Tomography Short Course
March 31-April 4, 2025
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. The 2023 offering resulted in a review on cryo-ET workflows (https://doi.org/10.3389/fmolb.2023.1296941).
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Short-course Agenda
Monday, March 31, 2025 |
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| Session | Type | Lecturer | Topic |
| Morning | Keynote | Wei Dai (Rutgers University) | Intro and overview of tomography [pdf] |
| Morning | Lecture 1 | Keith Hamilton (Rockefeller University) | Intro to technologies for cryo sample prep [pdf] |
| Morning | Lecture 2 | Alex de Marco (NYSBC/SEMC) | Applications of FIB-milling for cryoET investigations [pdf] |
| Morning | Roundtable 1 | Students | Flashtalks |
| Lunch | all attendees | Lunch | |
| Afternoon | Lecture 3 | Geoff Perumal (TFS) | Sample preparation workflows: Getting samples ready for tomography data collection [pdf] |
| Afternoon | Practical 1 | National Center staff | Sample preparation practicals and demos |
Tuesday, April 1, 2025 |
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| Session | Type | Lecturer | Topic |
| Morning | Lecture 4 | Misha Kopylov (NYSBC) | CryoET data acquisition strategies and software [pdf] |
| Morning | Lecture 5 & Practical 2 | Jose Luis Vilas Prieto (I2PC) | Scipion tomography pipeline [pdf] |
| Lunch | all attendees | Lunch | |
| Afternoon | Lecture 6 & Practical 3 | Alberto Bartesaghi (Duke University) | Cryo-ET data processing tutorial using nextPYP [pdf] |
Wednesday, April 2, 2025 |
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| Session | Type | Lecturer | Topic |
| Morning | Roundtable 2 | Alberto Bartesaghi (Duke University) | Cryo-ET data processing tutorial using nextPYP (on-the-fly processing) |
| Morning | Lecture 7 | Jake Johnston (Columbia University) | Data processing: segmentation and sub-volume averaging pipelines [pdf] |
| Morning | Lecture 8 | Alister Burt (Genentech) | A Hitchhikers Guide to Structural Cryo-ET [pdf] |
| Lunch | all attendees | ||
| Afternoon | Practical 4 | Alister Burt (Genentech) | Sub-Tomogram processing practical with WARP/RELION |
Thursday, April 3, 2025 |
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| Session | Type | Lecturer | Topic |
| Morning | Lecture 9 | Tianbo Zhai and Mark McClendon (TFS) | CryoET annotation and analysis & AMIRA demo |
| Morning | Roundtable 3 | National Center staff | EM challenges and new frontiers |
| Morning | Lecture 10 & Practical 5 | Matthew Swulius (Penn State University) | Training Generalized Segmentation Networks Using Real and Synthetic Data [pdf] |
| Lunch | all attendees | Lunch | |
| Afternoon | Practical 5 (cont) | Matthew Swulius (Penn State University) | CryoET annotation practical |
Friday, April 4, 2025 |
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| Session | Type | Lecturer | Topic |
| Morning | Roundtable 4 | National Center staff | What’s next – applying to NIH common fund cryoEM and cryoET centers |
| Morning | Practical 6 | National Center staff | Choose your adventure: deeper dive into waffle milling, cryoCLEM & data collection |
| Wrap up | all attendees | farewell | |
| Afternoon | bonus time | all attendees | additional time for cryoET data collection |
Yes. This will be an in-person on-site workshop.
See the 2023 offering of this workshop here.
Yes. All parts of the workshop will be recorded. We will post all learning materials on our website.