Publications

Cooke, Colin L., Kanghyun Kim, Shiqi Xu, Amey Chaware, Xing Yao, Xi Yang, Jadee Neff, et al. “Deep Optical Blood Analysis: COVID-19 Detection as a Case Study in Next Generation Blood Screening.” Cold Spring Harbor Laboratory, July 22, 2021. https://doi.org/10.1101/2021.07.18.21259553.

Vu, T., A. DiSpirito, D. Li, Z. Wang, X. Zhu, M. Chen, L. Jiang, et al. “Deep image prior for undersampling high-speed photoacoustic microscopy.” Photoacoustics 22 (June 1, 2021). https://doi.org/10.1016/j.pacs.2021.100266.

Fontes, Cassio M., Barbara D. Lipes, Jason Liu, Krystle N. Agans, Aiwei Yan, Patricia Shi, Daniela F. Cruz, et al. “Ultrasensitive point-of-care immunoassay for secreted glycoprotein detects Ebola infection earlier than PCR.” Sci Transl Med 13, no. 588 (April 7, 2021). https://doi.org/10.1126/scitranslmed.abd9696.

Liu, W., R. Qian, S. Xu, P. Chandra Konda, J. Jönsson, M. Harfouche, D. Borycki, et al. “Fast and sensitive diffuse correlation spectroscopy with highly parallelized single photon detection.” APL Photonics 6, no. 2 (February 1, 2021). https://doi.org/10.1063/5.0031225.

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 2021): 562–70. https://doi.org/10.1109/tmi.2020.3031541.

Cooke, C. L., F. Kong, A. Chaware, K. C. Zhou, K. Kim, R. Xu, D. M. Ando, S. J. Yang, P. C. Konda, and R. Horstmeyer. “Physics-Enhanced Machine Learning for Virtual Fluorescence Microscopy.” In Proceedings of the IEEE International Conference on Computer Vision, 3783–93, 2021. https://doi.org/10.1109/ICCV48922.2021.00378.

Yao, X., H. Xi, K. C. Zhou, A. Chaware, C. Cooke, Y. Li, T. Dunn, P. C. Konda, and R. Horstmeyer. “Increasing a microscope’s effective field of view via overlapped imaging and machine learning.” Optics InfoBase Conference Papers, January 1, 2021.

Sharma, S., A. Bègue, J. Doman, M. Harfouche, G. Horstmeyer, and R. Horstmeyer. “High throughput acquisition and analysis of bacterial colony features using gigapixel microscopy.” In Optics InfoBase Conference Papers, 2021.

Xu, S., X. Yang, P. C. Konda, and R. Horstmeyer. “Rapid imaging of deep-tissue motion with parallelized diffuse correlation spectroscopy.” In Optics InfoBase Conference Papers, 2021.

Zhou, K. C., C. Cooke, J. Park, R. Qian, R. Horstmeyer, J. A. Izatt, and S. Farsiu. “Mesoscopic photogrammetry with an unstabilized phone camera.” In Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 7531–41, 2021. https://doi.org/10.1109/CVPR46437.2021.00745.

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.

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.

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.

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.

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.

Loetgering, Lars, Margarita Baluktsian, Kahraman Keskinbora, Roarke Horstmeyer, Thomas Wilhein, Gisela Schütz, Kjeld S. E. Eikema, and Stefan Witte. “Generation and characterization of focused helical x-ray beams.” Science Advances 6, no. 7 (February 2020): eaax8836. https://doi.org/10.1126/sciadv.aax8836.

Dai, X., P. C. Konda, S. Xu, and R. W. Horstmeyer. “Towards a vectorial treatment of Fourier ptychographic microscopy.” In Optics InfoBase Conference Papers, 2020.

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.

Liu, W., S. Xu, R. Qian, P. C. Konda, and R. Horstmeyer. “Classifying decorrelation events hidden beneath scattering media via SPAD array detection.” In Optics InfoBase Conference Papers, 2020.

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.

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.

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.

Horstmeyer, R., I. M. Vellekoop, and B. Judkewitz. “Transmission matrix correlations.” In Wavefront Shaping for Biomedical Imaging, 315–28, 2019. https://doi.org/10.1017/9781316403938.014.

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.

Horstmeyer, Roarke, Richard Y. Chen, Barbara Kappes, and Benjamin Judkewitz. “Convolutional neural networks that teach microscopes how to image,” September 21, 2017.