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]]* |
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 | 68 | Anchi Cheng | ## *[[Direct Detector Frame Processing]]* |
11 | *** [[Gain/Dark correction of the raw frame with or without drift correction]] |
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12 | *** [[Catch up DD frame alignment]] on gpu-capable processing host |
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13 | ## *[[CTF Estimation]]* |
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14 | *** [[Ace Estimation]] |
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15 | *** [[Ace 2 Estimation]] |
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16 | *** [[CtfFind Estimation]] |
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17 | *** [[Phase plate CTF Estimation|Recommendations for phase plate CTF estimation]] |
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18 | *** [[Repeat from other session]] |
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19 | 32 | Anke Mulder | ## *[[Particle Selection]]* |
20 | *** [[Template Picking]] |
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21 | 40 | Amber Herold | *** [[Dog Picking]] |
22 | 38 | Anke Mulder | *** [[Manual Picking]] |
23 | *** [[Repeat from other session]] |
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24 | *** [[Random Conical Tilt Picking]] |
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25 | 67 | Anchi Cheng | **** [[Align and Edit Tilt Pairs]] |
26 | 38 | Anke Mulder | **** [[Auto Align Tilt Pairs]] |
27 | 40 | Amber Herold | ## *[[Stacks]]* |
28 | 38 | Anke Mulder | *** [[Stack creation]] |
29 | *** [[more stack tools]] |
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30 | **** [[Combine Stacks]] |
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31 | **** [[View Stacks]] |
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32 | 31 | Anke Mulder | ***** [[Filter by MeanSTDev]] |
33 | ***** [[Center Particles]] |
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34 | ***** [[Sort Junk]] |
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35 | 33 | Anke Mulder | ***** [[Create Substack]] |
36 | 38 | Anke Mulder | **** [[Alignment SubStacks]] |
37 | **** [[Jumpers SubStack]] |
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38 | 59 | Amber Herold | **** [[Convert Stack into Particle Picks]] |
39 | 40 | Amber Herold | **** [[Run DE Particle Frame Alignment]] |
40 | 3 | Anke Mulder | ## *[[Particle Alignment]]* |
41 | 34 | Anke Mulder | ### [[Run Alignment]] |
42 | **** [[Xmipp Maximum Likelihood Alignment]] |
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43 | 42 | Dmitry Lyumkis | **** [[Spider Reference-free Alignment]] |
44 | 34 | Anke Mulder | **** [[IMAGIC Multi Reference Alignment]] |
45 | **** [[Spider Reference-based Alignment]] |
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46 | **** [[Xmipp Reference-based Maximum Likelihood Alignment]] |
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47 | 57 | Amber Herold | **** [[Xmipp 3 Clustering 2D Alignment]] |
48 | 56 | Sargis Dallakyan | **** [[ISAC Iterative Stable Alignment and Clustering]] |
49 | 36 | Anke Mulder | ### [[Run Feature Analysis]] |
50 | **** [[Spider Coran Classification]] |
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51 | **** [[Xmipp Kerden Self-Organizing Map]] |
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52 | 45 | Amber Herold | **** [[IMAGIC Multivariate Statistical Analysis (MSA)]] |
53 | 3 | Anke Mulder | **** [[Xmipp Rotational Kerden Self-Organizing Map]] |
54 | 45 | Amber Herold | **** [[Cluster by Affinity Propogation]] |
55 | 3 | Anke Mulder | ### [[Run Particle Clustering]] |
56 | 40 | Amber Herold | ## *[[Ab Initio Reconstruction]]* |
57 | 38 | Anke Mulder | *** [[RCT Volume]] |
58 | *** [[OTR Volume]] |
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59 | *** [[EMAN Common Lines]] |
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60 | *** [[IMAGIC Angular Reconstitution]] |
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61 | 40 | Amber Herold | ## *[[Refine Reconstruction]]* |
62 | 38 | Anke Mulder | *** [[EMAN Refinement]] |
63 | *** [[Frealign Refinement]] |
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64 | *** [[SPIDER Refinement]] |
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65 | *** [[IMAGIC Refinement]] |
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66 | 43 | Amber Herold | *** [[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]] |
71 | *** [[Align Tilt-Series|Align Tilt-Series (Appion-Protomo)]] |
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72 | *** [[Upload full tomogram|Create & Upload Tomogram]] |
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73 | *** [[Create tomogram subvolume|Create Tomogram Subvolume]] |
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74 | *** [[Average tomogram subvolumes|Average Subvolumes]] |
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75 | 40 | Amber Herold | ## *[[Import Tools]]* |
76 | 38 | Anke Mulder | *** [[PDB to Model]] |
77 | *** [[EMDB to Model]] |
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78 | *** [[Upload Particles]] |
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79 | *** [[Upload Template]] |
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80 | *** [[Upload Model]] |
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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]] |
84 | 69 | Sargis Dallakyan | *** [[cryoSPARC]] |
85 | 40 | Amber Herold | ## *[[Image Assessment]]* |
86 | 38 | Anke Mulder | *** [[Web Img Assessment]] |
87 | 50 | Amber Herold | *** [[Multi Img Assessment]] |
88 | 40 | Amber Herold | *** [[Run Image Rejector]] |
89 | 38 | Anke Mulder | ## *[[Region Mask Creation]]* |
90 | 51 | Anchi Cheng | *** [[Manual Masking]] |
91 | *** [[Maskiton]] |
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92 | 52 | Anchi Cheng | ## *[[Synthetic Data]]* |
93 | 22 | Anke Mulder | *** [[Synthetic Dataset Creation]] |
94 | !http://emg.nysbc.org/attachments/282/Picture_83.png! |
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95 | 19 | Anke Mulder | !http://emg.nysbc.org/attachments/277/Picture_81.png! |
96 | 22 | Anke Mulder | |
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100 | 5 | Amber Herold | |
101 | 2 | Amber Herold | ______ |
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103 | [[Appion and Leginon Database Tools|< Appion and Leginon Database Tools]] |
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104 | |||
105 | ______ |