Appion Processing » History » Version 67
Anchi Cheng, 01/31/2018 02:46 AM
| 1 | 1 | Amber Herold | h1. Appion Processing |
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| 2 | |||
| 3 | 40 | Amber Herold | ## *[[Terminology]]* |
| 4 | ## *[[Common Workflow]]* |
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| 5 | 38 | Anke Mulder | *** [[Step by Step Guide]] |
| 6 | *** [[Quality Assessment]] |
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| 7 | 49 | Dmitry Lyumkis | *** [[Random-Conical Tilt (RCT) Reconstruction workflow]] |
| 8 | 55 | Dmitry Lyumkis | *** [[Trimer Processing workflow]] |
| 9 | 40 | Amber Herold | ## *[[Processing Cluster Login]]* |
| 10 | 41 | Amber Herold | ## *[[Particle Selection]]* |
| 11 | 38 | Anke Mulder | *** [[Template Picking]] |
| 12 | *** [[Dog Picking]] |
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| 13 | *** [[Manual Picking]] |
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| 14 | *** [[Repeat from other session]] |
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| 15 | *** [[Random Conical Tilt Picking]] |
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| 16 | 32 | Anke Mulder | **** [[Align and Edit Tilt Pairs]] |
| 17 | **** [[Auto Align Tilt Pairs]] |
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| 18 | 40 | Amber Herold | ## *[[CTF Estimation]]* |
| 19 | 38 | Anke Mulder | *** [[Ace Estimation]] |
| 20 | *** [[Ace 2 Estimation]] |
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| 21 | *** [[CtfFind Estimation]] |
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| 22 | 67 | Anchi Cheng | *** [[Phase plate CTF Estimation|Recommendations for phase plate CTF estimation]] |
| 23 | 38 | Anke Mulder | *** [[Repeat from other session]] |
| 24 | 40 | Amber Herold | ## *[[Stacks]]* |
| 25 | 38 | Anke Mulder | *** [[Stack creation]] |
| 26 | *** [[more stack tools]] |
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| 27 | **** [[Combine Stacks]] |
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| 28 | **** [[View Stacks]] |
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| 29 | 31 | Anke Mulder | ***** [[Filter by MeanSTDev]] |
| 30 | ***** [[Center Particles]] |
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| 31 | ***** [[Sort Junk]] |
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| 32 | 33 | Anke Mulder | ***** [[Create Substack]] |
| 33 | 38 | Anke Mulder | **** [[Alignment SubStacks]] |
| 34 | 58 | Sargis Dallakyan | **** [[Jumpers SubStack]] |
| 35 | 38 | Anke Mulder | **** [[Convert Stack into Particle Picks]] |
| 36 | 59 | Amber Herold | **** [[Run DE Particle Frame Alignment]] |
| 37 | 40 | Amber Herold | ## *[[Particle Alignment]]* |
| 38 | 3 | Anke Mulder | ### [[Run Alignment]] |
| 39 | 34 | Anke Mulder | **** [[Xmipp Maximum Likelihood Alignment]] |
| 40 | **** [[Spider Reference-free Alignment]] |
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| 41 | 42 | Dmitry Lyumkis | **** [[IMAGIC Multi Reference Alignment]] |
| 42 | 34 | Anke Mulder | **** [[Spider Reference-based Alignment]] |
| 43 | **** [[Ed's Iteration Alignment]] |
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| 44 | **** [[Xmipp Reference-based Maximum Likelihood Alignment]] |
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| 45 | 57 | Amber Herold | **** [[Xmipp 3 Clustering 2D Alignment]] |
| 46 | 56 | Sargis Dallakyan | **** [[ISAC Iterative Stable Alignment and Clustering]] |
| 47 | 36 | Anke Mulder | ### [[Run Feature Analysis]] |
| 48 | **** [[Spider Coran Classification]] |
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| 49 | **** [[Xmipp Kerden Self-Organizing Map]] |
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| 50 | 45 | Amber Herold | **** [[IMAGIC Multivariate Statistical Analysis (MSA)]] |
