2024/05/08 – Aaditya Rangan

Aaditya Rangan
Associate Professor, Courant Institute, New York University and Flatiron Institute.

Date and time: May 8th, 2024 Wednesday, at 8am PDT / 11am EDT / 3pm BST / 5pm CEST / 11pm China

Ab-initio Reconstruction from small datasets: using entropy-maximization and principal modes (EMPM).

In this talk I’ll describe a simple algorithm for obtaining a low-resolution model from a small number (~1000) picked-particle images. The algorithm (termed EMPM) is similar to classical alternating-minimization, but with a slight twist: the entropy of the viewing-angle distribution is maximized during the search. This entropy-maximization greatly improves robustness and accuracy, allowing EMPM to outperform many existing ab-initio reconstruction algorithms. Because of its low computational overhead, this algorithm could facilitate statistical strategies such as bootstrapping and cross-validation, along with the rapid assessment of particle quality.

2022/10/05 Daisuke Kihara

Daisuke Kihara

Professor of Biological Sciences, Computer Science, Purdue University

Date and time: September 7th, 2022
Wednesday, at 8am PT / 11am ET / 4pm BST / 5pm CEST / 11pm China

For the zoom and gather.town links, please join the One World Cryo-EM mailing list.

Validating and Building Protein Structure Models for cryo-EM Maps Using Deep Learning

Cryo-electron microscopy (cryo-EM) has become one of the main experimental methods for determining protein structures. Protein structure modeling from cryo-EM is in general more difficult than X-ray crystallography since the resolution of maps is often not high enough to specify atom positions. We have been developing a series of computational methods for modeling protein structures from cryo-EM maps. For maps at medium resolution, deep learning can provide useful structure information for structure validation and modeling. Particularly, we have recently developed a protein model quality assessment score, DAQ, which compares local density patterns captured by deep learning with amino acid positions in a model, and detect potential errors in the model. In a large-scale analysis of protein models from cryo-EM, we found that not a small number of models may have some errors. All the tools we developed are available at https://kiharalab.org/emsuites/.

2021/03/10-11: Pilot Poster Session

One World Cryo-EM Pilot Poster Session

Time and date: 3/10/2021
Live sessions:
March 10 11am-1pm EST,
March 10 8-10pm EST,
March 11 8am-10am EST
Location: gather.town (link available through our mailing list)

Information: https://cryoem.world/talks/2021-03-10-poster-session/

We are delighted to announce that we will be hosting a pilot virtual One World Cryo-EM Poster Session on March 10-11, 2021. This poster session, held on gather.town, will be a chance to discuss research with colleagues, share your own work, and socialize with others in the community.

A list of posters, presenters, and their availability can be found below or at the following link.

We have 3 live poster sessions on: March 10 11am-1pm EST, March 10 8-10pm EST, March 11 8am-10am EST. 

If you are interested in presenting, please submit your poster on this application form. With your poster, you may optionally submit a 3-5 minute video to be displayed alongside your poster for visitors outside of live poster sessions. More information and details are provided in the form.

Please make sure that you are on our mailing list. This is the only place where the links to the gather.town poster session will be posted. As always, you can find more information at https://cryoem.world

We are excited to host this poster session, and hope that you will join us.

Important Rules and Policies

As a participant, you agree that any information presented in the One World Cryo-EM poster session, whether in a poster, talk, video, or discussion, is private communication and that the information is not for public use.

You agree not to record the information by any means and not to quote or publish it without the written permission of the presenter. This includes posting information on social media, in publications, and on blogs. 

You understand that the posters are not peer-reviewed and not archivable.

You understand that it is up to each participant to follow these restrictions. The organizers are not responsible for enforcing these restrictions. 

Note that the list of poster titles and authors will be available on the OWCryo-EM website. Therefore, you may tweet a recommendation to visit poster #123 titled x by y (#OWCryoEMPosters) without referencing the content.

As a presenter, you may post your own poster on Twitter and invite people to retweet it and meet you at your poster #OWCryoEMPosters.


Q: What is gather.town? What do posters there look like?
A: This is what a poster looks like on gather.town: https://gather.town/app/5Qb5FSmPM0wtDvpd/sample_poster (the actual session is expected to have a slightly larger number of posters).

