Introduction to the Biophotonics Congress 2020 feature issue

Rainer A. Leitgeb, David Sampson, Regine Choe, Christine Hendon, Kevin Eliceiri, and James Tunnell

Biomed. Opt. Express 12(1), 509-510 (2021)  View: HTML | PDF

Applications of augmented reality in ophthalmology [Invited]

Güneş Aydındoğan, Koray Kavaklı, Afsun Şahin, Pablo Artal, and Hakan Ürey

Biomed. Opt. Express 12(1), 511-538 (2021)  View: HTML | PDF

Dual GRIN lens two-photon endoscopy for high-speed volumetric and deep brain imaging

Yu-Feng Chien, Jyun-Yi Lin, Po-Ting Yeh, Kuo-Jen Hsu, Yu-Hsuan Tsai, Shih-Kuo Chen, and Shi-Wei Chu

Biomed. Opt. Express 12(1), 162-172 (2021)  View: HTML | PDF  [Suppl. Mat. (2)]

Excitation-scanning hyperspectral video endoscopy: enhancing the light at the end of the tunnel

Craig M. Browning, Joshua Deal, Sam Mayes, Arslan Arshad, Thomas C. Rich, and Silas J. Leavesley

Biomed. Opt. Express 12(1), 247-271 (2021)  View: HTML | PDF

Lightsheet-based flow cytometer for whole blood with the ability for the magnetic retrieval of objects from the blood flow

Roman A. Verkhovskii, Anastasiia A. Kozlova, Olga A. Sindeeva, Ilya O. Kozhevnikov, Ekaterina S. Prikhozhdenko, Oksana A. Mayorova, Oleg V. Grishin, Mikhail A. Makarkin, Alexey V. Ermakov, Arkady S. Abdurashitov, Valery V. Tuchin, and Daniil N. Bratashov

Biomed. Opt. Express 12(1), 380-394 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Fundamental precision bounds for three-dimensional optical localization microscopy using self-interference digital holography

Abhijit Marar and Peter Kner

Biomed. Opt. Express 12(1), 20-40 (2021)  View: HTML | PDF

Linear diattenuation imaging of biological tissues with near infrared Mueller scanning microscopy

Matthieu Dubreuil, Florine Tissier, Sylvain Rivet, and Yann Le Grand

Biomed. Opt. Express 12(1), 41-54 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Hyperspectral microscopy combined with DAPI staining for the identification of hepatic carcinoma cells

Kunxing Liu, Sifan Lin, Siqi Zhu, Yao Chen, Hao Yin, Zhen Li, and Zhenqiang Chen

Biomed. Opt. Express 12(1), 173-180 (2021)  View: HTML | PDF

Artefact removal in ground truth deficient fluctuations-based nanoscopy images using deep learning

Suyog Jadhav, Sebastian Acuña, Ida S. Opstad, Balpreet Singh Ahluwalia, Krishna Agarwal, and Dilip K. Prasad

Biomed. Opt. Express 12(1), 191-210 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Comparative study of the influence of imaging resolution on linear retardance parameters derived from the Mueller matrix

Yuanxing Shen, Rongrong Huang, Honghui He, Shaoxiong Liu, Yang Dong, Jian Wu, and Hui Ma

Biomed. Opt. Express 12(1), 211-225 (2021)  View: HTML | PDF

Dynamic real-time subtraction of stray-light and background for multiphoton imaging

A. Fernández, A. Straw, M. Distel, R. Leitgeb, A. Baltuska, and A. J. Verhoef

Biomed. Opt. Express 12(1), 288-302 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Label-free imaging of fibroblast membrane interfaces and protein signatures with vibrational infrared photothermal and phase signals

Panagis D. Samolis, Daniel Langley, Breanna M. O’Reilly, Zay Oo, Geva Hilzenrat, Shyamsunder Erramilli, Allyson E. Sgro, Sally McArthur, and Michelle Y. Sander

Biomed. Opt. Express 12(1), 303-319 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Adaptive optics enables aberration-free single-objective remote focusing for two-photon fluorescence microscopy

Yuhan Yang, Wei Chen, Jiang Lan Fan, and Na Ji

Biomed. Opt. Express 12(1), 354-366 (2021)  View: HTML | PDF

Label-free and noninvasive method for assessing the metabolic status in type 2 diabetic rats with myocardium diastolic dysfunction

Kai Guo, Junxin Wu, Yawei Kong, Li Zhou, Wei Li, Yiyan Fei, Jiong Ma, and Lan Mi

Biomed. Opt. Express 12(1), 480-493 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Characterization of fibrillar collagen isoforms in infarcted mouse hearts using second harmonic generation imaging

