Home - phonchi/ASCEP GitHub Wiki

Welcome to the ASCEP wiki!

Features

  1. Benchmark, develop, simulate data, interactive
  2. for micrograph noise2noise, devonv
  3. for 2D mra, k-means(sklearn all?), r-sup, tsne(sklearn all? umap)
  4. for particles pca, mpca, hosvd
  5. simulation data (including data from continous conformation described here )

Import Data

  1. From EMPIAR
  2. From tutorial data set

Motion Correction

Whole Frame Alignment

  1. MotionCorr (MotionCorr2, Relion, Warp)
  2. Unblur (CisTEM)
  3. Full-frame motion correction (CryoSparc)
  4. Optical Flow (Xmipp)

Per-particle based alignment

  1. alignparts (CryoSparc(local, patch), alignparts-lmbfgs)
  2. Bayesian Polishing (Relion, 3D Reference required)

CTF Estimation

Whole Frame

  1. CTFFIND (CisTEM)
  2. gCTF

Patch-based/tilt data

  1. Patch-Based CTF Estimation (CryoSparc, Warp)
  2. goCTF

Per-particel

  1. CTF refinement (Relion/CisTEM, 3D Reference required)

Particle-pickeing

Semi-superviesd

  1. Topaz
  2. Cryolo

Template-based

  1. Relion, CryoSparc

Automatic

  1. DoG, LoG

2D classification

MRA-based

  1. ISAC
  2. CL2D
  3. EMAN2
  4. SPIDER

Maximum-likelihood

  1. Relion
  2. CryoSparc

Mixed

  1. ROME

Ab-initial

Using class-averages

  1. Simple

Using particles

  1. CryoSparc

3D Refinemnet

  1. Relion
  2. CryoSparc

3D classification

  1. Relion

3D Variability

  1. CryoSparc