Peer-reviewed Journal Papers

Complete list of publications is available in Google Scholar and ResearchGate.

2024

  1. Yiheng Lim, Shumpei Kojima, Pradipta Mukherjee, Ibrahim Abd El-Sadek, Shuichi Makita, and Yoshiaki Yasuno, “Developmental Imaging of Radish Sprouts Using Dynamic Optical Coherence Tomography,” Journal of Biophotonics, e202400254 (2024).

  2. Thitiya Seesan, Pradipta Mukherjee, Ibrahim Abd El-Sadek, Yiheng Lim, Lida Zhu, Shuichi Makita, and Yoshiaki Yasuno, “Optical-coherence-tomography-based deep-learning scatterer-density estimator using physically accurate noise model,” Biomedcal Optics Express, 15, 2832–2848 (2024).

  3. Ibrahim Abd El-Sadek, Rion Morishita, Tomoko Mori, Shuichi Makita, Pradipta Mukherjee, Satoshi Matsusaka, and Yoshiaki Yasuno, “Label-free visualization and quantification of the drug-type-dependent response of tumor spheroids by dynamic optical coherence tomography”, Scientific Reports 14, 3366 (2024).

  4. Lida Zhu, Shuichi Makita, Junya Tamaoki, Yiqiang Zhu, Pradipta Mukherjee, Yiheng Lim, Makoto Kobayashi, and Yoshiaki Yasuno, “Polarization-artifact reduction and accuracy improvement of Jones-matrix polarization-sensitive optical coherence tomography by multi-focus-averaging based multiple scattering reduction”, Biomedical Optics Express, 15, 256–276 (2024).

2023

  1. Pradipta Mukherjee, Shinichi Fukuda, Donny Lukmanto, Thi Hang Tran, Shuichi Makita, Ibrahim Abd El-Sadek, Yiheng Lim, and Yoshiaki Yasuno, “Renal tubular function and morphology revealed in kidney without labeling by three-dimensional dynamic optical coherence tomography”, Scientific Reports 13, 15324 (2023).

  2. Ibrahim Abd El-Sadek, Larina Tzu-Wei Shen, Tomoko Mori, Shuichi Makita, Pradipta Mukherjee, Antonia Lichtenegger, Satoshi Matsusaka, and Yoshiaki Yasuno, “Label-free drug response evaluation of human derived tumor spheroids using three-dimensional dynamic optical coherence tomography”, Scientific Reports 13, 15377 (2023).

  3. Kiriko Tomita, Shuichi Makita, Naoki Fukutake, Rion Morishita, Ibrahim Abd El-Sadek, Pradipta Mukherjee, Antonia Lichtenegger, Junya Tamaoki, Lixuan Bian, Makoto Kobayashi, Tomoko Mori, Satoshi Matsusaka and Yoshiaki Yasuno, “Theoretical model for enface optical coherence tomography imaging and its application to volumetric differential contrast imaging”, Biomedical Optics Express, 14, 3100–3124 (2023).

  4. Rion Morishita, Toshio Suzuki, Pradipta Mukherjee, Ibrahim Abd El-Sadek, Yiheng Lim, Antonia Lichtengger, Shuichi Makita, Kiriko Tomita, Yuki Yamamoto, Tetsuharu Nagamoto, and Yoshiaki Yasuno, “Label-free intratissue activity imaging of alveolar organoids with dynamic optical coherence tomography”, Biomedical Optics Express, 14, 2333-2351 (2023).

2022

  1. Pradipta Mukherjee, Shinichi Fukuda, Donny Lukmanto, Toshiharu Yamashita, Kosuke Okada, Shuichi Makita, Ibrahim Abd El-Sadek, Arata Miyazawa, Lida Zhu, Antonia Lichtenegger, Tetsuro Oshika, and Yoshiaki Yasuno, “Label-free metabolic imaging of non-alcoholic-fatty-liver-disease (NAFLD) liver by volumetric dynamic optical coherence tomography”, Biomedical Optics Express, 13, 4071-4086 (2022).

  2. Antonia Lichtenegger, Junya Tamaoki, Roxane Licandro, Tomoko Mori, Pradipta Mukherjee, Lixuan Bian, Shuichi Makita, Satoshi Matsusaka, Makoto Kobayashi, Bernhard Baumann, and Yoshiaki Yasuno, “Longitudinal investigation of a xenograft tumor zebrafish model using polarization-sensitive optical coherence tomography”, Scientific Reports 12, 15381 (2022).

