Publications

Kreiss, L., S. Jiang, X. Li, S. Xu, K. C. Zhou, K. C. Lee, A. Mühlberg, et al. “Digital staining in optical microscopy using deep learning - a review.” PhotoniX 4, no. 1 (December 1, 2023). https://doi.org/10.1186/s43074-023-00113-4.

Wu, Melissa M., Roarke Horstmeyer, and Stefan A. Carp. “scatterBrains: an open database of human head models and companion optode locations for realistic Monte Carlo photon simulations.” Journal of Biomedical Optics 28, no. 10 (October 2023): 100501. https://doi.org/10.1117/1.jbo.28.10.100501.

Mühlberg, Alexander, Paul Ritter, Simon Langer, Chloë Goossens, Stefanie Nübler, Dominik Schneidereit, Oliver Taubmann, et al. “SEMPAI: a Self-Enhancing Multi-Photon Artificial Intelligence for Prior-Informed Assessment of Muscle Function and Pathology.” Advanced Science (Weinheim, Baden-Wurttemberg, Germany) 10, no. 28 (October 2023): e2206319. https://doi.org/10.1002/advs.202206319.

Bian, Liheng, Haoze Song, Lintao Peng, Xuyang Chang, Xi Yang, Roarke Horstmeyer, Lin Ye, et al. “High-resolution single-photon imaging with physics-informed deep learning.” Nature Communications 14, no. 1 (September 2023): 5902. https://doi.org/10.1038/s41467-023-41597-9.

Harfouche, M., K. Kim, K. C. Zhou, P. C. Konda, S. Sharma, E. E. Thomson, C. Cooke, et al. “Imaging across multiple spatial scales with the multi-camera array microscope.” Optica 10, no. 4 (April 1, 2023): 471–80. https://doi.org/10.1364/OPTICA.478010.

Yang, Xi, Mark Harfouche, Kevin C. Zhou, Lucas Kreiss, Shiqi Xu, Pavan Chandra Konda, Kanghyun Kim, and Roarke Horstmeyer. “Multi-modal imaging using a cascaded microscope design.” Optics Letters 48, no. 7 (April 2023): 1658–61. https://doi.org/10.1364/ol.471380.

Zhou, Kevin C., Mark Harfouche, Colin L. Cooke, Jaehee Park, Pavan C. Konda, Lucas Kreiss, Kanghyun Kim, et al. “Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second.” ArXiv, January 19, 2023.

Kreiss, L., K. Zhou, K. Kim, M. Harfouche, S. Xu, J. Jönsson, K. C. Lee, et al. “High-throughput imaging across multiple spatial scales with the multi-camera array microscope (MCAM).” In Proceedings of SPIE - The International Society for Optical Engineering, Vol. 12622, 2023. https://doi.org/10.1117/12.2675451.

Thomson, Eric E., Mark Harfouche, Kanghyun Kim, Pavan C. Konda, Catherine W. Seitz, Colin Cooke, Shiqi Xu, et al. “Gigapixel imaging with a novel multi-camera array microscope.” Elife 11 (December 14, 2022). https://doi.org/10.7554/eLife.74988.

Tomas Aidukas, Felix Wechsler, Lars Loetgering, Kevin Zhou, Roarke Horstmeyer, Applications and Extensions of Fourier Ptychography, Microscopy Today, Volume 30, Issue 6, 1 November 2022, Pages 40–45, https://doi.org/10.1017/S1551929522001298

Gigan, S., O. Katz, H. B. De Aguiar, E. R. Andresen, A. Aubry, J. Bertolotti, E. Bossy, et al. “Roadmap on wavefront shaping and deep imaging in complex media.” JPhys Photonics 4, no. 4 (October 1, 2022). https://doi.org/10.1088/2515-7647/ac76f9.

Cooke CL, Kim K, Xu S, Chaware A, Yao X, Yang X, et al. (2022) A multiple instance learning approach for detecting COVID-19 in peripheral blood smears. PLOS Digit Health 1(8): e0000078. https://doi.org/10.1371/journal.pdig.0000078

Ayaz, Hasan, Wesley B. Baker, Giles Blaney, David A. Boas, Heather Bortfeld, Kenneth Brady, Joshua Brake, et al. “Optical imaging and spectroscopy for the study of the human brain: status report.” Neurophotonics 9, no. Suppl 2 (August 2022): S24001. https://doi.org/10.1117/1.nph.9.s2.s24001.

