Data processing tutorials

Appion is a “pipeline” for processing and analysis of EM images; it is integrated with Leginon data acquisition, but can also be used stand-alone after uploading images or particle stacks.

The slides from the tutorials are located in the forums. Register for the forums and request to be added to the NYSBC-SEMC User Group.

When is the next offering?
• Pre-register for the next Appion part I here.
• Pre-register for the next Appion part II here.
• Pre-register for the next Appion part II.5 here.

Appion Part 1: Basics and 2D SPA

This tutorial provides hands-on training for the Appion single-particle data processing workflow. Topics include analyzing the quality of your data collection, correcting the CTF, generating and cleaning up stacks, and generating 2D class averages.

Appion Part 2: 3D Reconstruction

This tutorial provides hands-on training with tools for 3D reconstruction and is a follow-on to Appion part 1. Advanced Appion tools and workflows to make use of the on-the-fly processing done concurrently with Leginon data collection in other packages. The majority of the workshop we will be using Amazon Web Services (AWS) - Cloud Computing Services and cryoSPARC.

Appion Part 2.5: 3D Reconstruction (cont.)

The Appion Part 2.5 Workshop is a follow-on to the Part 2 workshop and will focus on 3D initial models and refinement. Utilizing AWS Cloud services and RELION this workshop will provide an introduction to the SPA workflow. The workshop will be held over 2 afternoons with 2-3 hours of instruction and demonstration followed by self-paced individual practice. We will be using the same tutorial dataset as in Part 2 so you may compare workflows and outputs.

Appion Part 3: Tomography

This tutorial covers tilt-series collection in Leginon, fiducial-less tilt-series alignment within Appion with Protomo, and sub-tomogram averaging with Dynamo. With this knowledge you will be able to create de novo initial models for single particle projects that no reviewer can argue with after just 1 hour of collection or collect and process tilt-series of FIB/SEM lamella, and anything in between.