| 51 | 3 | Anke Mulder | **** [[Xmipp Rotational Kerden Self-Organizing Map]] |
| 52 | 45 | Amber Herold | **** [[Cluster by Affinity Propogation]] |
| 53 | 3 | Anke Mulder | ### [[Run Particle Clustering]] |
| 54 | 40 | Amber Herold | ## *[[Ab Initio Reconstruction]]* |
| 55 | 38 | Anke Mulder | *** [[RCT Volume]] |
| 56 | *** [[OTR Volume]] |
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| 57 | *** [[EMAN Common Lines]] |
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| 58 | *** [[IMAGIC Angular Reconstitution]] |
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| 59 | 40 | Amber Herold | ## *[[Refine Reconstruction]]* |
| 60 | 38 | Anke Mulder | *** [[EMAN Refinement]] |
| 61 | *** [[Frealign Refinement]] |
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| 62 | *** [[SPIDER Refinement]] |
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| 63 | *** [[IMAGIC Refinement]] |
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| 64 | 43 | Amber Herold | *** [[Refinement Post-processing Procedures]] |
| 65 | 47 | Lauren Fisher | ## *[[Helical Processing]]* |
| 66 | 62 | Anchi Cheng | *** Manual Helix Picker Feature #1771 |
| 67 | 40 | Amber Herold | ## *[[Tomography]]* |
| 68 | 64 | Alex Noble | *** [[Align Tilt Series|Auto align+reconstruction]] |
| 69 | *** [[Align Tilt-Series|Align Tilt-Series (Appion-Protomo)]] |
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| 70 | *** [[Upload full tomogram|Create & Upload Tomogram]] |
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| 71 | *** [[Create tomogram subvolume|Create Tomogram Subvolume]] |
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| 72 | *** [[Average tomogram subvolumes|Average Subvolumes]] |
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| 73 | 40 | Amber Herold | ## *[[Import Tools]]* |
| 74 | 38 | Anke Mulder | *** [[PDB to Model]] |
| 75 | *** [[EMDB to Model]] |
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| 76 | *** [[Upload Particles]] |
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| 77 | *** [[Upload Template]] |
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| 78 | *** [[Upload Model]] |
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| 79 | 66 | Anchi Cheng | *** [[Upload More Images]] ( or see [[Upload Images to a new Project Session]] ) |
| 80 | 38 | Anke Mulder | *** [[Upload Stack]] |
| 81 | 48 | Dmitry Lyumkis | *** [[Upload Refinement]] |
| 82 | 40 | Amber Herold | ## *[[Image Assessment]]* |
| 83 | 38 | Anke Mulder | *** [[Web Img Assessment]] |
| 84 | *** [[Multi Img Assessment]] |
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| 85 | *** [[Run Image Rejector]] |
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| 86 | 40 | Amber Herold | ## *[[Region Mask Creation]]* |
| 87 | 38 | Anke Mulder | *** [[Manual Masking]] |
| 88 | 50 | Amber Herold | *** [[Maskiton]] |
| 89 | 40 | Amber Herold | ## *[[Synthetic Data]]* |
| 90 | 38 | Anke Mulder | *** [[Synthetic Dataset Creation]] |
| 91 | 51 | Anchi Cheng | ## *[[Direct Detector Frame Processing]]* |
| 92 | *** [[Gain/Dark correction of the raw frame with or without drift correction]] |
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| 93 | 52 | Anchi Cheng | *** [[Catch up DD frame alignment]] on gpu-capable processing host |
| 94 | 22 | Anke Mulder | |
| 95 | !http://emg.nysbc.org/attachments/282/Picture_83.png! |
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| 96 | 19 | Anke Mulder | !http://emg.nysbc.org/attachments/277/Picture_81.png! |
| 97 | 22 | Anke Mulder | |
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| 101 | 5 | Amber Herold | |
| 102 | 2 | Amber Herold | ______ |
| 103 | |||
| 104 | [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] |
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| 105 | |||
| 106 | ______ |