Introduction
Dr Kirti Prakash is an interdisciplinary scientist working at the interface of microscopy, artificial intelligence and biology. His work develops data-driven methods for microscopy, digital pathology, spatial genomics and translational science.
Research interests
Nanoscale Bioimaging
Super-resolution microscopy for cellular architecture, structural biomarkers, cancer biology and neurodegeneration.
02AI-Driven Mathematical Modelling
Interpretable AI, causal inference and mathematical models for biological, biomedical and regulatory systems.
03Agency & Education Systems
Human agency, free will, university rankings and mathematics education improvement.
04DNA & Chromatin Architecture
Genome folding, epigenetics, chromatin structure, ageing, cancer and neurodegenerative disease.
Background
Kirti 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.
His research develops AI, machine learning and computational modelling approaches for high-dimensional scientific datasets, including large-scale imaging, digital pathology, spatial transcriptomics and super-resolution microscopy. He is an elected Fellow of the Royal Microscopical Society.
Teaching
Qualifications
- PhD in Biology, Ruprecht-Karls-Universität Heidelberg, Germany, 2016
- MSc in Computer Science, Aalto University with University of Helsinki, Finland, 2012
Selected publications
- Spengler et al. 2026. CLEAR-IT, a framework for contrastive learning to capture the immune composition of tumor microenvironments. Communications Biology.
- Prakash et al. 2024. Resolution in super-resolution microscopy: definition, trade-offs and perspectives. Nature Reviews Molecular Cell Biology.
- Prakash and Curd. 2023. Assessment of 3D MINFLUX data for quantitative structural biology in cells. Nature Methods.
- Hohlbein et al. 2022. Open microscopy in the life sciences: quo Vadis? Nature Methods.
Professional service
- Fellow of the Royal Microscopical Society, elected 2022
- Scientific Editor, Journal of Microscopy, Microscopy at a Glance poster article series
- Scientific Editor, Applied Physics Letters, Advances in Optical Microscopy for Bioimaging
- Scientific Editor, Philosophical Transactions of the Royal Society A, two special issues
- Expert panel member, FWO Molecular and Cellular Biology, 2025
Talks and outreach
- Invited talks at Essex, Isaac Newton Institute, Durham and Southampton.
- Workshops and lectures in super-resolution microscopy at Edinburgh and Leicester.
- Commentary quoted in Nature and New Scientist.
Links
Contact
I welcome conversations with students, researchers, prospective PhD students, and postdoctoral researchers interested in fellowship routes.