Workshop on real-time cryo-EM image processing with SIMPLE

Oxford, UK
9th - 10th January 2018



Course overview:

SIMPLE is a program package for cryo-EM image processing, featuring algorithms for all aspects of single-particle image analysis. A recent focus of the SIMPLE development team has been the establishment of a streaming pipeline, allowing real-time image processing of data directly from the microscope with a minimal computing setup.

Our SIMPLEstream package robustly motion-corrects the movies with automatic weighting of the frames using a correlation-based M-estimator, estimates the CTF with global differential evolution optimisation, identifies the particle images and preforms simultaneous 2D alignment and clustering with self-adaptive update of the number of classes based on the current number of particle images collected. The gold-standard FRC used to estimate the resolution of the 2D classes provides the necessary validation for rapid assessment of data quality.


Workshop material:



Lecture 1: Introduction to EM



Lecture 2: CTF and particle picking



Lecture 3: clustering in 2D and ab initio 3D reconstruction



Lecture 5: Refinement and heterogeneity



Lecture 6: Streaming



Tutorials:

tutorials.tar.gz