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Appion Processing » History » Version 69

Sargis Dallakyan, 03/06/2019 06:05 PM

1 1 Amber Herold
h1. Appion Processing
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3 40 Amber Herold
## *[[Terminology]]*
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## *[[Common Workflow]]*
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*** [[Step by Step Guide]]
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*** [[Quality Assessment]]
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*** [[Random-Conical Tilt (RCT) Reconstruction workflow]]
8 55 Dmitry Lyumkis
*** [[Trimer Processing workflow]]
9 40 Amber Herold
## *[[Processing Cluster Login]]*
10 68 Anchi Cheng
## *[[Direct Detector Frame Processing]]*
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*** [[Gain/Dark correction of the raw frame with or without drift correction]]
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*** [[Catch up DD frame alignment]] on gpu-capable processing host
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## *[[CTF Estimation]]* 
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*** [[Ace Estimation]]
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*** [[Ace 2 Estimation]]
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*** [[CtfFind Estimation]]
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*** [[Phase plate CTF Estimation|Recommendations for phase plate CTF estimation]]
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*** [[Repeat from other session]]
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## *[[Particle Selection]]*
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*** [[Template Picking]]
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*** [[Dog Picking]]
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*** [[Manual Picking]] 
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*** [[Repeat from other session]]
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*** [[Random Conical Tilt Picking]]
25 67 Anchi Cheng
**** [[Align and Edit Tilt Pairs]]
26 38 Anke Mulder
**** [[Auto Align Tilt Pairs]]
27 40 Amber Herold
## *[[Stacks]]* 
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*** [[Stack creation]]
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*** [[more stack tools]]
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**** [[Combine Stacks]]
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**** [[View Stacks]] 
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***** [[Filter by MeanSTDev]]
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***** [[Center Particles]]
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***** [[Sort Junk]]
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***** [[Create Substack]]
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**** [[Alignment SubStacks]]
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**** [[Jumpers SubStack]]
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**** [[Convert Stack into Particle Picks]]
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**** [[Run DE Particle Frame Alignment]]
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## *[[Particle Alignment]]* 
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### [[Run Alignment]]
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**** [[Xmipp Maximum Likelihood Alignment]]
43 42 Dmitry Lyumkis
**** [[Spider Reference-free Alignment]]
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**** [[IMAGIC Multi Reference Alignment]]
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**** [[Spider Reference-based Alignment]]
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**** [[Xmipp Reference-based Maximum Likelihood Alignment]]
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**** [[Xmipp 3 Clustering 2D Alignment]]
48 56 Sargis Dallakyan
**** [[ISAC Iterative Stable Alignment and Clustering]]
49 36 Anke Mulder
### [[Run Feature Analysis]]
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**** [[Spider Coran Classification]]
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**** [[Xmipp Kerden Self-Organizing Map]]
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**** [[IMAGIC Multivariate Statistical Analysis (MSA)]]
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**** [[Xmipp Rotational Kerden Self-Organizing Map]]
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**** [[Cluster by Affinity Propogation]]
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### [[Run Particle Clustering]]
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## *[[Ab Initio Reconstruction]]*
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*** [[RCT Volume]] 
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*** [[OTR Volume]] 
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*** [[EMAN Common Lines]] 
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*** [[IMAGIC Angular Reconstitution]] 
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## *[[Refine Reconstruction]]* 
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*** [[EMAN Refinement]]
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*** [[Frealign Refinement]]
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*** [[SPIDER Refinement]]
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*** [[IMAGIC Refinement]]
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*** [[Refinement Post-processing Procedures]]
67 47 Lauren Fisher
## *[[Helical Processing]]* 
68 62 Anchi Cheng
*** Manual Helix Picker Feature #1771
69 40 Amber Herold
## *[[Tomography]]*
70 64 Alex Noble
*** [[Align Tilt Series|Auto align+reconstruction]]
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*** [[Align Tilt-Series|Align Tilt-Series (Appion-Protomo)]]
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*** [[Upload full tomogram|Create & Upload Tomogram]]
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*** [[Create tomogram subvolume|Create Tomogram Subvolume]]
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*** [[Average tomogram subvolumes|Average Subvolumes]]
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## *[[Import Tools]]* 
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*** [[PDB to Model]]
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*** [[EMDB to Model]]
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*** [[Upload Particles]]
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*** [[Upload Template]]
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*** [[Upload Model]]
81 66 Anchi Cheng
*** [[Upload More Images]] ( or see [[Upload Images to a new Project Session]] )
82 38 Anke Mulder
*** [[Upload Stack]]
83 48 Dmitry Lyumkis
*** [[Upload Refinement]]
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*** [[cryoSPARC]]
85 40 Amber Herold
## *[[Image Assessment]]* 
86 38 Anke Mulder
*** [[Web Img Assessment]]
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*** [[Multi Img Assessment]]
88 40 Amber Herold
*** [[Run Image Rejector]]
89 38 Anke Mulder
## *[[Region Mask Creation]]*
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*** [[Manual Masking]] 
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*** [[Maskiton]] 
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## *[[Synthetic Data]]* 
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*** [[Synthetic Dataset Creation]]
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!http://emg.nysbc.org/attachments/282/Picture_83.png!
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!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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