  3. Lida Zhu, Shuichi Makita, Daisuke Oida, Arata Miyazawa, Kensuke Oikawa, Pradipta Mukherjee, Antonia Lichtenegger, Martin Distel, and Yoshiaki Yasuno, “Computational refocusing of Jones matrix polarization-sensitive optical coherence tomography and investigation of defocus-induced polarization artifacts”, Biomedical Optics Express, 13, 2975-2994 (2022).

  4. Antonia Lichtenegger, Pradipta Mukherjee, Lida Zhu, Rion Morishita, Kiriko Tomita, Daisuke Oida, Konrad Leskovar, Ibrahim Abd El-Sadek, Shuichi Makita, S. Kirchberger, Martin Distel, Bernhard Baumann, and Yoshiaki Yasuno, “Non-destructive characterization of adult zebrafish models using Jones matrix optical coherence tomography”, Biomedical Optics Express, 13, 2202-2223 (2022).

  5. Antonia Lichtenegger, Pradipta Mukherjee, Junya Tamaoki, Lixuan Bian, Lida Zhu, Ibrahim Abd El-Sadek, Shuichi Makita, Konrad Leskovar, Makoto Kobayashi, Bernhard Baumann, Yoshiaki Yasuno, “Multicontrast investigation of in vivo wildtype zebrafish in three development stages using polarization-sensitive optical coherence tomography”, Journal of Biomedical Optics 27, 016001 (2022).

  6. Thitiya Seesan, Ibrahim Abd El-Sadek, Pradipta Mukherjee, Lida Zhu, Kensuke Oikawa, Arata Miyazawa, Larina Tzu-Wei Shen, Satoshi Matsusaka, Prathan Buranasiri, Shuichi Makita, and Yoshiaki Yasuno, “Deep convolutional neural network-based scatterer density and resolution estimators in optical coherence tomography”, Biomedical Optics Express, 13, 168-183 (2022).

2021

  1. Ibrahim Abd El-Sadek, Arata Miyazawa, Larina Tzu-Wei Shen, Shuichi Makita, Pradipta Mukherjee, Antonia Lichtenegger, Satoshi Matsusaka, and Yoshiaki Yasuno, “Three-dimensional dynamics optical coherence tomography for tumor spheroid evaluation”, Biomedical Optics Express, 12, 6844-6863 (2021).

  2. Pradipta Mukherjee, Arata Miyazawa, Shinichi Fukuda, Toshiharu Yamashita, Donny Lukmanto, Kosuke Okada, Ibrahim Abd El-Sadek, Lida Zhu, Shuichi Makita, Tetsuro Oshika, and Yoshiaki Yasuno, “Label-free functional and structural imaging of liver microvascular complex in mice by Jones matrix optical coherence tomography”, Scientific Reports 11, 20054 (2021).

2020

  1. Ibrahim Abd El-Sadek, Arata Miyazawa, Larina Tzu-Wei Shen, Shuichi Makita, Shinichi Fukuda, Toshiharu Yamashita, Yuki Oka, Pradipta Mukherjee, Satoshi Matsusaka, Tetsuro Oshika, Hideki Kano, and Yoshiaki Yasuno, “Optical coherence tomography-based tissue dynamics imaging for longitudinal and drug response evaluation of tumor spheroids”, Biomedical Optics Express, 11, 6231-6248 (2020).

2019

  1. Pradipta Mukherjee, Tomohisa Horiguchi, Shuhei Shibata, Nathan Hagen, and Yukitoshi Otani, “Quantitative discrimination of biological tissues by micro-elastographic measurement using an epi-illumination Mueller matrix microscope”, Biomedical Optics Express, 10(8), 3847-3859 (2019).

  2. Pradipta Mukherjee, Nathan Hagen, and Yukitoshi Otani, “Glucose sensing in the presence of scattering by analyzing a partial Mueller matrix”, Optik, 180, 775-781 (2019).

  3. Pradipta Mukherjee, Shogo Ishida, Nathan Hagen, and Yukitoshi Otani, “Implementation of a complete Mueller matrix polarimeter using dual photoelastic modulators and rotating wave plates”, Optical Review, 26, 23-32 (2019).