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 |
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| 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 |
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| 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 |
Wednesday, April 12, 2023 |
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| 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 |
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| 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 |
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| 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 |
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.