Roarke Horstmeyer | Scholars@Duke

Roarke Horstmeyer
Assistant Professor of Biomedical Engineering

Roarke Horstmeyer is an assistant professor within Duke's Biomedical Engineering Department. He develops microscopes, cameras and computer algorithms for a wide range of applications, from forming 3D reconstructions of organisms to detecting neural activity deep within tissue. His areas of interest include optics, signal processing, optimization and neuroscience. Most recently, Dr. Horstmeyer was a guest professor at the University of Erlangen in Germany and an Einstein postdoctoral fellow at Charitè Medical School in Berlin. Prior to his time in Germany, Dr. Horstmeyer earned a PhD from Caltech’s electrical engineering department in 2016, a master of science degree from the MIT Media Lab in 2011, and a bachelors degree in physics and Japanese from Duke University in 2006.

Current Research Interests

Computational optics, machine learning, and designing new algorithms for image processing. A main focus is to improve how we capture and use images of microscopic phenomena within a range of biomedical contexts. In general, I like to create new optical devices that can improve the utility of the information that we can gather about the world around us.

Office Hours

Office hours for Fall 2020 - Spring 2021:

Wednesdays 10-11:30am
Thursdays 10am - 11:30am

Current Appointments & Affiliations

Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2018
Assistant Professor in the Department of Electrical and Computer Engineering, Electrical and Computer Engineering, Pratt School of Engineering 2018
Assistant Professor of Physics, Physics, Trinity College of Arts & Sciences 2019
Faculty Network Member of the Duke Institute for Brain Sciences, Duke Institute for Brain Sciences, University Institutes and Centers 2018

Contact Information

Box 90548, Durham, NC 27708-0548
Fitzpatrick Center (Ciemas) Room 2569, 101 Science Drive, Durham, NC 27701
roarke.w.horstmeyer@duke.edu (650) 686-1368
Computational Optics Lab
Deep Learning for Hardware Design

Background
Duke Appointment History
- Visiting Assistant Professor in the Department of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2018
Academic Positions Outside Duke
- Guest Professor, University of Erlangen . 2018 - 2022
Recognition
In the News
- NOV 20, 2019 Pratt School of Engineering
  
