Next-generation imaging for biology.

We work at the intersection of biophotonics, computational imaging, and deep learning to design the microscopes of the future.

Join Our Research

Meet the Team

The minds behind the research.

Current Members

Dr. Dushan N. Wadduwage

Dr. Dushan N. Wadduwage

Principal Investigator

Assistant Professor in Data Science, Computer Science, and Physics. Former John Harvard Distinguished Science Fellow.

Dineth Jayakody

Dineth Jayakody

Ph.D. Student

Researching on Computational Imaging, Computer Vision, and AI for Health.

Leonidas Zimianitis

Leonidas Zimianitis

Ph.D. Student

Researching on Differentiable Optics and Target-Agnostic Tracking.

Alumni

  • Mithunjha Anandakumar, Ph.D. Candidate, UIUC (Former Postbac Fellow)
  • Ramith Hettiarachchi, Ph.D. Student, CMU-Pitt (Former Postbac Fellow)
  • Jathurshan Pradeepkumar, Ph.D. Student, UIUC (Former Postbac Fellow)
  • Zhun Wei, Assistant Professor, Zhejiang Univ. (Former Postdoc)
  • Navodini Wijethilake, Ph.D. Student, King's College (Former PG Researcher)
  • Kithmini Herath, Ph.D. Student, UC Berkeley (Former Postbac Fellow)
  • Udith Haputhanthri, Ph.D. Student, Princeton (Former Research Asst.)
  • Hasindu Piyumantha, Ph.D. Student, Cornell (Former Postbac Fellow)
  • Ishan Baliyan, Undergraduate, Waterloo (Former High School Intern)
  • Liana Owen, (Former Undergrad Researcher)

Publications

  • 2026

  • Sharma, S., Zimianitis, L., Samanta, K., Ahluwalia, B. S., Joseph, J., & Wadduwage, D. N. (2026). Untrained Position-Encoded Multilayer Perceptron Network for Structured Illumination Microscopy Reconstruction. Chemical & Biomedical Imaging.
  • Kariyawasam, H., Hettiarachchi, R., Yang, Q., Matlock, A., Nambara, T., Kusaka, H., Kunai, Y., So, P.T., Boyden, E.S. & Wadduwage, D.N. (2026). QuATON: Quantization aware training of optical neurons. Optics Express, 34(1) (1-14).

  • 2025

  • Sivaroopan N., Galappaththige C. J., Ekanayake C., Watawana H., Rodrigo R., Edussooriya C. U.S. & Wadduwage, D. N.* (2025). Uncertainty Awareness Enables Efficient Labeling for Cancer Subtyping in Digital Pathology. IEEE/CVF Winter Conference on Applications of Computer Vision (WACV).

  • 2024

  • Xue, Y., Boivin, J. R., Wadduwage, D. N., Park, J. K., Nedivi, E., & So, P. T. (2024). Multiline orthogonal scanning temporal focusing (mosTF) microscopy for scattering reduction in in vivo brain imaging. Scientific Reports, 14(1) (10954).
  • Haputhanthri, U., Herath, K., Hettiarachchi, R., Kariyawasam, H., Ahmad, A., Ahluwalia, B. S., Acharya, G., Edussooriya, C. U., & Wadduwage, D. N.* (2024). Towards ultrafast quantitative phase imaging via differentiable microscopy. Biomedical Optics Express, 15(3) (1798-1812).

  • 2023

  • Wijethilake, N., Anandakumar, M., Zheng, C., So, P. T., Yildirim, M., & Wadduwage, D. N.* (2023). DEEP-squared: deep learning powered De-scattering with Excitation Patterning. Light: Science & Applications, 12(1) (228).
  • Das, S., Saxena, K., Tinguely, J.-C., Pal, A., Wickramasinghe, N. L., Khezri, A., Dubey, V., Ahmad, A., Perumal, V., & Ahmad, R. (2023). SERS nanowire chip and machine learning-enabled classification of wild-type and antibiotic-resistant bacteria at species and strain levels. ACS Applied Materials & Interfaces, 15(20) (24047-24058).
  • Arguello, H., Bacca, J., Kariyawasam, H., Vargas, E., Marquez, M., Hettiarachchi, R., Garcia, H., Herath, K., Haputhanthri, U., & Ahluwalia, B. S. (2023). Deep optical coding design in computational imaging: a data-driven framework. IEEE Signal Processing Magazine, 40(2) (75-88).
  • Ahmad, A., Hettiarachchi, R., Khezri, A., Singh Ahluwalia, B., Wadduwage, D. N., & Ahmad, R. (2023). Highly sensitive quantitative phase microscopy and deep learning aided with whole genome sequencing for rapid detection of infection and antimicrobial resistance. Frontiers in Microbiology, 14 (1154620).