Q: How do I view the gather.town session?
A: Please make sure that you are on our mailing list. This is the only place where the links to the gather.town poster session will be posted.

Q: What is the poster selection process?
A: In this pilot poster session, we expect to accept all novel work that satisfies the topic, quality, and form requirements.

Q: How do I submit a poster?
A: Please submit your completed poster on this application form. You are not required to submit a title and abstract before submitting the full poster.

Q: What are the requirements for the poster?
A: Posters should be in an image format (eg .png, .jpg, but not .pdf), and should be at least 4000×6000 pixels. You may resubmit posters up to 10 times until February 22nd. These will be collectively posted in gather.town, and we will let you know your poster ID number. Here is a poster size example.

Q: What are the requirements for the video?
A: Videos are optional, and should be between 3-5 minutes long and provide viewers a brief description of your poster. These will be posted next to your poster for visitors that cannot make the live session, or to provide visitors context about your poster.

2020/12/02: Alberto Bartesaghi: CryoET – high-speed or high-resolution? BISECT tackles both

Alberto Bartesaghi

Alberto Bartesaghi

Associate Professor of Computer Science, Biochemistry and Electrical and Computer Engineering, Duke University

CryoET – high-speed or high-resolution? BISECT tackles both

Date and time: Dec 2nd, 2020 Wednesday, at 8am PT / 11am ET / 4pm GMT / 5pm CET / Dec 3rd midnight China

For the zoom and gather.town links, please join the One World Cryo-EM mailing list.
Note that we no longer use the zoom registration system, so old zoom links may not work. The new links will be sent via the mailing list.

Tomographic reconstruction of cryo-preserved specimens followed by extraction and averaging of sub-volumes has been successfully used to determine the structure of macromolecules in their native environment.
Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. Delays introduced during mechanical navigation of the specimen and stage tilting, however, significantly slow down data collection thus limiting its practical value. Here, I present BISECT (beam image-shift electron cryo-tomography), a new protocol to accelerate tilt-series acquisition without sacrificing resolution. I also describe improvements to our constrained single particle tomography (CSPT) framework, leading to higher resolution reconstructions determined by sub-volume averaging.
For validation, we collected tilt-series from a low molecular weight target (~300kDa) using BISECT and processed them using CSPT to obtain a 3.6 Å resolution map where density for side chains is clearly resolved. These advances bring cryo-ET a step closer to becoming a high-throughput tool for in-situ structure determination at near-atomic resolution.

2020/11/18: Jane Richardson: The Challenge of Model Validation & Correction for 2.5-4Å CryoEM

Jane Shelby Richardson

James B. Duke Professor of Medicine
Professor of Biochemistry
Duke University

The Challenge of Model Validation & Correction for 2.5-4Å CryoEM

Date and time: Nov 18th, 2020 Wednesday, at 8am PT / 11am ET / 4pm GMT / 5pm CET / Nov 19th midnight China

Registration: https://yale.zoom.us/meeting/register/tJApcu6grD4iGdFaQsDVdpJEaGD1oE-3VOjB
If you registered to the previous talk your zoom link will still work.

Please register to our mailing list to receive updates. Please use institution/company email.

New! gather.town breakout room before the talk. Please register to our mailing list to receive the link.

2020/11/4: Bridget Carragher: CryoEM: Challenges and Opportunities

Bridget Carragher
Director, Simons Electron Microscopy Center,
New York Structural Biology Center, NY, NY, USA

CryoEM: Challenges and Opportunities

Date and time: Nov 4th, 2020 Wednesday, at 8am PT / 11am ET / 4pm BST / 5pm CET / Nov 5th midnight China

Bridget will talk about challenges and opportunities in cryoEM; then, we will invite participants to add their perspective. What are the things that existing algorithms and software cannot do currently? What would make experimental work better? What do we expect or hope to achieve in the coming years?