  A Microscope That Teaches Itself to Know the Best Settings for Diagnostic Images for Malaria
Expertise
Subject Headings
Global Scholarship
- Teaching
  - Germany (Country)
Research
Fellowships, Supported Research, & Other Grants
- Young Researcher Award in Optical Technologies awarded by School of Advanced Optical Technologies, University of Erlangen 2018 - 2020
External Relationships
- Kernel Inc.
- MITRE Corporation
- Microscopic Image Recognition Algorithm (MIRA) Inc.
- Ramona Optics Inc.
- SafineAI Inc.
Publications & Artistic Works
Selected Publications
- Academic Articles
  - DiSpirito, Anthony, Daiwei Li, Tri Vu, Maomao Chen, Dong Zhang, Jianwen Luo, Roarke Horstmeyer, and Junjie Yao. “Reconstructing Undersampled Photoacoustic Microscopy Images Using Deep Learning.” Ieee Transactions on Medical Imaging 40, no. 2 (February 3, 2021): 562–70. https://doi.org/10.1109/tmi.2020.3031541.
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  - Kim, Kanghyun, Pavan Chandra Konda, Colin L. Cooke, Ron Appel, and Roarke Horstmeyer. “Multi-element microscope optimization by a learned sensing network with composite physical layers.” Optics Letters 45, no. 20 (October 2020): 5684–87. https://doi.org/10.1364/ol.401105.
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  - Chaware, A., C. L. Cooke, K. Kim, and R. Horstmeyer. “Towards an intelligent microscope: Adaptively learned illumination for optimal sample classification.” Icassp, Ieee International Conference on Acoustics, Speech and Signal Processing Proceedings 2020-May (May 1, 2020): 9284–88. https://doi.org/10.1109/ICASSP40776.2020.9054477.
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  - Zhou, Kevin C., and Roarke Horstmeyer. “Diffraction tomography with a deep image prior.” Optics Express 28, no. 9 (April 2020): 12872–96. https://doi.org/10.1364/oe.379200.
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  - Konda, Pavan Chandra, Lars Loetgering, Kevin C. Zhou, Shiqi Xu, Andrew R. Harvey, and Roarke Horstmeyer. “Fourier ptychography: current applications and future promises.” Optics Express 28, no. 7 (March 2020): 9603–30. https://doi.org/10.1364/oe.386168.
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  - Del Hougne, Philipp, Mohammadreza F. Imani, Aaron V. Diebold, Roarke Horstmeyer, and David R. Smith. “Learned Integrated Sensing Pipeline: Reconfigurable Metasurface Transceivers as Trainable Physical Layer in an Artificial Neural Network.” Advanced Science (Weinheim, Baden Wurttemberg, Germany) 7, no. 3 (February 2020): 1901913. https://doi.org/10.1002/advs.201901913.
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  - Muthumbi, Alex, Amey Chaware, Kanghyun Kim, Kevin C. Zhou, Pavan Chandra Konda, Richard Chen, Benjamin Judkewitz, Andreas Erdmann, Barbara Kappes, and Roarke Horstmeyer. “Learned sensing: jointly optimized microscope hardware for accurate image classification.” Biomedical Optics Express 10, no. 12 (December 2019): 6351–69. https://doi.org/10.1364/BOE.10.006351.
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  - Kadobianskyi, M., I. N. Papadopoulos, T. Chaigne, R. Horstmeyer, and B. Judkewitz. “Scattering correlations of time-gated light.” Optica 5, no. 4 (April 20, 2018): 389–94. https://doi.org/10.1364/OPTICA.5.000389.
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  - Osnabrugge, G., R. Horstmeyer, I. N. Papadopoulos, B. Judkewitz, and I. M. Vellekoop. “Generalized optical memory effect.” Optica 4, no. 8 (August 20, 2017): 886–92. https://doi.org/10.1364/OPTICA.4.000886.
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  - Ryu, Donghun, Zihao Wang, Kuan He, Guoan Zheng, Roarke Horstmeyer, and Oliver Cossairt. “Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video.” Biomedical Optics Express 8, no. 3 (March 2017): 1981–95. https://doi.org/10.1364/boe.8.001981.
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  - Horstmeyer, Roarke, Richard Y. Chen, Barbara Kappes, and Benjamin Judkewitz. “Convolutional neural networks that teach microscopes how to image.” Corr abs/1709.07223 (2017).
  - Holloway, Jason, M Salman Asif, Manoj Kumar Sharma, Nathan Matsuda, Roarke Horstmeyer, Oliver Cossairt, and Ashok Veeraraghavan. “Toward Long-Distance Subdiffraction Imaging Using Coherent Camera Arrays.” Ieee Transactions on Computational Imaging 2, no. 3 (September 2016): 251–65. https://doi.org/10.1109/tci.2016.2557067.
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  - Horstmeyer, Roarke, Jaebum Chung, Xiaoze Ou, Guoan Zheng, and Changhuei Yang. “Diffraction tomography with Fourier ptychography.” Optica 3, no. 8 (August 2016): 827–35. https://doi.org/10.1364/optica.3.000827.
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  - Ou, Xiaoze, Jaebum Chung, Roarke Horstmeyer, and Changhuei Yang. “Aperture scanning Fourier ptychographic microscopy.” Biomedical Optics Express 7, no. 8 (August 2016): 3140–50. https://doi.org/10.1364/boe.7.003140.
