Appion Processing » History » Revision 67
Revision 66 (Anchi Cheng, 11/12/2015 02:51 PM) → Revision 67/69 (Anchi Cheng, 01/31/2018 02:46 AM)
h1. Appion Processing
## *[[Terminology]]*
## *[[Common Workflow]]*
*** [[Step by Step Guide]]
*** [[Quality Assessment]]
*** [[Random-Conical Tilt (RCT) Reconstruction workflow]]
*** [[Trimer Processing workflow]]
## *[[Processing Cluster Login]]*
## *[[Particle Selection]]*
*** [[Template Picking]]
*** [[Dog Picking]]
*** [[Manual Picking]]
*** [[Repeat from other session]]
*** [[Random Conical Tilt Picking]]
**** [[Align and Edit Tilt Pairs]]
**** [[Auto Align Tilt Pairs]]
## *[[CTF Estimation]]*
*** [[Ace Estimation]]
*** [[Ace 2 Estimation]]
*** [[CtfFind Estimation]]
*** [[Phase plate CTF Estimation|Recommendations for phase plate CTF estimation]]
*** [[Repeat from other session]]
## *[[Stacks]]*
*** [[Stack creation]]
*** [[more stack tools]]
**** [[Combine Stacks]]
**** [[View Stacks]]
***** [[Filter by MeanSTDev]]
***** [[Center Particles]]
***** [[Sort Junk]]
***** [[Create Substack]]
**** [[Alignment SubStacks]]
**** [[Jumpers SubStack]]
**** [[Convert Stack into Particle Picks]]
**** [[Run DE Particle Frame Alignment]]
## *[[Particle Alignment]]*
### [[Run Alignment]]
**** [[Xmipp Maximum Likelihood Alignment]]
**** [[Spider Reference-free Alignment]]
**** [[IMAGIC Multi Reference Alignment]]
**** [[Spider Reference-based Alignment]]
**** [[Ed's Iteration Alignment]]
**** [[Xmipp Reference-based Maximum Likelihood Alignment]]
**** [[Xmipp 3 Clustering 2D Alignment]]
**** [[ISAC Iterative Stable Alignment and Clustering]]
### [[Run Feature Analysis]]
**** [[Spider Coran Classification]]
**** [[Xmipp Kerden Self-Organizing Map]]
**** [[IMAGIC Multivariate Statistical Analysis (MSA)]]
**** [[Xmipp Rotational Kerden Self-Organizing Map]]
**** [[Cluster by Affinity Propogation]]
### [[Run Particle Clustering]]
## *[[Ab Initio Reconstruction]]*
*** [[RCT Volume]]
*** [[OTR Volume]]
*** [[EMAN Common Lines]]
*** [[IMAGIC Angular Reconstitution]]
## *[[Refine Reconstruction]]*
*** [[EMAN Refinement]]
*** [[Frealign Refinement]]
*** [[SPIDER Refinement]]
*** [[IMAGIC Refinement]]
*** [[Refinement Post-processing Procedures]]
## *[[Helical Processing]]*
*** Manual Helix Picker Feature #1771
## *[[Tomography]]*
*** [[Align Tilt Series|Auto align+reconstruction]]
*** [[Align Tilt-Series|Align Tilt-Series (Appion-Protomo)]]
*** [[Upload full tomogram|Create & Upload Tomogram]]
*** [[Create tomogram subvolume|Create Tomogram Subvolume]]
*** [[Average tomogram subvolumes|Average Subvolumes]]
## *[[Import Tools]]*
*** [[PDB to Model]]
*** [[EMDB to Model]]
*** [[Upload Particles]]
*** [[Upload Template]]
*** [[Upload Model]]
*** [[Upload More Images]] ( or see [[Upload Images to a new Project Session]] )
*** [[Upload Stack]]
*** [[Upload Refinement]]
## *[[Image Assessment]]*
*** [[Web Img Assessment]]
*** [[Multi Img Assessment]]
*** [[Run Image Rejector]]
## *[[Region Mask Creation]]*
*** [[Manual Masking]]
*** [[Maskiton]]
## *[[Synthetic Data]]*
*** [[Synthetic Dataset Creation]]
## *[[Direct Detector Frame Processing]]*
*** [[Gain/Dark correction of the raw frame with or without drift correction]]
*** [[Catch up DD frame alignment]] on gpu-capable processing host
!http://emg.nysbc.org/attachments/282/Picture_83.png!
!http://emg.nysbc.org/attachments/277/Picture_81.png!
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[[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]]
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