Interdisciplinary PhD in Structural and Computational Biology and Quantitative Biosciences

Jeremy Rogers

Assistant Professor, Department of Biomedical Engineering Lab Website 262-8357

9433 WI Institutes for Medical Research
1111 Highland Ave
Madison, WI 53705-2275


B.S., Michigan Technological University
M.S., University of Arizona
Ph.D., University of Arizona

Developing optical instrumentation and techniques for research, screening and detection of disease, and monitor therapy

Research in the Rogers lab explores the exciting ways in which we can use imaging and optics to enable discoveries in biology and medicine and to improve screening, diagnosis, and medical care. By combining aspects of theoretical modeling, computational simulation, and development of new optical instruments, we work to advance the state of the art and develop new medical technologies for a wide range of applications.

Photo of constructing instument


Current research projects include:

  • Adaptive Optics Scanning Light Ophthalmoscopy (AOSLO) for imaging retinal cells in humans and animal models
  • Optical Coherence Tomography including polarization sensitive OCT for imaging birefringence in collagen
  • Mueller Matrix Enhanced Backscattering Spectroscopy for detecting polarization dependent scattering properties in glaucoma
  • Dynamic Phase Optical Coherence Microscopy for quantifying cell function in retinal organoids
  • Fiber optic probe development for cancer screening and risk stratification through detection of field carcinogenesis via Enhanced Backscattering Spectroscopy
  • Quantification of lipofucsin autofluorescence spectral changes in Age-related Macular Degeneration
  • Imaging metabolic activity in differentiating retinal stem cells in vitro
  • Optical metrology of scattering properties of tissue

Optical methods used in our research include:

  • Microscopy
  • Spectroscopy
  • Polarization imaging
  • Coherent or Enhanced Backscattering
  • Interferometry and holography
  • Optical coherence tomography

Graph of light


As light propagates through tissue, the structure, distribution, and composition of cells, organelles, and extracellular matrix cause the light to be absorbed and scattered. By quantifying these scattering and absorption properties, we gain a wealth of information about the tissue composition. To relate the measured optical properties to tissue structure, we employ theoretical models based on a mass fractal organization of tissue.

See for example:


Simulating radiative transport in random media can be done in several ways. Analytical solutions only exist for very specialized geometries, so more general modeling uses either approximations (diffusion approximation, etc) or numerical solutions. Monte Carlo (MC) simulations have proven to be an effective and flexible method for computing a numerical solution to the radiative transport equation. An outstanding resource for Monte Carlo modeling of tissue, and THE place to start is the Oregon Medical Laser Center with great documentation and opensource code you can download and modify to suite your needs.

Our contributions to MC include:

  • Monte Carlo modeling of light transport in random/turbid media
  • Numerical simulation of LEBS
  • Parallel Monte Carlo for HPC clusters using openMPI
  • Add signal handling to allow interruptible or timed simulations instead of fixed number of rays/photons

We are also working to implement MC on High Throughput Computational (HTC) facilities such as open science grid.

See for example:
Andrew Radosevich’s website with open source code and Matlab scripts


  • Experimental LEBS
  • Spectral microscopy
  • Optical metrology
  • Refractometry of cells

Design and Engineering

  • Raytracing and optical design
  • Building prototype fiber optic probes for in vivo clinical trials
  • Stray light analysis and reduction in endoscopic instruments

Areas of Expertise

  • Computational Biology & Bioinformatics
  • Membrane & Cellular Biophysics
  • Personalized Medicine
  • Spectroscopy Microscopy Imaging