Workshops and Courses2018-09-27T13:54:21+00:00

Workshops and Courses

What follows is a list of the Workshops and Courses currently offered through the SEMC lab.  Workshops and Courses are open to interested persons from our member institutions and the scientific community.  Registration is completed through links on the Upcoming Events menu (see the menu on the left).

The Appion Workshop Series covers single particle and tomography processing focused on users at the facility and using Leginon to collect our data.  Themes are generalized and would be beneficial for anyone interested in the field.  To see when the upcoming Appion Workshops are scheduled, click on Upcoming Events in the menu on this page.

Appion Part 1 – Basics and 2D Single Particle Analysis

The Appion Part 1 Workshop provides hands-on training for the Appion single-particle data processing workflow. 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. Topics include analyzing the quality of your data collection, correcting the CTF, generating and cleaning up stacks, and generating 2D class averages. An Appion Part 2 Workshop will be offered in the future to provide training for making initial models and doing 3D reconstructions.

Appion Part 2 – 3D Reconstruction

This Appion Part 2 Workshop is a follow-on to the Part 1 workshop and focuses on 3D initial models and refinement.

Appion Part 3: Tomography

This Workshop 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.

Leginon Workshop: Krios Data Collection at SEMC

Subtitled How to get the most out of your Krios session!

Leginon is a system designed for automated collection of images from a transmission electron microscope.  This workshop is intended for active Krios users to more effectively and efficiently use the platform for high resolution single particle data collection.  We will also show the full sample handling process at SEMC from grid drop off to loading.

To learn when the next Leginon Workshop is scheduled, click on Upcoming Events in the menu on this page. 

The Winter-Spring 2019 EM Course

Electron microscopy in combination with image analysis is increasingly powerful in producing 3D structures of individual molecules and large macromolecular complexes that are unapproachable by other methods. This course is focused on the concepts and theories behind electron microscopy and will be taught in a reverse classroom format based on Grant Jensen’s online course (Getting Started in Cryo-EM from Caltech). Students will be responsible for watching these online lectures prior to class. Each week guest lecturers and SEMC staff lead discussions on the practice of solving molecular structures by electron microscopy.

To learn the details of when this course begins and how to register, click on Upcoming Events in the menu on this page. 

The Winter-Spring Course is recorded and made available on YouTube.  To see the list of the Winter 2018 courses and links the the videos, click here:  Winter Course 2018 Videos.