Anna Kreshuk

Anna Kreshuk is a computer scientist who applies machine learning to biological image analysis. She studied mathematics at Lomonosov Moscow State University, worked as a scientific programmer on CERN's ROOT framework, and completed a computer science PhD at Heidelberg University in 2012. At EMBL, her group develops ilastik for interactive bioimage analysis and methods for cell segmentation; in 2021, she contributed to a whole-animal atlas linking gene expression and cell morphology. She is a group leader and senior scientist at EMBL and has served as Interim Head of its Cell Biology and Biophysics Unit since 2024.

Now at: European Molecular Biology Laboratory

Timeline

2003–2008

Mathematics and CERN's ROOT

She earns a mathematics diploma at Lomonosov Moscow State University in 2003 and works at CERN from 2004 to 2007, then at the GSI Helmholtz Centre for Heavy Ion Research from 2007 to 2008. Between her degrees, she works at CERN as a scientific programmer for the ROOT framework.
2011

Automating synapse segmentation

In 2011, she coauthors a method for automated detection and segmentation of synapses in serial electron-microscopy images. The interactive machine-learning procedure needs only a few labeled synapses for training.
2012

A Heidelberg computer science PhD

She completes a computer science PhD at Heidelberg University's Heidelberg Collaboratory for Image Processing in 2012.
July 2018

Joining EMBL and building ilastik

She joins EMBL's Cell Biology and Biophysics Unit as a group leader in July 2018. Her group develops machine-learning methods for automated biological image analysis and the ilastik toolkit for interactive learning and segmentation.
2021

An atlas of a whole worm

In 2021, she works with an EMBL team on a Cell study that creates a multimodal atlas for the marine worm Platynereis dumerilii. The project combines electron microscopy with gene-expression data and uses machine learning to identify cell borders. In a 2021 seminar, she describes methods her team develops to segment all cells and nuclei in a volume of a six-day-old worm.
Since 2024

Leading EMBL's CBB unit

Since 2024, she serves as Interim Head of EMBL's Cell Biology and Biophysics Unit.
2025

An ELLIS Scholar

At the 2025 AI in Science Summit, ELLIS lists her as an ELLIS Scholar at EMBL.
As of October 2026

Leading the Kreshuk Group

As of October 2026, she is a Group Leader and Senior Scientist at EMBL and also serves as Interim Head of its Cell Biology and Biophysics Unit.