Advance registration is required: https://yale.zoom.us/meeting/register/tJApcu6grD4iGdFaQsDVdpJEaGD1oE-3VOjB

2020/10/21: Alex Noble: Neural network particle picking and denoising in cryoEM with Topaz

Alex Noble
National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center,
New York Structural Biology Center, NY, NY, USA

Neural network particle picking and denoising in cryoEM with Topaz

Date and time: 10/21/2020 Wednesday, at 8am PT / 11am ET/ 4pm BST / 5pm CEST / 11pm China

Single particle cryoEM projects are often hampered by low SNR particle views, which are missed by most particle pickers or severely de-prioritized causing junk to be preferentially picked. Moreover, for non-globular, small, asymmetric, and aggregated proteins, picking and centering such particles becomes critical. To solve these issues and more, we present Topaz particle picking using a novel positive-unlabelled framework and Topaz-Denoise using the Noise2Noise framework. We show that Topaz and Topaz-Denoise significantly increase the number of real particles picked, enable conventionally difficult projects, significantly decrease classification bias, and increase collection efficiency. We show the first in-depth analysis of pre-trained 2D and 3D denoising models for cryoEM and cryoET, which remove the characteristic sheets of noise in cryoEM micrographs of proteins and cryoET cellular tomograms. We also will highlight Topaz pre-trained picking models. In the past several months, Topaz has been used by numerous labs around the world to enable and optimize single particle cryoEM projects, including several SARS-CoV2 projects. These recent projects and more will be highlighted to show the unique and timely power of Topaz. We will also highlight Topaz integration into the most popular cryoEM suites: Relion, CryoSPARC, Scipion, and Appion.

2020/10/7: Jasenko Zivanov: Bayesian Particle-Polishing in Detail

Jasenko Zivanov
MRC Laboratory of Molecular Biology, Cambridge

Bayesian Particle-Polishing in Detail

Date and time: 10/7/2020 Wednesday, at 8am PT / 11am ET/ 4pm BST / 5pm CEST / 11pm China

Registration required: https://yale.zoom.us/meeting/register/tJApcu6grD4iGdFaQsDVdpJEaGD1oE-3VOjB
Please join our mailing list at https://mailman.yale.edu/mailman/listinfo/ow_cryoem

The beam-induced motion-correction method informally known as Bayesian Polishing will be discussed in detail. The method has been made available to the public in 2019 as part of Relion-3 and has been widely adopted since. The talk will focus on the Bayesian formulation of the problem and on the use of Gaussian processes to model our prior assumptions on the movement of particles embedded in the ice. A more recent adaptation of the method to estimate 3D motion in tomographic samples will also be briefly presented.

Zivanov, Jasenko, Takanori Nakane, and Sjors HW Scheres. “A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis.” IUCrJ 6.1 (2019): 5-17.

2020/09/23: Edward H Egelman: Cryo-EM and Helical Polymers: A Natural Affinity


Edward H Egelman
Professor, Biochemistry and Molecular Genetics, University of Virginia

Cryo-EM and Helical Polymers: A Natural Affinity

Date and time: 9/23/2020 Wednesday, at 8am PT / 11am ET/ 4pm BST / 5pm CEST / 11pm China

Link: please join our mailing list at https://mailman.yale.edu/mailman/listinfo/ow_cryoem

It was over fifty years ago that the first 3D reconstruction from electron microscopy was published (DeRosier and Klug, 1968), and this happened to be a helical phage tail. It was no accident that this was a helical specimen, and not just because helical polymers are so abundant in biology. From one point of view helical objects are the simplest to reconstruct: a single image of a helical filament may provide all of the information needed for a 3D reconstruction. Fourier-Bessel methods of reconstruction dominated the field for the next 30 years, but now real-space approaches have become the standard. With the advent of direct-electron detectors, reaching a near-atomic resolution for helical polymers has become the standard, rather than the exception. However, problems in determining the correct helical symmetry can persist even when one reaches a resolution of ~ 5 Å. I will discuss how the best approach to determining helical symmetry involves an averaged power spectrum from the images, and explain why the power spectrum of an averaged image (such as using Class2D) is not the same as the averaged power spectrum. In addition, the highly anisotropic environment present in thin films prior to vitrification, the compressional forces associated with these thin films, and fluid flow with associated shear, can all impact the structure of the filaments being examined. I will discuss these problems and potential solutions while giving an overview of some of our own efforts involving everything from viruses infecting hosts living in nearly boiling acid to microbial nanowires, with stops along the way at bacterial and archaeal flagellar filaments and bacterial and archaeal pili.

Images courtesy of Agnieszka Kawska.