Sushant P. Sahu, Qianglin Liu, Alisha Prasad, Syed Mohammad Abid Hasan, Qun Liu, Maria Ximena Bastidas Rodriguez, Orna Mukhopadhyay, David Burk, Joseph Francis, Supratik Mukhopadhyay, Xing Fu, and Manas Ranjan Gartia

Biomed. Opt. Express 12(1), 604-618 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Hyperspectral imaging and spectral unmixing for improving whole-body fluorescence cryo-imaging

Dennis Wirth, Brook Byrd, Boyu Meng, Rendall R. Strawbridge, Kimberley S. Samkoe, and Scott C. Davis

Biomed. Opt. Express 12(1), 395-408 (2021)  View: HTML | PDF

Uptake quantification of gold nanoparticles inside of cancer cells using high order image correlation spectroscopy

Delaram Katoozi, Andrew H. A. Clayton, David J. Moss, and James W. M. Chon

Biomed. Opt. Express 12(1), 539-552 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Deep-learning based multi-modal retinal image registration for the longitudinal analysis of patients with age-related macular degeneration

Tharindu De Silva, Emily Y. Chew, Nathan Hotaling, and Catherine A. Cukras

Biomed. Opt. Express 12(1), 619-636 (2021)  View: HTML | PDF

Detection of singlet oxygen luminescence for experimental corneal rose bengal photodynamic antimicrobial therapy

Jeffrey C. Peterson, Esdras Arrieta, Marco Ruggeri, Juan D. Silgado, Keenan J. Mintz, Ernesto H. Weisson, Roger M. Leblanc, Irene Kochevar, Fabrice Manns, and Jean-Marie Parel

Biomed. Opt. Express 12(1), 272-287 (2021)  View: HTML | PDF

Laser-induced corneal injury: validation of a computer model to predict thresholds

Mathieu Jean, Karl Schulmeister, David J. Lund, and Bruce E. Stuck

Biomed. Opt. Express 12(1), 336-353 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Positive role of the long luminescence lifetime of upconversion nanophosphors on resonant surfaces for ultra-compact filter-free bio-assays

Duc Tu Vu, Thanh-Thu Vu Le, Chia-Chen Hsu, Ngoc Diep Lai, Christophe Hecquet, and Henri Benisty

Biomed. Opt. Express 12(1), 1-19 (2021)  View: HTML | PDF

Systematic analysis of video-based pulse measurement from compressed videos

Ewa M. Nowara, Daniel McDuff, and Ashok Veeraraghavan

Biomed. Opt. Express 12(1), 494-508 (2021)  View: HTML | PDF

Maximum a posteriori signal recovery for optical coherence tomography angiography image generation and denoising

Lennart Husvogt, Stefan B. Ploner, Siyu Chen, Daniel Stromer, Julia Schottenhamml, A. Yasin Alibhai, Eric Moult, Nadia K. Waheed, James G. Fujimoto, and Andreas Maier

Biomed. Opt. Express 12(1), 55-68 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

OCT-OCTA segmentation: combining structural and blood flow information to segment Bruch’s membrane

Julia Schottenhamml, Eric M. Moult, Stefan B. Ploner, Siyu Chen, Eduardo Novais, Lennart Husvogt, Jay S. Duker, Nadia K. Waheed, James G. Fujimoto, and Andreas K. Maier

Biomed. Opt. Express 12(1), 84-99 (2021)  View: HTML | PDF

Intrinsic spectrally-dependent background in spectroscopic visible-light optical coherence tomography

Ian Rubinoff, Roman V. Kuranov, and Hao F. Zhang

Biomed. Opt. Express 12(1), 110-124 (2021)  View: HTML | PDF

Correction of circumferential and longitudinal motion distortion in high-speed catheter/endoscope-based optical coherence tomography

Tan Huu Nguyen, Osman Oguz Ahsen, Kaicheng Liang, Jason Zhang, Hiroshi Mashimo, and James G. Fujimoto

Biomed. Opt. Express 12(1), 226-246 (2021)  View: HTML | PDF

Vascular morphology and blood flow signatures for differential artery-vein analysis in optical coherence tomography of the retina

Tae-Hoon Kim, David Le, Taeyoon Son, and Xincheng Yao

Biomed. Opt. Express 12(1), 367-379 (2021)  View: HTML | PDF  [Suppl. Mat. (3)]

Optimizing 3D retinal vasculature imaging in diabetic retinopathy using registration and averaging of OCT-A

Arman Athwal, Chandrakumar Balaratnasingam, Dao-Yi Yu, Morgan Heisler, Marinko V. Sarunic, and Myeong Jin Ju

