Appion Processing¶

1. Terminology
2. Common Workflow
   1. Step by Step Guide
   2. Quality Assessment
3. Processing Cluster Login
4. Particle Selection
   1. Template Picking
   2. Dog Picking
   3. Manual Picking
   4. Repeat from other session
   5. Random Conical Tilt Picking
      • Align and Edit Tilt Pairs
      • Auto Align Tilt Pairs
5. CTF Estimation
   1. Ace Estimation
   2. Ace 2 Estimation
   3. CtfFind Estimation
   4. Repeat from other session
6. Stacks
   1. Stack creation
   2. more stack tools
      1. Combine Stacks
      2. View Stacks
         • Filter by MeanSTDev
         • Center Particles
         • Sort Junk
         • Create Substack
      3. Alignment SubStacks
      4. Jumpers SubStack
      5. Convert Stack into Particle Picks

1. Particle Alignment
   1. Run Alignment
      • Xmipp Maximum Likelihood Alignment
      • Spider Reference-free Alignment
      • Spider Reference-based Alignment
      • Ed's Iteration Alignment
      • Xmipp Reference-based Maximum Likelihood Alignment

1. Run Feature Analysis
2. Run Particle Clustering

1. Ab Initio Reconstruction
   1. RCT Volume
   2. OTR Volume
   3. EMAN Common Lines
   4. IMAGIC Angular Reconstitution
2. Refine Reconstruction
   1. EMAN Refinement
   2. Frealign Refinement
   3. SPIDER Refinement
   4. IMAGIC Refinement
3. Tomography
   1. Align tilt series
   2. Create full tomogram
   3. Upload tomogram
   4. Create tomogram subvolume
   5. Average subvolumes
4. Import Tools
   1. PDB to Model
   2. EMDB to Model
   3. Upload Particles
   4. Upload Template
   5. Upload Model
   6. Upload More Images
   7. Upload Stack
5. Image Assessment
   1. Web Img Assessment
   2. Multi Img Assessment
   3. Run Image Rejector
6. Region Mask Creation
   1. Manual Masking
7. Synthetic Data
   1. Synthetic Dataset Creation

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