# CryoCollege: A CryoEM Learning Community
## Introduction
We can see living atoms with electrons. Electron microscopes use hundreds of thousands of volts to accelerate single electrons to nearly three-quarters the speed of light, giving them picometer wavelengths that can resolve the distances between atoms in biomolecules. Electron cryomicroscopy (cryoEM) has revolutionized structural biology, earning the Nobel prize in Chemistry in 2017. This community aims to open up the computational "black box" of cryoEM by focusing on electron optics and forward modeling in image formation, crucial for inferring intrepretable and identifiable 3D information from 2D images.
Researchers are encouraged to engage with these discussions with the theory and coding resources from [Learning CryoEM Math](https://github.com/geoffwoollard/learn_cryoem_math/).
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## Topics
- **Modelling**:
- **Electron optics**: Contrast transfer function, inelastic and elastic scattering, Ewald sphere curvature, projection assumption, weak-phase object approximation, multislice, phase plate
- **Noise**: Water models of amorphous ice, sample damage, detectors, noise models
- **Specimen**: Dynamics, atom coordinates to electron density
- **Inference**: 3D reconstruction priors, simulaiton based inference, Bayesian inference, optimization, identifiability, resolution
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## Upcoming Meetings
| **Date** | **Time (ET)** | **Time (PT)** | **Presenter** | **Resource** | **Topics/Questions** | **Additional References** |
|-----------------|-----------------|-----------------|---------------|-------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Thursday 4 Dec 2025 | 3-4 PM | 12-1 PM | Geoff | Lobato, I., & Van Dyck, D. (2014). An accurate parameterization for scattering factors, electron densities and electrostatic potentials for neutral atoms that obey all physical constraints. Acta Crystallographica Section A: Foundations and Advances, 70(2014), 636–649. http://doi.org/10.1107/S205327331401643X | Forward model of atoms to potential |
| Thursday 15 Jan 2025 | 3-4 PM | 12-1 PM | David | CryoSPARC Team, Structura Biotechnology Inc. (2025). End-to-end automation of repeat-target cryo-EM structure determination in CryoSPARC, 1–47. https://www.biorxiv.org/content/10.1101/2025.10.17.682689v1 | Automation and reproducability |
| Thursday 15 Jan 2025 | 3-4 PM | 12-1 PM | Serena | |
| Thursday 12 Feb 2025 | 3-4 PM | 12-1 PM | | |
| Thursday 12 March 2025 | 3-4 PM | 12-1 PM | | |
| Thursday 16 April 2025 | 3-4 PM | 12-1 PM | | |
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## Suggested Papers
- CryoGEM: Physics-Informed Generative Cryo-Electron Microscopy, https://neurips.cc/virtual/2024/poster/94256
- Li, J., Chen, Y., Zheng, S., McDonald, A., Sedat, J. W., Agard, D. A., & Cheng, Y. (2025). Deconvolution to restore cryo-EM maps with anisotropic resolution. https://www.biorxiv.org/content/10.1101/2025.02.23.639707v1 | Preferred orientation correction. |
- Raghu, R., Levy, A., Wetzstein, G., & Zhong, E. D. (2025). Multiscale guidance of AlphaFold3 with heterogeneous cryo-EM data. https://arxiv.org/abs/2506.04490 | Foundation model prior. CryoBoltz |
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## Past Meetings
| **Date** | **Time (ET)** | **Time (PT)** | **Presenter** | **Resource** | **Topics/Questions** | **Additional References** |
|-----------------|-----------------|-----------------|---------------|-------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Thursday 16 Oct 2025 | 3-4 PM | 12-1 PM | Qiyu | Mancl, J., Wu, X., Zhao, M., & Tang, W.-J. (2025). Dimerization and dynamics of angiotensin-I converting enzyme revealed by cryo-EM and MD simulations. BioRxiv. https://www.biorxiv.org/content/10.1101/2025.01.09.632263v6.full.pdf | Interpretation of heterogeneity (is this blob really there?) |
| 9 July 2025 | 3-4 PM ET | 12-1 PM PT | Yikai | Li, Y., Zhou, Y., Yuan, J., Ye, F., & Gu, Q. (2024). CryoSTAR: leveraging structural priors and constraints for cryo-EM heterogeneous reconstruction. Nature Methods. http://doi.org/10.1038/s41592-024-02486-1 | Structural (coordinated based) prior elastic network model. CryoSTAR. |
