Advanced Bioimaging Capabilities and Biomedical Research Opportunities at the Department of Energy (DOE) and the NIH

A Dialog Series Between the NIH and DOE Communities for Technology Development and Biomedical Research

Objectives:

  • Characterize the current state of high-resolution bioimaging technology
  • Identify significant biomedical challenges that would benefit from bioimaging
  • Identify novel technology that could advance biomedical imaging
  • Provide a forum to cross-fertilize ideas from technology developers and biomedical researchers

Initial efforts include webinars that focus on bioimaging techniques with resolutions from sub-nanometer to micrometer and would be applied to biological samples from nanometer to millimeter size.

NIH-DOE Bioimaging Webinar, March 11, 2020:
Data Acquisition and Available Techniques

3D image of actin in a cell. It forms a dense network of thin filaments. 

DOE, NIGMS, NIBIB Introduction and Resources

Based on data in figure 4: Fluorescence maps and ptychographic image of a frozen-hydrated C. reinhardtii alga obtained from 167 × 151-point scan data. (A) Elemental distributions of P, S, K, and Ca within the cell. Phase image reconstructed via ptychography. 

Stefan Vogt, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory

Synchrotron-based X-ray Imaging for Biology: Visualization of Trace Elements to Cellular Structure

(A) Isosurface representation of the T20S map. (B) An a-helical segment from one ß subunit is shown in ribbon representation docked into the corresponding region of the reconstruction. (C) Same a-helical segment as in (B) shown in atom representation docked into the corresponding region of the reconstruction. Several water molecules are visible. 

Bridget Carragher, Simons Electron Microscopy Center, New York Structural Biology Center

An Introduction to Cryo-electron Microscopy (cryo-EM)

Figure 4 AKAP95 forms dynamic foci in cell nucleus. Immunostaining of endogenous AKAP95 (red) and DNA (DAPI, blue) in indicated cancer cell lines and primary MEFs from WT and Akap95 KO embryos. 

Enrico Gratton, Laboratory for Fluorescence Dynamics, University of California, Irvine

Dynamic Super-resolution in Optical Microscopy

NIH-DOE Bioimaging Webinar, April 15, 2020:
Imaging Data Analysis, Management, and Knowledge

3D image of actin in a cell. It forms a dense network of thin filaments.  

Advanced Bioimaging Capabilities and Biomedical Research Opportunities Introduction

Three database icons lined up in a row. 

Belinda Seto, Office of Data Science Strategy, National Institutes of Health

Adaptive Optics Imaging: A Case for Technology and Biomedical Data Management

High-throughput imaging experiments generate extremely large, multidimensional data sets with quantifiable phenotypic information for every individual cell. Using machine learning, including deep learning, we mine this rich, latent information to identify patterns resulting from chemical or genetic perturbations to probe the causes and cures for various diseases. 

Anne E. Carpenter, Broad Institute of Harvard and Massachusetts Institute of Technology

Image Analysis for the Modern Biologist: Why and How?

The Math Group has solved a 60 year old open question on the limiting form of extreme standing water waves. The new result or answer is that the wave crests of extreme standing waves do not sharpen to a corner in a self-similar fashion as predicted, but instead develop an oscillatory structure on small scales near the crest. 

James Sethian, Dept. of Mathematics, University of California at Berkeley and Lawrence Berkeley Laboratory

Building Mathematical Algorithms for Inversion, Reconstruction, and Classification from Biological Image Data

Open Microscopy Environment Logo. OMERO is client-server software for managing, visualizing and analyzing microscopy images and associated metadata. 

Jason Swedlow, Open Microscopy Environment, School of Life Sciences, University of Dundee

Making BioImage Data FAIR

Department of Energy (DOE) Information

A vector map of the measured deflections of an atomic-sized electron beam scanned across different polar domains in the ferroelectric bismuth ferrite. 

Basic Energy Sciences (BES) User Facilities

X-ray Fluorescence (XRF) image of cobalt (red), calcium (green) and potassium (blue) in a leaf of Alyssum murale acquired using the MAIA detector developed at Brookhaven National Laboratory 

Biological and Environmental Research (BER) Structural Biology and Imaging Resources at Synchrotron and Neutron Facilities

National Institute of Biomedical Imaging and Bioengineering (NIBIB) Information

Rendered 3D model of a malaria-infected erythrocyte obtained by scanning transmission electron tomography. 

Intramural Labs at NIBIB

Combined physiological and biochemical measurements in a PET/MR anatomical image. 

Extramural Resource Centers for Medical Imaging

Multiphoton microscopy of amyloid deposits in mouse model of Alzheimer's Disease. 

NIBIB Exploratory Research Funding

National Institutes of General Medical Sciences (NIGMS) Information

Mouse retina, delicately snipped to lay flat and sparkling with fluorescent molecules. 

NIGMS Overview: Biomedical Technology

Multi-colored specs are cells on the surface of a zebrafish scale. 

NIGMS Technology Development Programs (R21 and R01)

NIH Common Fund Initiatives

A guiding principle of the NIH Strategic Plan for Data Science, and the approach of the ODSS, is that all biomedical research data should adhere to FAIR principles. This means data should be findable, accessible, interoperable, and reusable (FAIR). 

NIH Data Science Biomedical Data Repositories and Knowledgebases

Composite image of E. coli beta-galactosidase using cryo-EM. 

Transformative High Resolution Cryo-Electron Microscopy