New User Features 3.0¶

Gatan K2 Summit support¶

• Acquire summed frame image thru Leginon
• Trigger raw frame saving
• Transfer raw frame images off solide-state drive of DE-12 during data collection to a network drive.
• Compile gain corrected movie stack thru Appion

Direct Detector Frame alignment (Appion) (K2 or DE)¶

• Parallel gpu processing using program from Li et. al. Nature Methods.

Microcondenser mode setting in presets manager¶

Target Navigation:¶

1. 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

Automatic Target Finding:¶

1. 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.
2. 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.

Focusing¶

1. 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.

RCT Acquisition:¶

1. Tilt Test Tool
   • Usage: For testing if the grid bars will block the intended targets when tilted.
     1. Send the preset using for defining the RCT targets to scope with Presets Manager.
     2. Each click of the Tilt Test Tool will take the goniometer to the next tilt defined in RCT settings and acquire an image.