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  - Chung, Jaebum, Jinho Kim, Xiaoze Ou, Roarke Horstmeyer, and Changhuei Yang. “Wide field-of-view fluorescence image deconvolution with aberration-estimation from Fourier ptychography.” Biomedical Optics Express 7, no. 2 (February 2016): 352–68. https://doi.org/10.1364/boe.7.000352.
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  - Horstmeyer, R., R. Heintzmann, G. Popescu, L. Waller, and C. Yang. “Standardizing the resolution claims for coherent microscopy.” Nature Photonics 10, no. 2 (February 1, 2016): 68–71. https://doi.org/10.1038/nphoton.2015.279.
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  - Judkewitz, B., R. Horstmeyer, I. M. Vellekoop, I. N. Papadopoulos, and C. Yang. “Translation correlations in anisotropically scattering media.” Nature Physics 11, no. 8 (July 31, 2015): 684–89. https://doi.org/10.1038/nphys3373.
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  - Horstmeyer, Roarke, Xiaoze Ou, Guoan Zheng, Phil Willems, and Changhuei Yang. “Digital pathology with Fourier ptychography.” Computerized Medical Imaging and Graphics : The Official Journal of the Computerized Medical Imaging Society 42 (June 2015): 38–43. https://doi.org/10.1016/j.compmedimag.2014.11.005.
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  - Horstmeyer, Roarke, Richard Y. Chen, Xiaoze Ou, Brendan Ames, Joel A. Tropp, and Changhuei Yang. “Solving ptychography with a convex relaxation.” New Journal of Physics 17 (May 2015). https://doi.org/10.1088/1367-2630/17/5/053044.
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  - Ou, Xiaoze, Roarke Horstmeyer, Guoan Zheng, and Changhuei Yang. “High numerical aperture Fourier ptychography: principle, implementation and characterization.” Optics Express 23, no. 3 (February 2015): 3472–91. https://doi.org/10.1364/oe.23.003472.
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  - Holloway, Jason, M Salman Asif, Manoj Kumar Sharma, Nathan Matsuda, Roarke Horstmeyer, Oliver Cossairt, and Ashok Veeraraghavan. “Toward Long Distance, Sub-diffraction Imaging Using Coherent Camera Arrays.” Corr abs/1510.08470 (2015).
  - Horstmeyer, Roarke, Haowen Ruan, and Changhuei Yang. “Guidestar-assisted wavefront-shaping methods for focusing light into biological tissue.” Nature Photonics 9 (January 2015): 563–71. https://doi.org/10.1038/nphoton.2015.140.
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  - Zheng, G., R. Horstmeyer, and C. Yang. “Erratum : Wide-field, high-resolution Fourier ptychographic microscopy (Nature Photonics (2013)7, (739-745)).” Nature Photonics 9, no. 9 (January 1, 2015): 621. https://doi.org/10.1038/nphoton.2015.148.
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  - Horstmeyer, Roarke, Xiaoze Ou, Jaebum Chung, Guoan Zheng, and Changhuei Yang. “Overlapped Fourier coding for optical aberration removal.” Optics Express 22, no. 20 (October 2014): 24062–80. https://doi.org/10.1364/oe.22.024062.
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  - Dong, Siyuan, Roarke Horstmeyer, Radhika Shiradkar, Kaikai Guo, Xiaoze Ou, Zichao Bian, Huolin Xin, and Guoan Zheng. “Aperture-scanning Fourier ptychography for 3D refocusing and super-resolution macroscopic imaging.” Optics Express 22, no. 11 (June 2014): 13586–99. https://doi.org/10.1364/oe.22.013586.
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  - Hollmann, Joseph L., Roarke Horstmeyer, Changhuei Yang, and Charles A. DiMarzio. “Diffusion model for ultrasound-modulated light.” Journal of Biomedical Optics 19, no. 3 (March 2014): 35005. https://doi.org/10.1117/1.jbo.19.3.035005.
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  - Horstmeyer, Roarke, and Changhuei Yang. “A phase space model of Fourier ptychographic microscopy.” Optics Express 22, no. 1 (January 2014): 338–58. https://doi.org/10.1364/oe.22.000338.
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  - Zheng, G., X. Ou, R. Horstmeyer, J. Chung, and C. Yang. “Fourier pt ychographic microscopy.” Optics and Photonics News 25, no. 4 (January 1, 2014): 26–33. https://doi.org/10.1364/OPN.25.4.000026.
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  - Horstmeyer, Roarke, Benjamin Judkewitz, Ivo M. Vellekoop, Sid Assawaworrarit, and Changhuei Yang. “Physical key-protected one-time pad.” Scientific Reports 3 (December 18, 2013): 3543. https://doi.org/10.1038/srep03543.
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  - Ou, Xiaoze, Roarke Horstmeyer, Changhuei Yang, and Guoan Zheng. “Quantitative phase imaging via Fourier ptychographic microscopy.” Optics Letters 38, no. 22 (November 2013): 4845–48. https://doi.org/10.1364/ol.38.004845.
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  - Zheng, Guoan, Roarke Horstmeyer, and Changhuei Yang. “Wide-field, high-resolution Fourier ptychographic microscopy.” Nature Photonics 7, no. 9 (September 2013): 739–45. https://doi.org/10.1038/nphoton.2013.187.
