Remote Cross-training Central
Tentative Round Table Schedule
Round table registration will be open to a larger group but embedded trainees have priority to available seats. Round tables are open forums that start with a 5-10 intro from a SEMC staff member to kick off the discussion, followed by open Q&A, an opportunity to share data/intermediate results, and discussion amongst the group.
Tuesdays at 3:30
Remote cryoEM Master Class
NCCAT’s Remote Master class aims to ensure a trainee’s foundational concepts in the art and science in the field of cryoEM by focusing on applied theory and practicals to reinforce core knowledge.
Remote Sample Preparation Module
Remote microscope operations cannot completely replace in-person instruction, but it aims to educate and familiarize trainees with the tools of the trade through virtual shadowing for EM specimen preparation focused on single particle analysis applications in a TEM.
Proficiency badges in cryoEM sample preparation
We have broken the sample preparation module into merit badges to help organize the training program. Each merit badge has a worksheet with information on the requirements necessary to be completed for the badge. Users should contact the NCCAT User Office to begin working on a particular merit badge. Once the requirements are completed, the user may meet with your User Coordinator to complete the theoretical portion and arrange an appointment to demonstrate the practical portion of the worksheet. After successful completion of the merit badge requirements, the user can then receive a merit badge.
Remote Microscope Operation Module
Remote microscope operations cannot completely replace in-person instruction, but it aims to educate and familiarize trainees with the tools of the trade through virtual shadowing and remote operations using Leginon.
Leginon Remote – Remote Krios operations
Remote Pre-processing Module
Remote data collection pre-processing feedback at NCCAT and data analysis tools.
Appion pre-processing pipeline
cryoSPARC Live and data analysis workflow
Case studies (a reading list)
Aim: To review the origins, developments, and applications of cryo-EM methods and concepts.
NCCAT virtual tour
See what happens daily at a national cryoEM facility.
General Cross-training Components
Embedded Cross-training Modules
Learn about different parameters during grid preparation that affect sample quality and ice thickness.
• Reproducible sample preparation of a test sample with the Vitrobot Mark IV, Leica GP, and/or CP3.
• Identify sample preparation conditions for an applicant’s driving biological project and to prepare grids reproducibly.
Learn about the operation of screening microscopes and Krios microscopes. Learn which alignments are important for obtaining high-quality data on an EM, how to check if it is aligned correctly and how to do the alignments.
• Check the alignments on an EM and be able to adjust them if necessary.
• Know the most common errors occurring on an EM during operation and how to deal with them.
Learn to assess if a sample is ready for data collection, what to check on the microscope before starting a long data collection, and how to operate the Leginon acquisition software. Furthermore, judging how many micrographs would be necessary for a reasonably good structure by looking at the micrographs and pre-processed data.
• Set up a data collection from a test sample and obtain enough data to get a high-resolution structure.
• Determine data acquisition parameters for applicant’s sample and collect enough data for an initial 3D model.
Learn how to use on-the-fly processing through Appion to optimize a data collection experiment in real time. After data collection is complete learn to process data with commonly used software packages and pipelines (RELION3 and cryoSPARC) from motion correction to 3D model refinement.
• Obtain a high-resolution structure from a test data set with commonly used software packages.
• Process a data set from the applicant’s own sample and obtain a 3D model.