Dr Kirti Prakash

Kirti Prakash trained across computer science and biology, with an MSc from Aalto University, and a PhD from Heidelberg University. His doctoral research on DNA and chromatin architecture was nominated as an outstanding PhD thesis and later published by Springer Nature as Chromatin Architecture. He is an elected Fellow of the Royal Microscopical Society and has published in leading journals including Nature Methods, PNAS, Nature Neuroscience and Nature Reviews Molecular Cell Biology.

His research develops AI, machine learning and computational modelling approaches for high-dimensional scientific datasets, especially large-scale imaging, digital pathology, spatial transcriptomics and super-resolution microscopy. He has worked at the University of Cambridge, National Physical Laboratory, Institute of Cancer Research, Max Planck Institute, Royal Marsden Hospital, TU Delft, University of Edinburgh and MHRA.

Kirti welcomes opportunities to engage with students and researchers and collaborate on innovative, interdisciplinary projects. He is also pleased to hear from prospective PhD students and postdoctoral researchers interested in applying for international fellowship funding.

• English
• Hindi

• Nanoscale Bioimaging
• AI-Driven Mathematical Modelling
• Agency & Education Systems
• DNA & Chromatin Architecture

• Artificial Intelligence, Machine Learning and Semantic Technologies
• Programming and data analysis using Python, R and MATLAB
• Biomedical image analysis and advanced microscopy

• PhD in Biology, Ruprecht-Karls-Universität Heidelberg, Germany, 2016
• MSc (Tech.) in Computer Science, Aalto University with University of Helsinki, Finland, 2012

• Fellow of the Royal Microscopical Society (FRMS), elected 2022
• Royal Microscopical Society Ambassador
• Scientific Editor, Journal of Microscopy, Microscopy at a Glance poster article series, 2023 onwards
• Scientific Editor, Applied Physics Letters: Advances in Optical Microscopy for Bioimaging, 2023
• Scientific Editor, Philosophical Transactions of the Royal Society A, two special issues, 2021 and 2022
• Expert panel member, Fonds Wetenschappelijk Onderzoek Vlaanderen (FWO), Molecular and Cellular Biology, 2025
• Regular reviewer for journals including Nature Communications, PNAS, Scientific Reports, APL, Communications Biology, Journal of Microscopy and Philosophical Transactions

Spengler, D., Korovin, S., Prakash, K., Bankhead, P., Debets, R., Balcioglu, H. E., & Smith, C. 2026. CLEAR-IT, a framework for contrastive learning to capture the immune composition of tumor microenvironments. Communications Biology.

Prakash, K., Baddeley, D., Eggeling, C., Fiolka, R., Heintzmann, R., Manley, S., Radenovic, A., Smith, C., Shroff, H. and Schermelleh, L., 2024. Resolution in super-resolution microscopy: definition, trade-offs and perspectives. Nature Reviews Molecular Cell Biology.

Prakash, K. and Curd, A., 2023. Assessment of 3D MINFLUX data for quantitative structural biology in cells. Nature Methods.

Hohlbein, J., Diederich, B., Marsikova, B., Reynaud, E. G., Holden, S., Jahr, W., ... & Prakash, K. 2022. Open microscopy in the life sciences: quo Vadis? Nature Methods.

Prakash, K. 2021. Laser-free super-resolution microscopy. Philosophical Transactions of the Royal Society A.

Bayraktar, O. A., ..., Prakash, K., et al., 2020. Astrocyte layers in the mammalian cerebral cortex revealed by a single cell in situ transcriptomic map. Nature Neuroscience.

• Commentary quoted in Nature, “Making samples one billion times bigger lets simple microscopes pinpoint amino acids”, 2026.
• Commentary quoted in New Scientist, “Tiniest ruler ever measures distances as small as an atom’s width”, 2024.
• Public engagement through Microscopy Wonderland STEM Hub outreach talks, 2021.

Recent invited talks

• Pure Math’s in the Age of AI. University of Essex, Essex, UK
• Foundations of Causal Inference. Isaac Newton Institute for Mathematical Sciences, Cambridge, UK
• Physics of Life Summer School, Durham, UK
• Southampton Imaging Conference: Illuminating All Things Big and Small, UK
• ESRIC summer school, lecture and Hands-on Superresolution Workshop, University of Edinburgh, UK
• Lecture and Hands-on Superresolution Workshop, University of Leicester, UK

Conference organisation

• ORBIT: Organization of Genome in Space and Time, TU Delft, 2025
• Imaging ONEWORLD international online microscopy series, 2020-2023
• Royal Society SIMposium conference, 2021
• Next Generation Imaging workshop, CRUK Cambridge, 2019