R01GM143805

Automated, Optimized, Intelligent Data Collection for Cryo-EM - Project Summary

Cryo-electron microscopy (Cryo-EM) is now a widely established and indispensable method for determining the high-resolution structures of biomedically important molecules. Given that thousands of images, often acquired over the course of several days, are required to obtain such structures, automation software has played a critical role in the large-scale adoption of this method by the scientific community.

In just the past five years, Cryo-EM has revolutionized our understanding of entire biological systems and, in 2020, provided the first molecular descriptions of SARS-CoV-2 interaction with neutralizing antibodies. The widespread adoption of Cryo-EM recently prompted the NIH to invest in three national centers through the Transformative High Resolution Cryo-Electron Microscopy Program, providing free, high-end electron microscope access to biologists across the country.

The exponential increase in the popularity of Cryo-EM has led to an astonishing number of developments in sample preparation methodologies and image processing algorithms, which have improved attainable resolution of single particle reconstructions. However, comparatively little progress has been made in optimizing the quality of the Cryo-EM data being collected.

The pioneering software packages Leginon and Appion demonstrated the power of automated data acquisition and real-time processing, respectively, and there are now numerous programs for automated data acquisition and real-time processing. Despite advances in automation, optimally extracting the highest quality data from an EM sample still requires manual involvement of an expert electron microscopist. User intervention and expertise are necessary to run the appropriate image analyses, interpret the results, and make informed decisions on how the processed results relate to the ongoing data collection.

However, even experts must contend with the fact that the "best grid regions" differ drastically from sample to sample, and there are no established tools for automatically and quickly assessing the quality of the specimen across the various microenvironments of an EM grid.

Given the ever-increasing incorporation of Cryo-EM into labs' research programs, it is imperative that data collection and processing be streamlined to match the growing needs of the structural community. We propose to develop a second-generation Leginon/Appion software package, "Magellon," to overcome existing bottlenecks and provide an avenue toward fully automated data acquisition that bypasses the need for user input during data collection.

Importantly, this software will support the computational infrastructure to enable real-time image processing results to inform and modify the ongoing data collection regime by learning where to acquire images in regions that will yield the highest resolution structures. We will develop and incorporate new, fast image assessment routines while also providing an application programming interface to enable the incorporation of extensions and plugins from developers in the community.

Furthermore, Magellon will enable straightforward, seamless import and export of data from its database to accommodate remote data acquisition at any of the regional or national Cryo-EM centers.

Scripps Research Institute

THE NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES (NIGMS) SUPPORTS BASIC RESEARCH THAT INCREASES OUR UNDERSTANDING OF BIOLOGICAL PROCESSES AND LAYS THE FOUNDATION FOR ADVANCES IN DISEASE DIAGNOSIS, TREATMENT, AND PREVENTION. NIGMS ALSO SUPPORTS RESEARCH IN SPECIFIC CLINICAL AREAS THAT AFFECT MULTIPLE ORGAN SYSTEMS: ANESTHESIOLOGY AND PERI-OPERATIVE PAIN, CLINICAL PHARMACOLOGY ?COMMON TO MULTIPLE DRUGS AND TREATMENTS, AND INJURY, CRITICAL ILLNESS, SEPSIS, AND WOUND HEALING.? NIGMS-FUNDED SCIENTISTS INVESTIGATE HOW LIVING SYSTEMS WORK AT A RANGE OF LEVELSFROM MOLECULES AND CELLS TO TISSUES AND ORGANSIN RESEARCH ORGANISMS, HUMANS, AND POPULATIONS. ADDITIONALLY, TO ENSURE THE VITALITY AND CONTINUED PRODUCTIVITY OF THE RESEARCH ENTERPRISE, NIGMS PROVIDES LEADERSHIP IN SUPPORTING THE TRAINING OF THE NEXT GENERATION OF SCIENTISTS, ENHANCING THE DIVERSITY OF THE SCIENTIFIC WORKFORCE, AND DEVELOPING RESEARCH CAPACITY THROUGHOUT THE COUNTRY.

93.859 - Biomedical Research and Research Training

National Institute of General Medical Sciences (NIGMS) [HHS - NIH]

La Jolla, California 920371000 United States

Single Zip Code

Focused Technology Research and Development (R01 Clinical Trial Not Allowed) (PAR-22-127)

Amendment Since initial award the End Date has been extended from 06/30/25 to 08/31/29 and the total obligations have increased 612% from $655,046 to $4,662,806.