Einstein Postdoctoral Fellow
Charitè Medical School
Humboldt University of Berlin
Bioimaging and Neurophotonics Laboratory


e-mail:
roarke (at) charite (dot) de

Short Biography

I am a recent PhD graduate from Caltech’s electrical engineering department and am currently an Einstein postdoctoral fellow with the Judkewitz lab at Charitè Medical School in Berlin. I mostly work with optics and algorithms. Please check out some of my papers in the "Publications" section linked above.

I also have a website for my Computational Optics Lab that I am starting at Duke University, so I will probably update this site less often in the future.


September 2017: Designing microscopes with deep learning

Deep learning algorithms have become a popular way to extract useful information from images (e.g., to classify, segment and track objects). We've come up with a slightly different application for deep learning: we're using it to extract more useful information from the physical world, as opposed to just images of the world. By modifying the pipeline of a convolutional neural network, we can now optimize the physical layout of an imaging device itself - namely, the illumination of an optical microscope - to extract more useful information from a collection of cells that are infected with the malaria virus than would otherwise be possible with an alternative microscope layout. Our CNN-designed microscope offers better cell infection classification accuracies than all tested alternatives, so hopefully it'll be pretty useful in the future!

Convolutional neural networks that teach microscopes how to image
R. Horstmeyer, R. Y. Chen, B. Kappes and B. Judkewitz, (2017) (In submission, pre-print on arXiv)

July 2017: Young Researcher Award

I was recently awarded a nice price from Friedrich-Alexander University (FAU) in Erlangen: the SAOT Young Researcher Award, which comes with some prize money and a guest professor appointment. I will spend the beginning of 2018 as a Guest Professor at both the Graduate School in Advanced Optical Technologies and the Max Planck Institute for the Science of Light, where I will be collaborating with several different groups. Please let me know if you are in the Erlangen/Nuremberg/Munich area next year and would like to meet up!

July 2017: Optical scattering in tissue - 2 new papers

We've been working hard trying to figure out some better ways to scan light around deep within tissue. We are hoping that these scanning methods will be useful to neuroscientists, who aim to image neurons deep within the brain. The first paper below describes a way to tilt and shift light around to help scan out images quickly. The second discusses how it might be possible to use many different colors of light to increase this scanning range even more.

The generalized optical memory effect
G. Osnabrugge*, R. Horstmeyer*, I.N. Papadopoulos, B. Judkewitz and I. M. Vellekoop, Optica (2017) (*shared 1st authorship).

Scattering correlations of time-gated light
M. Kadobianskyi, I. N. Papadopoulos, T. Chaigne, R. Horstmeyer and B. Judkewitz (2017) (In submission, pre-print on Arxiv).

March 2017: My new Duke website

While I'll try my best to keep this page updated as well, I now have a new website for the Computational Optics Lab that I am starting at Duke University:

horstmeyer.pratt.duke.edu

Please be sure to check out this new site for updates about me and my research!

February 2017: Einstein Foundation article and video

The Einstein Foundation Berlin just wroteup a short piece about me and my research. They also made a video about some of my work at the intersection of optics and neuroscience.

February 2017: New paper about on-chip holographic video

We have a new method that can take really fast videos of small micro-organisms that swim around on top of a sensor. It is based on a modified phase retrieval algorithm, which you can read about more here:

Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video
D. Ryu, Z. Wang, K. He, G. Zheng, R. Horstmeyer and O. Cossairt, Biomedical Optics Express 8, 1981-1995 (2017).

June 2016: Eventually heading back to to Duke!

I will join Duke University's Biomedical Engineering Department as an assistant professor in 2018, after finishing my postdoctoral fellowship in Berlin. If you hope to start graduate school or a postdoc in a couple of years and find my work interesting, please feel free to get in touch!

May 2016: Awarded Charles Wiltz prize at Caltech

I was awarded this prize from Caltech for "outstanding research in electrical engineering towards a PhD", which you can read more about here.

February 2016: New paper about microscope resolution

Characterizing the resolution of a microscope can be a little bit tricky. In the following paper, we outline a set of guidelines and propose a common resolution standard for a particular class of microscopes that image with coherent light:

Standardizing the resolution claims for coherent microscopy
R. Horstmeyer, R. Heintzmann, G. Popescu, L. Waller and C. Yang, Nature Photonics 9, 68-71 (2016).

November 2015: I just graduated with my PhD!

Over the past 6 months, I've mostly been working on a way to extend our Fourier ptychographic method to operate in 3D. Now, we can use a regular microscope and an LED array to capture the full volume of a thick biological specimen:

Diffraction tomography with Fourier ptychography
R. Horstmeyer and C. Yang, Optica 8, 827-835 (2016).

September 2015: Three new papers

The first two papers below are about some tricks we use to control the behavior of light, deep within tissue, to image very small things (like cells). The third paper is an improved algorithm to reconstruct ptychographic images.

Guidestar-assisted wavefront shaping methods for focusing light into biological tissue
R. Horstmeyer, H. Ruan and C. Yang, Nature Photonics 9, 563-571 (2015)

Translation correlations in anisotropically scattering media
B. Judkewitz*, R. Horstmeyer*, I. M. Vellekoop, I. N. Papadopoulos and C. Yang, Nature Physics 11, 684-689 (2015) (*shared 1st authorship, and its the cover article!)
Related news: Nature news and views

Solving ptychography with a convex relaxation
R. Horstmeyer, R. Y. Chen, X. Ou, B. Ames, J. A. Tropp and C. Yang, New Journal of Physics 15, 053044 (2015).

Videos of my research

If you're more into watching clips (instead of reading academic papers), then you might like to learn more about my research through some videos.

First, I recently had the honor of giving an Everhart Lecture at Caltech. In this talk, I summarize my lab's work creating microscopes that capture gigapixel-scale images. You can find more information about this lecture here, or watch it for free at iTunes U at the link below:

Computational microscopy: turning megapixels into gigapixels

Second, I was lucky enough to feature some of my research on cryptography on the Science Channel show, Through the Wormhole, with Morgan Freeman. Check out my explanation of how one-time pads and physical unclonable functions work!

The third video you might like is a great educational tutorial on how a camera works, created by Stephanie Li Xian Seo and her team for young and curious students at scienceqanda.com. If anyone else would like to animate any other optics-related subjects, please let me know!