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M. Applegate, K. Kose, S. Ghimire, M. Rajadhyaksha, J. Dy "Self-supervised denoising of Nyquist-sampled volumetric images via deep learning." J. of Medical Imaging, 2023.
M. Applegate, R. Amelard, C. Gomez, D. Roblyer, "Real-Time Handheld Probe Tracking and Image Formation Using Digital Frequency-Domain Diffuse Optical Spectroscopy." IEEE Trans Biomed Eng, 2021.
M. Applegate, S. Spink, D. Roblyer, "Dual-DMD hyperspectral spatial frequency domain imaging (SFDI) using dispersed broadband illumination with a demonstration of blood stain spectral monitoring." Biomed Opt Express, 2021.
M. B. Applegate, R. E. Istfan, S. Spink, A. Tank, and D. Roblyer, "Recent advances in high speed diffuse optical imaging in biomedicine", APL Photonics 5, 040802 (2020)
Applegate, M. B., Gómez, C. A., & Roblyer, D. M. (2021). Modulation frequency selection and efficient look-up table inversion for frequency domain diffuse optical spectroscopy. Journal of biomedical optics, 26(3), 036007.
D. Adams, A. Miller, M. Applegate, J. Cho, D. Hamilos, A. Chee, J. Holz, M. Szabari, L. Hariri, R. Harris, J. Griffith, A. Luster, B. Medoff, M. Suter, "Quantitative assessment of airway remodelling and response to allergen in asthma." Respirology, 2019.
L. Hariri, D. Adams, M. Applegate, A. Miller, B. Roop, M. Villiger, B. Bouma, M. Suter, "Distinguishing Tumor from Associated Fibrosis to Increase Diagnostic Biopsy Yield with Polarization-Sensitive Optical Coherence Tomography." Clin Cancer Res, 2019.
M. Applegate, Y. Zhao, R. Istfan, A. Pande, D. Roblyer, "Quantitative real-time pulse oximetry with ultrafast frequency-domain diffuse optics and deep neural network processing." Biomed Opt Express, 2018.
M. Applegate, D. Roblyer, "Multi-distance diffuse optical spectroscopy with a single optode via hypotrochoidal scanning." Opt Lett, 2018.
M. Applegate, D. Roblyer, "High-speed spatial frequency domain imaging with temporally modulated light." J Biomed Opt, 2017.
P. Tseng, B. Napier, S. Zhao, A. Mitropoulos, M. Applegate, B. Marelli, D. Kaplan, F. Omenetto, "Directed assembly of bio-inspired hierarchical materials with controlled nanofibrillar architectures." Nat Nanotechnol, 2017.
M. Landry, M. Applegate, O. Bushuyev, F. Omenetto, D. Kaplan, M. Cronin-Golomb, C. Barrett, "Photo-induced structural modification of silk gels containing azobenzene side groups." Soft Matter, 2017.
P. Tseng, S. Zhao, A. Golding, M. Applegate, A. Mitropoulos, D. Kaplan, F. Omenetto, "Evaluation of Silk Inverse Opals for "Smart" Tissue Culture." ACS Omega, 2017.
B. Partlow, M. Applegate, F. Omenetto, D. Kaplan, "Dityrosine Cross-Linking in Designing Biomaterials." ACS Biomater Sci Eng, 2016.
S. Zhao, Y. Chen, B. Partlow, A. Golding, P. Tseng, J. Coburn, M. Applegate, J. Moreau, F. Omenetto, D. Kaplan, "Bio-functionalized silk hydrogel microfluidic systems." Biomaterials, 2016.
M. B. Applegate, C. Alonzo, I. Georgakoudi, D. L. Kaplan, and F. G. Omenetto, "A simple model of multiphoton micromachining in silk hydrogels", Appl. Phys. Lett. 108, 241903 (2016)
M. Applegate, B. Partlow, J. Coburn, B. Marelli, C. Pirie, R. Pineda, D. Kaplan, F. Omenetto, "Photocrosslinking of Silk Fibroin Using Riboflavin for Ocular Prostheses." Adv Mater, 2016.
M. Applegate, G. Perotto, D. Kaplan, F. Omenetto, "Biocompatible silk step-index optical waveguides." Biomed Opt Express, 2015.
A. Mitropoulos, B. Marelli, C. Ghezzi, M. Applegate, B. Partlow, D. Kaplan, F. Omenetto, "Transparent, Nanostructured Silk Fibroin Hydrogels with Tunable Mechanical Properties." ACS Biomater Sci Eng, 2015.
M. Applegate, J. Coburn, B. Partlow, J. Moreau, J. Mondia, B. Marelli, D. Kaplan, F. Omenetto, "Laser-based three-dimensional multiscale micropatterning of biocompatible hydrogels for customized tissue engineering scaffolds." Proc Natl Acad Sci U S A, 2015.
B. Partlow, C. Hanna, J. Rnjak-Kovacina, J. Moreau, M. Applegate, K. Burke, B. Marelli, A. Mitropoulos, F. Omenetto, D. Kaplan, "Highly tunable elastomeric silk biomaterials." Adv Funct Mater, 2014.
M. Applegate, B. Marelli, D. Kaplan, F. Omenetto, "Determination of multiphoton absorption of silk fibroin using the Z-scan technique." Opt Express, 2013.
L. Hariri, M. Mino-Kenudson, M. Applegate, E. Mark, G. Tearney, M. Lanuti, C. Channick, A. Chee, M. Suter, "Toward the guidance of transbronchial biopsy: identifying pulmonary nodules with optical coherence tomography." Chest, 2013.
L. Hariri, M. Applegate, M. Mino-Kenudson, E. Mark, B. Medoff, A. Luster, B. Bouma, G. Tearney, M. Suter, "Volumetric optical frequency domain imaging of pulmonary pathology with precise correlation to histopathology." Chest, 2013.
L. Hariri, M. Villiger, M. Applegate, M. Mino-Kenudson, E. Mark, B. Bouma, M. Suter, "Seeing beyond the bronchoscope to increase the diagnostic yield of bronchoscopic biopsy." Am J Respir Crit Care Med, 2013.
L. Hariri, M. Applegate, M. Mino-Kenudson, E. Mark, B. Bouma, G. Tearney, M. Suter, "Optical frequency domain imaging of ex vivo pulmonary resection specimens: obtaining one to one image to histopathology correlation." J Vis Exp, 2013.
K. Tan, M. Shishkov, A. Chee, M. Applegate, B. Bouma, M. Suter, "Flexible transbronchial optical frequency domain imaging smart needle for biopsy guidance." Biomed Opt Express, 2012.
Talk at Biomedical Engineering Society Annual Meeting, Seattle, WA
Talk at Conference on Lasers and Electro Optics, San Jose, CA
Talk at Advanced Photonics Congress, Boston, MA
Talk at ECI Advances in Optics for Biotechnology, Snowmass, CO
Talk at SPIE Photonics West, San Francisco, CA
Talk at SPIE Photonics West, San Francisco, CA
Talk at OSA Biophotonics Congress: Biomedical Optics, Virtual
Talk at Photonics West, Virtual
Talk at Photonics West, Virtual