University of Texas at Austin
Enhanced resolution for 3DEM analysis of synapses across brain regions and taxa

This Neurotechnology Hub is motivated by challenges in understanding synapses, tiny points of inter-neuronal communication. The variance in synapse dimensions, connectivity and subcellular content across species is simply not known, yet required to determine whether model systems represent human brain functions. Current approaches are limited by resolution, inefficient data collection, and analysis bottlenecks. These limitations restrict use and dissemination. We are addressing these challenges by: (1) developing transmission-mode scanning electron microscope (tSEM) approaches to improve axial resolution to 10nm while maintaining in-plane resolution of 1-2 nm; (2) updating automated and interactive tools that speed analysis of large data volumes; (3) integrating the enhanced tSEM data collection and tools with high performance computing; and (4) demonstrating the approach by imaging hippocampus and prefrontal cortex in mice, rats, non-human primates, and humans in existing brain samples. In this way, we will provide real-time feedback during image collection; disseminate images, analyses, metadata, and software; and provide a venue to build tSEM communities, so output can integrate with existing cell type and brain databases.

Key Research Resources Being Developed and Disseminated

  • Well-documented and shared improvements to tSEM better identify and characterize the shape of the molecular structures to be analyzed and incorporated into computational simulations. These include enhancing resolution techniques and perfecting staining techniques across multiple species.
  • Re-engineered software (e.g. Reconstruct and neuropil tools) to better handle larger datasets, and to be accessible via web browser.
  • A dissemination portal that will allow access to a 3DEM brain image data repository for neuroscientists, researchers, educators, and students. The portal is integrated with high performance computing resources to allow data access and analysis in a collaborative workspace. Through this resource, neuroscientists around the world will be able to access our discovery environment and collaborate with other researchers via an on-line workplace that will have the ability to store and manage the data being analyzed.
  • This Neurotechnology Hub will also provide the neuroscience community with reference data and atlases to support their hypotheses and advance their discoveries.

Our primary resource for disseminating information will be our web portal. The main portal page will include direct access to resources such as documentation, public datasets, reference atlases, and online workshops. We will supplement the release of new portal content with coordinated information release via associated websites (e.g. synapseweb, online forums), networking events (e.g., meetings, conferences, workshops, etc.), user interactions, word-of-mouth (email correspondences, face-to-face interactions), course teachings, trainings, and more as is determined to be impactful and appropriate.  Key target groups include project personnel, collaborators, neuroscience researchers, engineers and developers in overlapping areas of technical interest, and the general public.

Reaching Out to the Community

Methods to reach out to the community may include, but not limited to, the following: community workshops, seminars, course material, on-line training videos, and online forums.

Bob Kuczewski
Co-Principal Investigator
Tracy Brown
Co-Principal Investigator
Masa Kuwajima
Co-Principal Investigator
Kristen Harris
Principal Investigator
Terry Sejnowski
Co-Principal Investigator
John Mendenhall
Co-Principal Investigator
James Carson
Co-Principal Investigator
Tom Bartol
Co-Principal Investigator
Project Managers
Anna-Maria Escherich
Project Manager
University of Texas at Austin
110 Inner Campus Drive
Austin, TX 78712