| 18 June 2025 | 3-4 PM ET | 12-1 PM PT | David | Möbius, J. L., & Habeck, M. (2024). Diffusion priors for Bayesian 3D reconstruction from incomplete measurements. http://arxiv.org/abs/2412.14897 | Diffusion prior. |
| 30 May 2025 | 3-4 PM ET | 12-1 PM PT | Geoff | Chen, M. (2024, September 27). Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks. BioRxiv. http://doi.org/10.1101/2024.09.27.615511 | Atomic model prior (per residue and full atom geometry regularizations). EMAN2 GMM. | Chen, M., Toader, B., & Lederman, R. (2023). Integrating Molecular Models Into CryoEM Heterogeneity Analysis Using Scalable High-resolution Deep Gaussian Mixture Models. Journal of Molecular Biology, 435(9), 168014. http://doi.org/10.1016/j.jmb.2023.168014
| 8 May 2025 | 4-5 PM ET | 1-2 PM PT | David | Igaev, M., Kutzner, C., Bock, L. V., Vaiana, A. C., & Grubmüller, H. (2019). Automated cryo-EM structure refinement using correlation-driven molecular dynamics. ELife, 8, 1–33. http://doi.org/10.7554/eLife.43542 | Structural (atomic model) prior. Correlation-driven molecular dynamics |
| 23 Apr 2025 | 4-5 PM ET | 1-2 PM PT | Geoff | Prins, V., Diepeveen, W., Bekkers, E. J., & Oktem, O. (2024). Physics-informed geometric regularization of heterogeneous reconstructions in cryo-EM. GEM Workshop, ICLR 2024, (i), 1–14. https://openreview.net/forum?id=41zNERm0J9 | Normal mode prior. Geometry degradation loss |
| 9 Apr 2025 | 4-5 PM ET | 1-2 PM PT | Minhuan | Kimanius, D., Jamali, K., Wilkinson, M. E., Lövestam, S., Velazhahan, V., Nakane, T., & Scheres, S. H. W. (2024). Data-driven regularization lowers the size barrier of cryo-EM structure determination. Nature Methods, 21(7), 1216–1221. http://doi.org/10.1038/s41592-024-02304-8 | Data-driven denoising prior. Relion's Blush|
| 5 Mar 2025 | 4-5 PM ET | 1-2 PM PT | Minhuan | [1] Singer, A. (2021). Wilson statistics: derivation, generalization and applications to electron cryomicroscopy. Acta Crystallographica Section A Foundations and Advances, 77(5), 472–479. http://doi.org/10.1107/S205327332100752X [2] Gilles, M. A., & Singer, A. (2022). A Molecular Prior Distribution for Bayesian Inference Based on Wilson Statistics, 1–11.| Wilson prior |
| 27 Feb 2025 | 4-5 PM ET | 1-2 PM PT | Geoff | [1] “Theoretical background” section in Scheres, S. H. W. (2012). RELION: Implementation of a Bayesian approach to cryo-EM structure determination. Journal of Structural Biology, 180(3), 519–530. http://doi.org/10.1016/j.jsb.2012.09.006 [2] “Theory” section in Scheres, S. H. W. (2012). A bayesian view on cryo-EM structure determination. Journal of Molecular Biology, 415(2), 406–418. http://doi.org/10.1016/j.jmb.2011.11.010 | Reconstruction. Diagonel spectral prior |
| 16 Jan 2025 | 4-5 PM ET | 1-2 PM PT | Luke | Gilles & Singer (2023) RECOVAR: Principal component analysis (PCA) computed via REgularized COVARiance estimation | Linear subspace models for inferring heterogeneneity (part 2) | - Gilles, M. A., & Singer, A. (2023). *A Bayesian Framework for Cryo-EM Heterogeneity Analysis using Regularized Covariance Estimation*, 1–27. https://www.biorxiv.org/content/10.1101/2023.10.28.564422v4
- Tagare, H. D., Kucukelbir, A., Sigworth, F. J., Wang, H., & Rao, M. (2015). *Directly reconstructing principal components of heterogeneous particles from cryo-EM images.* Journal of Structural Biology, 191(2), 245–262. http://doi.org/10.1016/j.jsb.2015.05.007
| 5 Dec 2024 | 4-5 PM ET | 1-2 PM PT | David | Gilles & Singer (2023) RECOVAR: Principal component analysis (PCA) computed via REgularized COVARiance estimation | Linear subspace models for inferring heterogeneneity | - Gilles, M. A., & Singer, A. (2023). *A Bayesian Framework for Cryo-EM Heterogeneity Analysis using Regularized Covariance Estimation*, 1–27. https://www.biorxiv.org/content/10.1101/2023.10.28.564422v4
- Tagare, H. D., Kucukelbir, A., Sigworth, F. J., Wang, H., & Rao, M. (2015). *Directly reconstructing principal components of heterogeneous particles from cryo-EM images.* Journal of Structural Biology, 191(2), 245–262. http://doi.org/10.1016/j.jsb.2015.05.007