Xu, Shiqi, Xi Yang, Wenhui Liu, Joakim Jönsson, Ruobing Qian, Pavan Chandra Konda, Kevin C. Zhou, et al. “Imaging Dynamics Beneath Turbid Media via Parallelized Single-Photon Detection.” Advanced Science (Weinheim, Baden-Wurttemberg, Germany) 9, no. 24 (August 2022): e2201885. https://doi.org/10.1002/advs.202201885.

Dai, Xiang, Shiqi Xu, Xi Yang, Kevin C. Zhou, Carolyn Glass, Pavan Chandra Konda, and Roarke Horstmeyer. “Quantitative Jones matrix imaging using vectorial Fourier ptychography.” Biomed Opt Express 13, no. 3 (March 1, 2022): 1457–70. https://doi.org/10.1364/BOE.448804.

Glass, Carolyn, Kyle J. Lafata, William Jeck, Roarke Horstmeyer, Colin Cooke, Jeffrey Everitt, Matthew Glass, David Dov, and Michael A. Seidman. “The Role of Machine Learning in Cardiovascular Pathology.” Can J Cardiol 38, no. 2 (February 2022): 234–45. https://doi.org/10.1016/j.cjca.2021.11.008.

Kevin C Zhou, Tomas Aidukas, Lars Loetgering, Felix Wechsler, Roarke Horstmeyer, Introduction to Fourier Ptychography: Part I, Microscopy Today, Volume 30, Issue 3, 1 May 2022, Pages 36–41, https://doi.org/10.1017/S1551929522000670

Xu, S., X. Yang, J. Jönsson, H. Chang, and R. Horstmeyer. “Speckle contrast diffuse correlation spectroscopy with parallelized single photon detection.” In Optics InfoBase Conference Papers, 2022.

Yao, Xing, Vinayak Pathak, Haoran Xi, Amey Chaware, Colin Cooke, Kanghyun Kim, Shiqi Xu, et al. “Increasing a microscope's effective field of view via overlapped imaging and machine learning.” Optics Express 30, no. 2 (January 2022): 1745–61. https://doi.org/10.1364/oe.445001.

Feiger, B., E. Lorenzana-Saldivar, C. Cooke, R. Horstmeyer, M. Bishawi, J. Doberne, G. C. Hughes, D. Ranney, S. Voigt, and A. Randles. “Evaluation of U-Net Based Architectures for Automatic Aortic Dissection Segmentation.” ACM Transactions on Computing for Healthcare 3, no. 1 (January 1, 2022). https://doi.org/10.1145/3472302.

Zhou, K. C., M. Harfouche, C. Cooke, J. Park, P. Konda, J. Doman, P. Reamey, et al. “Gigapixel-per-second, wide-field 3D topographic imaging with physics-supervised learning.” In Optics InfoBase Conference Papers, 2022.

Kim, K., K. C. Zhou, M. Harfouche, and R. Horstmeyer. “Parallelized 16-gigapixel microscopy for rapid imaging of multiple whole slides.” In Optics InfoBase Conference Papers, 2022.

Xu, S., X. Dai, X. Yang, K. C. Zhou, K. Kim, V. Pathak, C. Glass, and R. Horstmeyer. “Tensorial tomographic differential phase-contrast microscopy.” In IEEE International Conference on Computational Photography, ICCP 2022, 2022. https://doi.org/10.1109/ICCP54855.2022.9887674.

Xu, Shiqi, Wenhui Liu, Xi Yang, Joakim Jönsson, Ruobing Qian, Paul McKee, Kanghyun Kim, et al. “Transient Motion Classification Through Turbid Volumes via Parallelized Single-Photon Detection and Deep Contrastive Embedding.” Frontiers in Neuroscience 16 (January 2022): 908770. https://doi.org/10.3389/fnins.2022.908770.

YANG, X., P. C. KONDA, S. XU, L. BIAN, and R. HORSTMEYER. “Quantized Fourier ptychography with binary images from SPAD cameras.” Photonics Research 9, no. 10 (October 1, 2021): 1958–69. https://doi.org/10.1364/PRJ.427699.