Avinash Upadhya

Research Interests

Microscopy Optics

Avinash Upadhya

School of Biological Sciences

College of Science

Eligible to supervise Masters and PhD (as Co-Supervisor) - email supervisor to discuss availability.

Avinash is currently a post-doctoral researcher working across both the Centre of Light for Life as well as the Reproductive Success Group at the Robinson Research Institute. He focuses on developing gentle optical imaging techniques for long-term monitoring of various biological samples, from single cells, to oocytes and embryos. For this, he employs advanced methods such as Bessel beam two-photon light sheet microscopy, hyperspectral imaging, and innovative acquisition strategies like compressed sensing. Together with members from the Reproductive Success Group, he has developed novel optical instrumentation tailored to the study of the preimplantation mammalian embryo development. Avinash earned his PhD in 2023 at the John Curtin School of Medical Research, Australian National University. During his doctoral studies, he investigated novel optical strategies to structure light for single-particle tracking and live-cell imaging. His expertise includes coherent and fluorescence optical imaging and wavefront shaping.

Date Position Institution name
2022 - ongoing Postdoctoral Researcher University of Adelaide

Language Competency
English Can read, write, speak, understand spoken and peer review
Kannada Can read, write, speak and understand spoken

Date Institution name Country Title
Australian National University Australia Bachelor of Engineering (Research and Development)
Australian National University Australia Bachelor of Science

Year Citation
2025 Peterkovic, Z., Upadhya, A., Perrella, C., Bajraktarevic, A., Bautista Gonzalez, R. E., Lim, M., . . . Dholakia, K. (2025). Optimizing image capture for low-light widefield quantitative fluorescence microscopy. APL Photonics, 10(3), 031102-1-031102-28.
DOI Scopus3 WoS3
2024 Chow, D. J. X., Schartner, E. P., Corsetti, S., Upadhya, A., Morizet, J., Gunn-Moore, F. J., . . . Dholakia, K. (2024). Quantifying DNA damage following light sheet and confocal imaging of the mammalian embryo. Scientific Reports, 14(1), 20760-1-20760-12.
DOI Scopus6 WoS6 Europe PMC5
2024 Chow, D. J. X., Tan, T. C. Y., Upadhya, A., Lim, M., Dholakia, K., & Dunning, K. R. (2024). Viewing early life without labels: optical approaches for imaging the early embryo†. Biology of Reproduction, 110(6), 1157-1174.
DOI Scopus6 WoS6 Europe PMC4
2020 Zhang, Z., Zheng, Y., Xu, T., Upadhya, A., Lim, Y. J., Mathews, A., . . . Lee, W. M. (2020). Holo-UNet: hologram-to-hologram neural network restoration for high fidelity low light quantitative phase imaging of live cells. Biomedical Optics Express, 11(10), 5478-5487.
DOI Scopus30 WoS29 Europe PMC10
2019 Upadhya, A., Zheng, Y., Li, L., & Lee, W. M. (2019). Structured Back Focal Plane Interferometry (SBFPI). Scientific Reports, 9(1), 20273-1-20273-10.
DOI Scopus2 WoS2
2017 Humar, M., Upadhya, A., & Yun, S. H. (2017). Spectral reading of optical resonance-encoded cells in microfluidics. Lab on A Chip, 17(16), 2777-2784.
DOI Scopus25 WoS24 Europe PMC12
2016 Zhu, W., Eckerskorn, N., Upadhya, A., Li, L., Rode, A. V., & Lee, W. M. (2016). Dynamic axial control over optically levitating particles in air with an electrically-tunable variable-focus lens. Biomedical Optics Express, 7(7), 2902-2911.
DOI Scopus6 WoS6 Europe PMC1
2014 Lee, W. M., Upadhya, A., Reece, P. J., & Phan, T. G. (2014). Fabricating low cost and high performance elastomer lenses using hanging droplets. Biomedical Optics Express, 5(5), 1626-1635.
DOI Scopus84 WoS80 Europe PMC28

Year Citation
2022 Upadhya, A., Xu, T., Zhang, J., Lim, Y. J., Linnenberger, A., Mitchell, N., . . . Lee, W. M. (2022). Full-field imaging contrast with spatial interpixel light modulation for lightsheet. In Optics InfoBase Conference Papers. Online: Optica Publishing Group (formerly OSA).
2021 Upadhya, A., Zheng, Y., Li, L., & Lee, W. M. (2021). Extending tracking range through structured back focal plane interferometry. In Proceedings of SPIE - The International Society for Optical Engineering Vol. 11701 (pp. 8 pages). Online: SPIE.
DOI
2021 Zhang, J., Upadhya, A., Xu, T., Zhang, Z., & Lee, W. M. (2021). INEXPENSIVE IMMERSIVE DISPLAY FOR 3D IMAGING FLOW ASSAYS. In MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences (pp. 1541-1542).
2014 Lee, W. M., Upadhya, A., & Phan, T. (2014). Mobile microscopy on the move. In N. Sampat, R. Tezaur, S. Battiato, B. A. Fowler, T. G. Georgiev, F. H. Imai, . . . D. Wuller (Eds.), Proceedings of SPIE the International Society for Optical Engineering Vol. 9023 (pp. 7 pages). CA, San Francisco: SPIE-INT SOC OPTICAL ENGINEERING.
DOI

Year Citation
2019 Upadhya, A., Zheng, Y., Li, L., & Lee, W. M. (2019). Structured back focal plane interferometry (S-BFPI). Poster session presented at the meeting of Proceedings of SPIE 11202, Biophotonics Australasia. Bellingham, Washington: Society of Photo-optical Instrumentation Engineers.
DOI WoS1

Year Citation
- Dholakia, K., Hughes, E., & Upadhya, A. (n.d.). Supporting information for Figure 3.
DOI

Year Citation
2025 Monteiro, G. B., Lim, M., Tan, T. C. Y., Upadhya, A., Liang, Z., Agnew, B., . . . Dholakia, K. (2025). A neuromorphic camera for tracking passive and active matter with lower
data throughput.
2024 Peterkovic, Z., Upadhya, A., Perrella, C., Bajraktarevic, A., Gonzalez, R. B., Lim, M., . . . Dholakia, K. (2024). Optimising image capture for low-light widefield quantitative
fluorescence microscopy.
2023 Chow, D. J. X., Schartner, E. P., Corsetti, S., Upadhya, A., Morizet, J., Gunn-Moore, F. J., . . . Dholakia, K. (2023). Assessing DNA damage during optical imaging of the preimplantation embryo: a comparison between light sheet and confocal microscopy.
DOI

Date Role Research Topic Program Degree Type Student Load Student Name
2025 Co-Supervisor Optimisation of low-light quantum imaging with single-photon detectors and computational algorithms Doctor of Philosophy Doctorate Full Time Mr Admir Bajraktarevic
2024 Co-Supervisor Visualising images at depth using patterned illumination Doctor of Philosophy Doctorate Full Time Miss Emi Cora Valmai Hughes

Date Role Membership Country
2019 - ongoing Member Society of Photo-Optical Instrumentation Engineers Australia

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