computer so that more images can be acquired automatically.  If you choose to only "align frames" but not "save frames", this script delete the frames generated by DM without transferring them.

Another python script in leginon directory "cleanddraw.py" can help you clean up the transferred raw frames when you start to run out of disk space, too.  See Feature #1784 for more details.

Here are some notes on odd things that we have to do:

# Make sure your camera configuration is set to [[Leginon image orientation]] and instruments.cfg matches that resulting orientation and dimension.

# We use DM's hardware Dark/Gain correction in counted and super-resolution mode.  DM will only give usable dark reference when the camera is unflipped and unrotated.

Therefore, it is necessary to switch between flip/rotate and unflip/unrotate to maintain [[Leginon image orientation]] convention and preparing dark/gain reference in DM, respectively.  Many new users forget to switch at first and need reminder several times.

# You will still need to do gain/dark correction in Leginon to correct in DM so called software correction.  WIthout it, the image of long exposure shows artifact even in counted and supre-resolution mode.

# K2's dose fractionation only works with full camera dimension without binning.

# K2 interface in DM restricts the exposure time to multiple of some set number, depending on the mode.  When you enter in DM an invalid number, it automatically change it to the valid one when you click the acquire button.  pyscope/dmsem.py has hard-coded values for these precision. Compare them to the precision of the DM version you have since it may change.

# K2 frame save frame rate is currently hard-coded in pyscope/dmsem.py as the variable self.dosefrac_frame_time = 0.200.  You may change this number to get different frame time.