Selected Publications

Multiplexed imaging such as multicolor immunofluorescence staining, multiplexed immunohistochemistry or cyclic immunofluorescence enables deep assessment of cellular complexity in situ and, in conjunction with standard histology stains like hematoxylin and eosin (H&E), can help to unravel the complex molecular relationships and spatial interdependencies that undergird disease states. However, these multiplexed imaging methods are costly and can degrade both tissue quality and antigenicity with each successive cycle of staining. In addition, computationally intensive image processing such as image registration across multiple channels is required. We have developed a novel method, speedy histopathological-to-immunofluorescent translation (SHIFT) of whole slide images (WSIs) using conditional generative adversarial networks. This approach is rooted in the assumption that specific patterns captured in IF images by stains like DAPI, pan-cytokeratin, or alpha-smooth muscle actin are encoded in H&E images, such that a SHIFT model can learn useful feature representations or architectural patterns in the H&E stain that help generate relevant IF stain patterns. We demonstrate that the proposed method is capable of generating realistic tumor marker IF WSIs conditioned on corresponding H&E-stained WSIs with up to 94.5% accuracy in a matter of seconds. Thus, this method has the potential to not only improve our understanding of the mapping of histological and morphological profile into protein expression pro files, but also greatly increase the efficiency of diagnostic and prognostic decision-making.
In Proc. SPIE 10581, 2018

Recent & Upcoming Talks

SPIE Medical Imaging 2018
Feb 10, 2018 4:00 PM

Recent Posts

Our SHIFT paper was published in Proceedings of SPIE Medical Imaging!

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Projects

Structural Biology

My graduate research is focused on structural biology in the context of the nervous system.

Deep Learning

Development and advancement of deep learning applications in medical imaging and electron microscopy data analysis.

Teaching

Graduate Teaching Fellow

  • BI121: Introduction to Human Physiology
  • September 2016 – December 2016
  • Department of Biology | University of Oregon | Eugene, OR

Science Literacy Lecturer

  • BI121: Introduction to Human Genetics
  • January 2015 – March 2015
  • Department of Biology | University of Oregon | Eugene, OR

Teaching Laboratory Assistant and Tutor

  • BI281H: Honors Biology: Cells, Biochemistry, and Physics
  • September 2014 - December 2014
  • Department of Biology | University of Oregon | Eugene, OR

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