• 1 week.

  • Morning lectures.

  • Afternoon practicals.

  • April 10-14, 2023.

  • At no cost.

  • Room and board NOT included.

For more information email nccatuseroffice [at] nysbc.org

see the 2021 shortcourse

Tomography Short Course
April 10-14, 2023

NCITU & NCCAT will be offering a 1 week workshop focused on the theory and practice of tomographic methods. Cryo-electron tomography (cryo-ET) is still emerging as a technique for directly visualizing macromolecular associations and organization in native cells. This course will step through each stage of the cryo-ET workflow (specimen preparation, data acquisition, computational processing, and national infrastructure) and present methodologies that participating trainees could implement at their home institutions. The course curriculum will cover cutting-edge methods in cryo-ET and help attendees accelerate their research with exposure to these methods. The mornings involve lectures and stimulating round table discussions. The afternoons offer hands-on practicals to reinforce fundamental concepts and topics covered earlier in the day. Users are welcome to bring their own samples and/or data.

Short-course Agenda

Monday, April 10, 2023

Session Type Lecturer Topic
Morning Lecture 1 Alex Noble Intro and overview of tomography [pdf]
Morning Flashtalks students Flash talks from students
Afternoon Roundtable 1 NCITU/NCCAT staff Choosing the right in situ target and model system
Afternoon Practical 1 NCITU/NCCAT staff Group 1: Aquilos 2
Group 2: Krios
Group 3: Data processing

Tuesday, April 11, 2023

Session Type Lecturer Topic
Morning Lecture 2 Daija Bobe Sample preparation and FIB-milling for cryoET investigations
Afternoon Roundtable 2 NCITU/NCCAT staff Plunge-freezing vs Waffle method vs Lift-out – what to use and when?
Afternoon Practical 2 NCITU/NCCAT staff Group demo: High-pressure freezing/waffle method

Group 3: Aquilos 2
Group 1: Krios
Group 2: Data processing

Wednesday, April 12, 2023

Session Type Lecturer Topic
Morning Lecture 3 Misha Kopylov CryoET data acquisition strategies
Morning Roundtable 3 NCITU/NCCAT staff Choosing the right hardware and scope setup
Afternoon Group demo Alex Noble Dynamo overview
Afternoon Practical 3 NCITU/NCCAT staff Group 2: Aquilos 2
Group 3: Krios
Group 1: Data processing

Thursday, April 13, 2023

Session Type Lecturer Topic
Morning Lecture 4 Reza Paaran Data processing: segmentation and sub-volume averaging pipelines
Morning Lecture 5 Jack Turner (EMDB & EMPIAR) archiving of cryo-ET data and results in EMDB and EMPIAR [pdf]
Morning Group demo NCITU/NCCAT staff Segmentation with AMIRA
Lunch Roundtable 4 NCITU/NCCAT staff EM challenges and new frontiers
Afternoon Practical 4 NCITU/NCCAT staff What to expect from your tomo session: advanced data collection strategies and on-the-fly processing
Dinner all attendees Group dinner

Friday, April 14, 2023

Session Type Lecturer Topic
Morning Roundtable 5 Elina Kopylov & Ed Eng What’s next – applying to NIH common fund cryoEM and cryoET centers
Morning Practical 5 NCITU/NCCAT staff Choose your adventure: deeper dive into processing, waffle milling, cryoCLEM & PRIMO
Lunch all attendees Box lunch to go (or stay) and farewell
Afternoon bonus time all attendees additional time for cryoET data collection

This workshop is offered at NO COST, but is limited to 8 attendees.
Attendees are encouraged to bring samples and data.

Email the NCCAT User Office for more information.

We will reach out to participants by end of January to confirm acceptance into the short course. For further inquiries please email the NCCAT User Office.

Yes. This will be an in-person on-site workshop. All attendees should be prepared to provide a CDC vaccination card or show their New York State Excelsior Pass showing proof of COVID-19 vaccination.

A copy of the NYSBC’s COVID-19 policies may be found here.

Yes. All parts of the workshop will be recorded. We will post all learning materials on our website.