New User Features 30 » History » Revision 4
Revision 3 (Anchi Cheng, 12/19/2013 04:53 PM) → Revision 4/9 (Anchi Cheng, 12/19/2013 04:59 PM)
h1. New User Features 3.0 h2. Instrument function: h2. 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 h2. 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.