Professional Education


  • Doctor of Philosophy, Stanford University, CS-PHD (2017)
  • Master of Engineering, Massachusetts Institute of Technology, Electrical Eng. & Comp. Sci. (2005)
  • Bachelor of Science, Massachusetts Institute of Technology, Electrical Eng. & Comp. Sci. (2005)

All Publications


  • SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function CELL Tomer, R., Lovett-Barron, M., Kauvar, I., Andalman, A., Burns, V. M., Sankaran, S., Grosenick, L., Broxton, M., Yang, S., Deisseroth, K. 2015; 163 (7): 1796-1806

    Abstract

    The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca(2+) imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function.

    View details for DOI 10.1016/j.cell.2015.11.061

    View details for Web of Science ID 000366854200024

    View details for PubMedID 26687363

  • Enhancing the performance of the light field microscope using wavefront coding OPTICS EXPRESS Cohen, N., Yang, S., Andalman, A., Broxton, M., Grosenick, L., Deisseroth, K., Horowitz, M., Levoy, M. 2014; 22 (20): 24817-24839
  • Wave optics theory and 3-D deconvolution for the light field microscope OPTICS EXPRESS Broxton, M., Grosenick, L., Yang, S., Cohen, N., Andalman, A., Deisseroth, K., Levoy, M. 2013; 21 (21): 25418-25439

    Abstract

    Light field microscopy is a new technique for high-speed volumetric imaging of weakly scattering or fluorescent specimens. It employs an array of microlenses to trade off spatial resolution against angular resolution, thereby allowing a 4-D light field to be captured using a single photographic exposure without the need for scanning. The recorded light field can then be used to computationally reconstruct a full volume. In this paper, we present an optical model for light field microscopy based on wave optics, instead of previously reported ray optics models. We also present a 3-D deconvolution method for light field microscopy that is able to reconstruct volumes at higher spatial resolution, and with better optical sectioning, than previously reported. To accomplish this, we take advantage of the dense spatio-angular sampling provided by a microlens array at axial positions away from the native object plane. This dense sampling permits us to decode aliasing present in the light field to reconstruct high-frequency information. We formulate our method as an inverse problem for reconstructing the 3-D volume, which we solve using a GPU-accelerated iterative algorithm. Theoretical limits on the depth-dependent lateral resolution of the reconstructed volumes are derived. We show that these limits are in good agreement with experimental results on a standard USAF 1951 resolution target. Finally, we present 3-D reconstructions of pollen grains that demonstrate the improvements in fidelity made possible by our method.

    View details for DOI 10.1364/OE.21.025418

    View details for Web of Science ID 000326085600097

    View details for PubMedID 24150383