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  - Zheng, Guoan, Xiaoze Ou, Roarke Horstmeyer, and Changhuei Yang. “Characterization of spatially varying aberrations for wide field-of-view microscopy.” Optics Express 21, no. 13 (July 2013): 15131–43. https://doi.org/10.1364/oe.21.015131.
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  - Judkewitz, Benjamin, Ying Min Wang, Roarke Horstmeyer, Alexandre Mathy, and Changhuei Yang. “Speckle-scale focusing in the diffusive regime with time-reversal of variance-encoded light (TROVE).” Nature Photonics 7, no. 4 (April 2013): 300–305. https://doi.org/10.1038/nphoton.2013.31.
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  - Hollmann, Joseph L., Roarke Horstmeyer, Changhuei Yang, and Charles A. DiMarzio. “Analysis and modeling of an ultrasound-modulated guide star to increase the depth of focusing in a turbid medium.” Journal of Biomedical Optics 18, no. 2 (February 2013): 25004. https://doi.org/10.1117/1.jbo.18.2.025004.
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  - Kim, J., R. Horstmeyer, I. J. Kim, and R. Raskar. “Highlighted depth-of-field photography: Shining light on focus.” Acm Transactions on Graphics 30, no. 3 (May 1, 2011). https://doi.org/10.1145/1966394.1966403.
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  - Horstmeyer, Roarke, Se Baek Oh, and Ramesh Raskar. “Iterative aperture mask design in phase space using a rank constraint.” Optics Express 18, no. 21 (October 2010): 22545–55. https://doi.org/10.1364/oe.18.022545.
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  - Rubin, R. H., G. J. Ferland, E. E. Chollet, and R. Horstmeyer. “¹²C/¹³C ratio in planetary nebulae from the IUE archives.” Astrophysical Journal 605, no. 2 I (April 20, 2004): 784–92. https://doi.org/10.1086/382528.
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  - Horstmeyer, Roarke, Se Baek Oh, and Ramesh Raskar. “View-Dependent Displays and the Space of Light Fields,” n.d.
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  - Horstmeyer, Roarke, Sid Assawaworrarit, and Changhuei Yang. “Reconfigurable random bit storage using polymer-dispersed liquid crystal,” n.d.
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  - Ryu, Donghun, Zihao Wang, Kuan He, Roarke Horstmeyer, and Oliver Cossairt. “Subsampled Phase Retrieval for On-chip Lensless Holographic Video,” n.d.
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- Book Sections
  - Horstmeyer, R., I. M. Vellekoop, and B. Judkewitz. “Transmission matrix correlations.” In Wavefront Shaping for Biomedical Imaging, 1–14, 2019. https://doi.org/10.1017/9781316403938.014.
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- Conference Papers
  - Liu, W., R. Qian, S. Xu, P. C. Konda, and R. Horstmeyer. “Fast sensitive diffuse correlation spectroscopy with a SPAD array.” In Optics Infobase Conference Papers, Vol. Part F179-OTS-2020, 2020. https://doi.org/10.1364/OTS.2020.SM3D.3.
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  - Harfouche, M., T. W. Dunn, E. A. Naumann, and R. Horstmeyer. “Imaging the behavior and neural activity of freely moving organisms with a gigapixel microscope.” In Optics Infobase Conference Papers, Vol. Part F169-BRAIN 2019, 2019. https://doi.org/10.1364/BRAIN.2019.BT3A.3.
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  - Zhong, L., P. C. Konda, M. Harfouche, and R. Horstmeyer. “Depth tracking using a multi-aperture microscope.” In Optics Infobase Conference Papers, Vol. Part F170-COSI 2019, 2019. https://doi.org/10.1364/COSI.2019.CM1A.CTh4A.2.
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  - Wang, Z., D. Ryu, K. He, R. Horstmeyer, A. Katsaggelos, and O. Cossairt. “High-speed holographic imaging using compressed sensing and phase retrieval.” In Proceedings of Spie the International Society for Optical Engineering, Vol. 10222, 2017. https://doi.org/10.1117/12.2262737.
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  - Wang, Z., Q. Dai, D. Ryu, K. He, R. Horstmeyer, A. K. Katsaggelos, and O. Cossairt. “Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video.” In Optics Infobase Conference Papers, Vol. Part F46-COSI 2017, 2017. https://doi.org/10.1364/COSI.2017.CTu2B.3.
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  - Chung, Jaebum, Jinho Kim, Xiaoze Ou, Roarke Horstmeyer, and Changhuei Yang. “Simultaneous fluorescence and high-resolution bright-field imaging with aberration correction over a wide field-of-view with Fourier ptychographic microscopy (FPM) (Conference Presentation).” In Three Dimensional and Multidimensional Microscopy: Image Acquisition and Processing Xxiii. SPIE, 2016. https://doi.org/10.1117/12.2211974.
