Publications

2026

1. Quantifying the spatio-temporal image degradation under motion blur in fluorescence microscopy

   Serafim Korovin , Kutay Ugurlu , Dylan Kalisvaart , and 4 more authors

   bioRxiv, 2026

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   A study of how motion blur degrades spatial information in fluorescence microscopy and how image-quality measures capture spatio-temporal trade-offs.

2. CLEAR-IT, a framework for contrastive learning to capture the immune composition of tumor microenvironments

   Daniel Spengler , Serafim Korovin , Kirti Prakash , and 4 more authors

   Communications Biology, 2026

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   A contrastive-learning framework for capturing immune composition in tumour microenvironments using multiplexed tissue images.

2025

1. Resolution in super-resolution microscopy–facts, artifacts, technological advancements and biological applications

   Kirti Prakash, David Baddeley , Christian Eggeling , and 7 more authors

   Journal of Cell Science, 2025

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   A perspective on the practical interpretation of resolution, artefacts, technological advances and biological applications in super-resolution microscopy.

2024

1. Resolution in super-resolution microscopy–definition, trade-offs and perspectives

   Kirti Prakash, David Baddeley , Christian Eggeling , and 7 more authors

   Nature Reviews Molecular Cell Biology, 2024

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   A viewpoint clarifying how resolution is defined and interpreted in super-resolution microscopy, including practical trade-offs in labelling, instrumentation and analysis.

2. Unraveling the Histone Code: Exploring the Dynamic Relationship Between DNA and Chromatin Structure in Epigenetic Signaling

   Kirti Prakash, and David Fournier

   In Epigenetics in Biological Communication, 2024

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3. Unveiling the limits of precision in iterative MINFLUX

   Carlas Smith , Dylan Kalisvaart , and Kirti Prakash

   Journal of Microscopy, 2024

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2023

1. Assessment of 3D MINFLUX data for quantitative structural biology in cells

   Kirti Prakash, and Alistair P. Curd

   Nature Methods, 2023

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   A reanalysis of 3D MINFLUX data for quantitative structural biology in cells, focusing on the interpretation of molecular-scale localisation data.

2. Correlative superresolution microscopy with deep UV reactivation

   Kirti Prakash

   Journal of Microscopy, 2023

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3. Opinions on imaging and cutting-edge developments in light microscopy for biomedical applications

   Kirti Prakash, Rainer Heintzmann , Uri Manor , and 1 more author

   Applied Physics Letters, 2023

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2022

1. Super-resolution microscopy: a brief history and new avenues

   Kirti Prakash, Benedict Diederich , Rainer Heintzmann , and 1 more author

   Philosophical Transactions of the Royal Society A, 2022

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2. Open microscopy in the life sciences: quo vadis?

   Johannes Hohlbein , Benedict Diederich , Barbora Marsikova , and 5 more authors

   Nature Methods, 2022

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   A community perspective on open microscopy, accessibility and the future of imaging in the life sciences.

3. At the molecular resolution with MINFLUX?

   Kirti Prakash

   Philosophical Transactions of the Royal Society A, 2022

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2021

1. Super-resolution structured illumination microscopy: past, present and future

   Kirti Prakash, Benedict Diederich , Stefanie Reichelt , and 2 more authors

   Philosophical Transactions of the Royal Society A, 2021

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   A review of structured illumination microscopy, its history, technical development and future directions.

2. Laser-free super-resolution microscopy

   Kirti Prakash

   Philosophical Transactions of the Royal Society A, 2021

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   A review of laser-free approaches for super-resolution microscopy and accessible optical imaging.

2020

1. Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

   Omer Ali Bayraktar , Theresa Bartels , Staffan Holmqvist , and 8 more authors

   Nature Neuroscience, 2020

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2019

1. Correlative STED and SMLM, without demons

   Kirti Prakash

   In Focus on Microscopy, 2019

2018

1. Evidence for the implication of the histone code in building the genome structure

   Kirti Prakash, and David Fournier

   Biosystems, 2018

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2017

1. Chromatin Architecture: Advances From High-resolution Single Molecule DNA Imaging

   Kirti Prakash

   Springer Nature, 2017

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2. Histone code and higher-order chromatin folding: A hypothesis

   Kirti Prakash, and David Fournier

   Genomics and Computational Biology, 2017

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2016

1. The periodic and dynamic structure of chromatin

   Kirti Prakash

   PhD thesis, 2016

2. Quantitative super-resolution localization microscopy of DNA in situ using Vybrant DyeCycle Violet fluorescent probe

   Dominika Zurek-Biesiada , Aleksander T. Szczurek , Kirti Prakash , and 7 more authors

   Data in Brief, 2016

2015

1. Localization microscopy of DNA in situ using Vybrant DyeCycle Violet fluorescent probe: A new approach to study nuclear nanostructure at single molecule resolution

   Dominika Zurek-Biesiada , Aleksander T. Szczurek , Kirti Prakash , and 6 more authors

   Experimental Cell Research, 2015

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2. A transient ischemic environment induces reversible compaction of chromatin

   Ina Kirmes , Aleksander Szczurek , Kirti Prakash , and 8 more authors

   Genome Biology, 2015

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3. Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes

   Kirti Prakash, David Fournier , Stefan Redl , and 8 more authors

   Proceedings of the National Academy of Sciences, 2015

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2014

1. Single molecule localization microscopy of the distribution of chromatin using Hoechst and DAPI fluorescent probes

   Aleksander T. Szczurek , Kirti Prakash, Hyun-Keun Lee , and 6 more authors

   Nucleus, 2014

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2012

1. A binary combinatorial histone code

   Kirti Prakash

   Master thesis, 2012