Leginon

h1. New User Features 3.0

h2. [[Gatan K2 Summit support]]

 * Acquire summed frame counted, super-resolution, or linear mode image thru Leginon

 * Trigger raw frame saving

 * [[DDD_raw_frame_file_transfer|Transfer raw frame images off hard drive of K2 during data collection to a network drive]].

 * [[appion:GainDark_correction_of_the_raw_frame_with_or_without_drift_correction|Compile gain corrected movie stack thru Appion]]

h2. [[appion:Direct_Detector_Frame_Processing|Direct Detector Frame alignment (Appion) (K2 or DE)]]

 * Parallel gpu processing using program from "Li et. al. Nature Methods (2013)":http://dx.doi.org/doi:10.1038/nmeth.2472.

h2. Microcondenser mode setting in presets manager

h2. Target Navigation:

# Option of using parent image move type to move to target during target adjustment.

** This improves the targeting accuracy and minimize image-shift-induced beam-tilt in image-shifted final exposure if queuing is used in Exposure Targeting and Navigator iterative move is used in acquiring its parent image.

** Activate it at /Leginon/Exposure/Settings/Advanced Settings:  Use ancestor image mover in adjustment

h2. Automatic Target Finding:

# Limit number of focusing performed on a series of images.

** For example, focus once every 5 hl images that processed by Exposure Targeting node.

** Iterator is reset at new parent so that hl image from a new square will always be focused.

** Activate at /Leginon/Exposure Targeting/Settings/Advanced Settings/Hole Finder(or Raster Finder) Settings: Focus every nnn image.  Default=1 meaning no skipping.

# Option to threshold very low intensity part of the image (grid bar or thick contaminant before template correlation in JAHCFinder used in MSI-T application

** This has the effect of reducing false-positive in template-based hole finding.

** Enter the threshold value at /Leginon/Exposure(or Hole) Targeting/Template Correlation Settings: Fill image values below n with mean before correlation.

h2. Focusing

# Repeat same beam-tilt-based focusing step with the exactly same setting except not to drift checking will improve the focusing when the first adjustment is large

** The first focusing step brings the defocus close to the range ideal for the algorithm for the repeat.

** A bug fix makes this approach reliable and is recommended if defocus is really critical and speed of data acquisition does not out-weight it.

h2.  RCT Acquisition:

# Tilt Test Tool !http://emg.nysbc.org/software/leginon/images/icons/alpha.png!

** Usage: For testing if the grid bars will block the intended targets when tilted.

**# Send the preset using for defining the RCT targets to scope with Presets Manager.

**# Each click of the Tilt Test Tool will take the goniometer to the next tilt defined in RCT settings and acquire an image.