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  - Horstmeyer, R., S. Assawaworrarit, U. Ruhrmair, and C. Yang. “Physically secure and fully reconfigurable data storage using optical scattering.” In Proceedings of the 2015 Ieee International Symposium on Hardware Oriented Security and Trust, Host 2015, 157–62, 2015. https://doi.org/10.1109/HST.2015.7140255.
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  - Horstmeyer, R. “Volumetric phase imaging using Fourier ptychography.” In Optics Infobase Conference Papers, 2014. https://doi.org/10.1364/LSC.2016.LM4B.1.
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  - Hollmann, J. L., R. Horstmeyer, C. Yang, and C. A. DiMarzio. “A model for ultrasound modulated light in a turbid medium.” In Progress in Biomedical Optics and Imaging Proceedings of Spie, Vol. 8949, 2014. https://doi.org/10.1117/12.2041179.
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  - Horstmeyer, R., G. Zheng, X. Ou, and C. Yang. “Modeling extensions of fourier ptychographic microscopy.” In Microscopy and Microanalysis, 20:370–71, 2014. https://doi.org/10.1017/S1431927614003572.
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  - Horstmeyer, R., B. Judkewitz, I. Vellekoop, and C. Yang. “Secure storage of cryptographic keys within random volumetric materials.” In Cleo: Applications and Technology, Cleo at 2013, 2013.
  - Horstmeyer, R., B. Judkewitz, I. Vellekoop, and C. Yang. “Secure storage of cryptographic keys within random volumetric materials.” In 2013 Conference on Lasers and Electro Optics, Cleo 2013, 2013. https://doi.org/10.1364/cleo_at.2013.af1h.6.
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  - Yang, C., R. Horstmeyer, and G. Zheng. “Fourier ptychographic microscopy: A method for pushing standard microscope beyond its physical limitations.” In Asia Communications and Photonics Conference, Acp, 2013.
  - Yang, C., R. Horstmeyer, and G. Zheng. “Fourier ptychographic microscopy: A method for pushing standard microscope beyond its physical limitations.” In Asia Communications and Photonics Conference, Acp, 2013. https://doi.org/10.1364/acpc.2013.ath3j.4.
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  - Horstmeyer, Roarke, Richard Y. Chen, Benjamin Judkewitz, and Changhuei Yang. “Markov speckle for efficient random bit generation.” In Optics Express, 20:26394–410, 2012. https://doi.org/10.1364/oe.20.026394.
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  - Horstmeyer, R., S. B. Oh, O. Gupta, and R. Raskar. “Partially coherent ambiguity functions for depth-variant point spread function design.” In Progress in Electromagnetics Research Symposium, 267–72, 2011.
  - Cuypers, T., R. Horstmeyer, S. B. Oh, P. Bekaert, and R. Raskar. “Validity of Wigner distribution function for ray-based imaging.” In 2011 Ieee International Conference on Computational Photography, Iccp 2011, 2011. https://doi.org/10.1109/ICCPHOT.2011.5753129.
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  - Horstmeyer, R., and S. B. Oh. “Creating aperture masks in phase space.” In Optics Infobase Conference Papers, 2010.
  - Horstmeyer, R., G. Euliss, and R. Athale. “Flexible multimodal camera using a light field architecture.” In 2009 Ieee International Conference on Computational Photography, Iccp 09, 2009. https://doi.org/10.1109/ICCPHOT.2009.5559016.
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  - Horstmeyer, R., R. Athale, and G. Euliss. “Modified light field architecture for reconfigurable multimode imaging.” In Proceedings of Spie the International Society for Optical Engineering, Vol. 7468, 2009. https://doi.org/10.1117/12.828653.
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  - Morrison, R. L., R. A. Stack, G. W. Euliss, R. A. Athale, B. F. Necioglu, R. W. Horstmeyer, and C. Reese. “Dual-band imaging system based on a compact coaxial folded optic architecture.” In Optics Infobase Conference Papers, 2009.
  - Morrison, R. L., R. A. Stack, G. W. Euliss, R. A. Athale, B. F. Necioglu, R. W. Horstmeyer, and C. Reese. “Dual-band imaging system based on a compact coaxial folded optic architecture.” In Optics Infobase Conference Papers, 2009. https://doi.org/10.1364/cosi.2009.cwb6p.
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  - Horstmeyer, R., G. W. Euliss, R. A. Athale, R. L. Morrison, R. A. Stack, and J. Ford. “Pupil plane multiplexing for multi-domain imaging sensors.” In Proceedings of Spie the International Society for Optical Engineering, Vol. 7096, 2008. https://doi.org/10.1117/12.797772.
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Teaching & Mentoring
Recent Courses

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Duke Appointment History

Academic Positions Outside Duke

In the News

Subject Headings

Global Scholarship

Teaching

Fellowships, Supported Research, & Other Grants

External Relationships

Selected Publications

Academic Articles

Book Sections

Conference Papers

Recent Courses