Biomed. Opt. Express 12(1), 553-570 (2021)  View: HTML | PDF  [Suppl. Mat. (2)]

Quantitative measurement of mechanical properties in wound healing processes in a corneal stroma model by using vibrational optical coherence elastography (OCE)

Yilong Zhang, Yuting Ling, Duo Zhang, Mingkai Wang, Christine Purslow, Ying Yang, Chunhui Li, and Zhihong Huang

Biomed. Opt. Express 12(1), 588-603 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Accurately motion-corrected Lissajous OCT with multi-type image registration

Shuichi Makita, Masahiro Miura, Shinnosuke Azuma, Toshihiro Mino, Tatsuo Yamaguchi, and Yoshiaki Yasuno

Biomed. Opt. Express 12(1), 637-653 (2021)  View: HTML | PDF

On-chip absorption spectroscopy enabled by graded index fiber tips

Kamalpreet K. Gill, Nicolas Riesen, Craig Priest, Nicholas Phillips, Bin Guan, and David G. Lancaster

Biomed. Opt. Express 12(1), 181-190 (2021)  View: HTML | PDF

Histopathology for Mohs micrographic surgery with photoacoustic remote sensing microscopy

Benjamin R. Ecclestone, Kevan Bell, Saad Abbasi, Deepak Dinakaran, Muba Taher, John R. Mackey, and Parsin Haji Reza

Biomed. Opt. Express 12(1), 654-665 (2021)  View: HTML | PDF

Single-wavelength water muted photoacoustic system for detecting physiological concentrations of endogenous molecules

Chao Xu, Shazzad Rassel, Steven Zhang, Abdulrahman Aloraynan, and Dayan Ban

Biomed. Opt. Express 12(1), 666-675 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Terahertz dielectric spectroscopy of human brain gliomas and intact tissues ex vivo: double-Debye and double-overdamped-oscillator models of dielectric response

A. A. Gavdush, N. V. Chernomyrdin, G. A. Komandin, I. N. Dolganova, P. V. Nikitin, G. R. Musina, G. M. Katyba, A. S. Kucheryavenko, I. V. Reshetov, A. A. Potapov, V. V. Tuchin, and K. I. Zaytsev

Biomed. Opt. Express 12(1), 69-83 (2021)  View: HTML | PDF

Light transport modeling in highly complex tissues using the implicit mesh-based Monte Carlo algorithm

Yaoshen Yuan, Shijie Yan, and Qianqian Fang

Biomed. Opt. Express 12(1), 147-161 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Direct measurement of the scattering coefficient

Martin Hohmann, Benjamin Lengenfelder, Daniel Muhr, Moritz Späth, Maximilian Hauptkorn, Florian Klämpfl, and Michael Schmidt

Biomed. Opt. Express 12(1), 320-335 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]

Direct mapping from diffuse reflectance to chromophore concentrations in multi-fx spatial frequency domain imaging (SFDI) with a deep residual network (DRN)

Yanyu Zhao, Yue Deng, Shuhua Yue, Ming Wang, Bowen Song, and Yubo Fan

Biomed. Opt. Express 12(1), 433-443 (2021)  View: HTML | PDF  [Suppl. Mat. (2)]

Effect of adipose tissue thickness and tissue optical properties on the differential pathlength factor estimation for NIRS studies on human skeletal muscle

Ileana Pirovano, Simone Porcelli, Rebecca Re, Lorenzo Spinelli, Davide Contini, Mauro Marzorati, and Alessandro Torricelli

Biomed. Opt. Express 12(1), 571-587 (2021)  View: HTML | PDF

Dual-DMD hyperspectral spatial frequency domain imaging (SFDI) using dispersed broadband illumination with a demonstration of blood stain spectral monitoring

Matthew B. Applegate, Samuel S. Spink, and Darren Roblyer

Biomed. Opt. Express 12(1), 676-688 (2021)  View: HTML | PDF  [Suppl. Mat. (2)]

Multi-layer Shack-Hartmann wavefront sensing in the point source regime

Vyas Akondi and Alfredo Dubra

Biomed. Opt. Express 12(1), 409-432 (2021)  View: HTML | PDF

Two-photon microperimetry with picosecond pulses

Marcin J. Marzejon, Łukasz Kornaszewski, Jakub Bogusławski, Piotr Ciąćka, Miłosz Martynow, Grażyna Palczewska, Sebastian Maćkowski, Krzysztof Palczewski, Maciej Wojtkowski, and Katarzyna Komar

Biomed. Opt. Express 12(1), 462-479 (2021)  View: HTML | PDF  [Suppl. Mat. (1)]