| 7 Nov 2024 | 2-3 PM ET | 11-12 PM PT | Robert | Parkhurst et al. (2024) Simulating water in cryo-EM | Solvation models | - Parkhurst, J. M., Cavalleri, A., Dumoux, M., Basham, M., Clare, D., Siebert, C. A., … Essex, J. W. (2024). Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples. Ultramicroscopy, 256(October 2023), 113882. http://doi.org/10.1016/j.ultramic.2023.113882 |
| 11 Sept 2024 | 4-5 PM ET | 1-2 PM PT | Pilar | Derivation of the Contrast Transfer Function | Contrast transfer in electron optics | - Wade, R. H. (1992). "A brief look at imaging and contrast transfer"
- Hawkes & Kasper (2022) *Principles of Electron Optics* chapters 60 & 65 |
| 29 August 2024 | 4-5 PM ET | 1-2 PM PT | Geoff | Remis et al. (2024). Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage | Laser phase plate, sample damage | - Remis, J., Petrov, P. N., Jessie, T., Axelrod, J. J., & Cheng, H. (2024). *Cryo-EM phase-plate images reveal unexpected levels of apparent specimen damage*, 1–28. |
| 7 August 2024 | 4-5 PM ET | 1-2 PM PT | Geoff | Kirkland, Chapter 6, Theory of Calculation of Images of Thick Specimens | Multislice wave propagation and cryo-TEM simulations | - Himes & Grigorieff (2021) *Cryo-TEM simulations using multislice wave propagation*
- Kirkland (2016), "Multislice: the FFT approach"
- Koeck & Karshikoff (2015) *Limitations of the linear and projection approximations in 3D TEM of hydrated proteins* |
| 10 July 2024 | 4-5 PM ET | 1-2 PM PT | Kwanghwi | Kirkland, Chapter 5, Calculation of Images of Thin Specimens | Image simulations of thin specimens | |
| 7 June 2024 | 1-2 PM ET | 10-11 AM PT | Niko | Henderson (1995) Appendix, The Potential and Limitations of Neutrons, Electrons and X-Rays | Atomic resolution microscopy of unstained biological molecules | |
| 22 May 2024 | 4-5 PM ET | 1-2 PM PT | Miro | Kirkland, Chapter 2, The Transmission Electron Microscope | Optical aberrations and Ewald sphere curvature | - Zivanov, Nakane, Scheres "4.8 Optical aberrations and Ewald sphere curvature"
- Chris Russo (2023), *Electron Cryomicroscope hardware: past, present, and future* |
| 1 May 2024 | 4-5 PM ET | 1-2 PM PT | Office Hours | Vulović et al. (2014) When to use the projection assumption and the weak-phase object approximation | Follow-up discussion on scattering in electron optics | |
| 17 April 2024 | 4-5 PM ET | 1-2 PM PT | Geoff | Glaeser, Chiu, Nogales. 1.2 Recovery of 3D structures from images of weak-phase objects | Inelastic and elastic scattering: physical basis, conservation of energy and momentum, inelastic always damaging? | - Hawkes & Casper, chapter 69
- Vulović et al. (2014) "When to use the projection assumption and the weak-phase object approximation"
- Fred Sigworth video lectures
- Robert Glaeser, *Electron Crystallography of Biological Macromolecules* |
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## Recommended Reading
- Vulović, M. et al. (2013). *Image formation modeling in cryo-electron microscopy*. Journal of Structural Biology, 183(1), 19–32. http://doi.org/10.1016/j.jsb.2013.05.008
- Rullgård, H. et al. (2011). *Simulation of transmission electron microscope images of biological specimens*. Journal of Microscopy, 243(3), 234–256. http://doi.org/10.1111/j.1365-2818.2011.03497.x
- Himes, B., & Grigorieff, N. (2021). *Cryo-TEM simulations of radiation-sensitive samples using multislice wave propagation*. IUCrJ, 8(6), 943–953. http://doi.org/10.1107/S2052252521008538
- Koeck, P. J. B. (2023). *Alternative Forward Models for Imaging Thick Specimens in TEM*. Microscopy and Microanalysis, 29(3), 1071–1076. http://doi.org/10.1093/micmic/ozad038
- Wade, R. H. (1992). *A brief look at imaging and contrast transfer*. Ultramicroscopy, 46(1–4), 145–156. http://doi.org/10.1016/0304-3991(92)90011-8
- Zhang, X., & Hong Zhou, Z. (2011). *Limiting factors in atomic resolution cryoEM*. Journal of Structural Biology, 175(3), 253–263. http://doi.org/10.1016/j.jsb.2011.05.004
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## Organizer
Geoffrey Woollard