Leginon

h1. Using Gatan K2 Summit in Leginon

The main use of K2 Summit is in Counted or Super-resolution mode in combination with dose fractionation (frame saving).

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.

 * [[K2 Summit introduction]]

 * [[K2 acquire image|Acquiring summed frame image thru Leginon]]

 * [[K2 gain correction|Gain and Dark Correction]] *This involves both DM and Leginon*

 * [[K2 calibration|Pixel and Matrix Calibrations]]

 * [[K2 raw frame saving|Trigger raw frame saving]]

 * [[DDD raw frame file transfer|Transferring raw frame images]] off the hard drive of K2 Summit during data collection to a network drive.

 * [[Make DDD movie stack|Compiling corrected movie stack]] with Appion using bright and dark images acquired in Leginon

h2. Operation

# Typical frame saving preset parameters for counted/super-resolution: 0.2 s frame exposure time, 4-5 s total exposure time at 8-10 e/physical pixel/s (Some argues that 5 e/physical pixel/s is better).  You can use DM's reading of dose rate while it is in counted mode and *UNBINNed* to get a reasonable estimate.

# 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.

# /myami/rawtransfer.py should be run on the file server to transfer the raw frames and give them names that are synced with the integrated image as it is produced. See [[DDD_raw_frame_file_transfer]].  K2 frames are saved as mrc stacks.

# See [[appion:Direct_Detector_Frame_Processing]] for tools used for processing the frames.

# To gain correct and align the frames, start parallel instances of Appion makeDDRawFrameStack.py See [[appion:GainDark correction of the raw frame with or without drift correction]].

h2. Warning

* Because of a delay in communication with DM when Leginon is started, camera configuration shown in Correction Node settings may not corresponds to what is used last time when you quit Leginon.  Make sure you check this.

h2. Leginon functions that do not work with K2 camera

h3. General functions

# The dose matching tool in Preset Manager.  K2's exposure time is not fine grained enough to make small adjustment according to the small dose deviation.  You will have to use fixed exposure time and adjust beam intensity by hand to achieve the right dose.  We find out the equivalent screen reading from the microscope for the acceptable 8-10 e/physical pixel/s dose rate for the detector and make adjustment there.

# Tomography correlation algorithm only takes square images.  Until that is changed, Frame saving is not possible since only a full size unbinned image can be paired with frame saving.

h3. Frame saving camera functions

# The image returned to Leginon display is always integrated over all the frames with K2 summit camera.  Selection of frames to use as in DE series does not work here.

# Readout delay is not adjustable on K2.  Leave it at 0.

h2. Clean up

Frame saving generates a lot of files during acquisition and during processing.

# 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.  See Feature #1784 for more details.

# Selective removal of aligned frame stack in Appion runs is still to be written.