Image Processing for cryo EM (2-12 September 2019)
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Mon 2nd Sept |
Lecture 1 | EM preparation methods
- Carolyn Moores |
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| Lecture (pm) | Setting up an EM lab
- Dave Bhella, Glasgow |
pdf1; pdf2; talk | |
| Guest Lecture | Wah Chiu, Stanford | (no documents) | |
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Tues 3rd Sept |
Lecture 2 | Basic concepts of Fourier analysis
- Giulia Zanetti, BBK |
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| Lecture 3 | Concepts of convolution, point spread, and cross-correlation
- Elena Orlova, BBK |
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| Guest Lecture | Anthony Roberts | (no documents) | |
| Practical 1 | Images and transforms, filtering, CTF, diffraction spacings, filter design, EMAN 2 Initial steps in processing, Scipion/motion corr/dose fractionation
- Helen Saibil, BBK ; Jose Miguel de la Rosa Trevin, Marta Carroni, Stockholm, Guendalina Marini, Scott Gardner BBK |
eman | |
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Weds 4th Sept |
Lecture 4 | Principles of TEM image formation
- Chris Russo, MRC-LMB |
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| Lecture 5 | Contrast transfer & CTF correction (phase contrast) (eBIC)
- Dan Clare, Diamond |
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| Lecture (pm) | Think Cold: Pushing the SPA Resolution Limit with CryoARM 300
- Bart Marzec, JEOL |
(no documents) | |
| Practical 2 | Scipion preprocessing pipeline cont’d: CTF find4, phase contrast, Gautomatch, article picking, examples of good and bad images, effects of dose and filtering
- Jose Miguel de la Rosa Trevin, Marta Carroni, Stockholm. Dan Clare, Diamond |
scipion | |
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Thurs 5th Sept |
Lecture 6 | Tomography and CLEM
- Kay Grünewald, Hamburg |
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| Lecture 7 | Subtomogram averaging, 3D CTF correction
- John Briggs, MRC-LMB |
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| Lecture (pm) | Micro ED
- Andreas Förster, Dectris |
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| Guest Lecture | Gabriel Waksman, BBK | (no documents) | |
| Practical 3 | Tomography and segmentation
- Daven Vasishtan, Oxford. Mauro Maiorca, Guendalina Marini, Josh Hutchings, Claudine Bisson, BBK |
imod | |
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Fri 6th Sept |
Lecture 8 | FIB milling /phase plate imaging
- Julia Mahamid, EMBL-HD |
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| Lecture 9 | Detectors, noise, frame alignment principles, particle detection
- Helen Saibil, BBK |
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| Lecture (pm) | Micro ED: EPU-D results and perspectives
- Ieva Drulyte, Thermo Fisher |
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| Practical 4 | Subtomogram averaging and 3D CTF correction, Dynamo
- Daniel Castano, Giulia Zanetti, Daven Vasishtan, Josh Hutchings, Claudine Bisson |
dynamo | |
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Sat 7th Sept |
Lecture 10 | Single particle analysis, reconstruction principles
- John Rubinstein, Toronto |
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| Lecture 11 | Using symmetry, viruses, helices, extracting asymmetric parts
- Doryen Bubeck, IC |
pdf; mov; ppt | |
| Guest Lecture | Hao Wu, Harvard | (no documents) | |
| Practical 5 | Single particle analysis: cryosparc: initial model by SGD, 2D & 3D classification, refinement. Map inspection with Chimera
- John Rubinstein, Ali Punjani, Marina Ivanova, Scott Gardner, BBK |
cryosparc | |
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Mon 9th Sept |
Lecture 12 | Single particle (Bayesian methods, particle classification)
- Sjors Scheres, MRC-LMB |
pdf; ppt |
| Lecture 13 | Microscopes and automated data collection
- Bridget Carragher, NYSBC |
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| Lecture (pm) | Direct electron detectors
- Paul Mooney, Gatan |
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| Guest Lecture | CryoEM structures of virus assemblies in vitro and in cells
- Peijun Zhang, Diamond |
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| Practical 6 | Relion advanced topics in single particle analysis: 3D refinement with focussed classification, signal subtraction, postprocessing, sharpening, local filtering
- Sjors Scheres, Kat Toropova, Giulia Zanetti, Scott Gardner |
relion | |
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Tues 10th Sept |
Lecture 14 | Validation of 3D EM reconstructions, post processing
- Peter Rosenthal, Crick |
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| Lecture 15 | Interpretation of maps, docking of atomic structures
- Maya Topf, BBK |
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| Practical 7 | Fitting of structures, flexible fitting (Flex-EM), model validation (TEMPy)
- Tom Burnley, Maya Topf, Colin Palmer, Agnel Praveen Joseph, Sony Malhotra, Tristan Cragnolini, Aaron Sweeney |
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Weds 11th Sept |
Lecture 16 | High resolution refinement, model assessment
- Arjen Jakobi, Delft |
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| Lecture 17 | Cryo EM in the pharmaceutical industry
- Claudio Ciferri, Genentech; Ilaria Ferlenghi, GSK |
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| Practical 8 | Local sharpening (LocScale), de novo structure building (CCP-EM, REFMAC)
- Arjen Jakobi, Tom Burnley, Colin Palmer, Sony Malhotra, Tristan Cragnolini, Aaron Sweeney |
locscale | |
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Thurs 12th Sept |
Lecture 18 | MDB Data deposition, EMPIAR, eBIC
- Gerard Kleywegt & Osman Salih, EMDB |
pdf1; pdf2 |
| Guest Lecture | Future prospects for cryo EM
- Richard Henderson, MRC LMB |
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