  • 2021

  • Zheng, C., Park, J. K., Yildirim, M., Boivin, J. R., Xue, Y., Sur, M., So, P. T., & Wadduwage, D. N.* (2021). De-scattering with excitation patterning enables rapid wide-field imaging through scattering media. Science Advances, 7(28) (eaay5496).
  • Kay, J. E., Mirabal, S., Briley, W. E., Kimoto, T., Poutahidis, T., Ragan, T., So, P. T., Wadduwage, D. N., Erdman, S. E., & Engelward, B. P. (2021). Analysis of mutations in tumor and normal adjacent tissue via fluorescence detection. Environmental and molecular mutagenesis, 62(2) (108-123).
  • Kay, J. E., Corrigan, J. J., Armijo, A. L., Nazari, I. S., Kohale, I. N., Torous, D. K., Avlasevich, S. L., Croy, R. G., Wadduwage, D. N., & Carrasco, S. E. (2021). Excision of mutagenic replication-blocking lesions suppresses cancer but promotes cytotoxicity and lethality in nitrosamine-exposed mice. Cell reports, 34(11).

  • 2020

  • Agbleke, A. A., Amitai, A., Buenrostro, J. D., Chakrabarti, A., Chu, L., Hansen, A. S., Koenig, K. M., Labade, A. S., Liu, S., & Nozaki, T. (2020). Advances in chromatin and chromosome research: perspectives from multiple fields. Molecular cell, 79(6) (881-901).

  • 2019

  • Coucheron, D. A., Wadduwage, D. N., Murugan, G. S., So, P. T., & Ahluwalia, B. S. (2019). Chip-based resonance Raman spectroscopy using tantalum pentoxide waveguides. IEEE Photonics Technology Letters, 31(14) (1127-1130).

  • 2018

  • Xue, Y., Berry, K. P., Boivin, J. R., Wadduwage, D., Nedivi, E., & So, P. T. (2018). Scattering reduction by structured light illumination in line-scanning temporal focusing microscopy. Biomedical Optics Express, 9(11) (5654-5666).
  • Wadduwage, D. N.*, Kay, J., Singh, V. R., Kiraly, O., Sukup-Jackson, M. R., Rajapakse, J., Engelward, B. P., & So, P. T. (2018). Automated fluorescence intensity and gradient analysis enables detection of rare fluorescent mutant cells deep within the tissue of RaDR mice. Scientific Reports, 8(1) (12108).

  • 2017

  • Wadduwage, D. N., Singh, V. R., Choi, H., Yaqoob, Z., Heemskerk, H., Matsudaira, P., & So, P. T. (2017). Near-common-path interferometer for imaging Fourier-transform spectroscopy in wide-field microscopy. Optica, 4(5) (546-556).

  • 2015

  • Choi, H., Wadduwage, D. N., Tu, T. Y., Matsudaira, P., & So, P. T. (2015). Three‐dimensional image cytometer based on widefield structured light microscopy and high‐speed remote depth scanning. Cytometry Part A, 87(1) (49-60).
  • Wadduwage, D. N., Parrish, M., Choi, H., Engelward, B. P., Matsudaira, P., & So, P. T. (2015). Subnuclear foci quantification using high-throughput 3D image cytometry. European Conference on Biomedical Optics.

  • 2014

  • Sukup-Jackson, M. R., Kiraly, O., Kay, J. E., Na, L., Rowland, E. A., Winther, K. E., Chow, D. N., Kimoto, T., Matsuguchi, T., & Jonnalagadda, V. S. (2014). Rosa26-GFP direct repeat (RaDR-GFP) mice reveal tissue-and age-dependence of homologous recombination in mammals in vivo. PLoS genetics, 10(6) (e1004299).
  • Choi, H., Wadduwage, D., Matsudaira, P. T., & So, P. T. (2014). Depth resolved hyperspectral imaging spectrometer based on structured light illumination and Fourier transform interferometry. Biomedical Optics Express, 5(10) (3494-3507).

Patents

  • Wadduwage, D.N., Harvard University, 2024. "Randomized Machine-learning Framework for Image-based Biomarker Discovery" (Provisional Patent Applied).
  • Wadduwage, D.N., Kanaththage, H.P., Haputhanthri, U., Harvard University, 2024. "Differentiable Optical Processors" (Patent Applied).
  • So, P.T., Yaqoob, Z., Lyzwa, D., Singh, V. and Wadduwage, D.N., MIT 2021. Phase Cancellation Microscopy. U.S. Patent Application 17/140,558 (Patent Granted).
  • Park, J.K., Wadduwage, D.N., Xue, Y., Nedivi, E., So, P.T., Rowlands, C. and Berry, K., MIT, 2020. Systems and Methods to Reduce Scattering in Temporal Focusing Multiphoton Microscopy. U.S. Patent Application 16/844,323 (Patent Granted).

Funding