4D Life Sciences Seminar

Léo Guignard is a computational biologist from the Marseille Developmental Biology Institute in France, working at the interface of computer science and developmental biology. His research focuses on understanding how cells organize, communicate, and change over space and time during embryonic development. Thereby his Group addresses a fundamental question in developmental biology: how can an organism reliably build the same complex form despite the inherent variability of biological systems? To answer this question, he develops computational approaches that transform complex imaging and spatial data into quantitative descriptions of morphogenesis. By reconstructing development across space and time and comparing developmental trajectories between individuals and species, his research provides a quantitative framework for understanding how biological form emerges and how reproducible development really is.

In his talk 'A quantitative view of cell lineages' Léo Guignard will take you to the world of Lineage tracing, which has long been the holy grail for biologists aiming to unravel how a single cell develops into a complex organism. While John Sulston’s pioneered manual reconstruction of C. elegans lineages and showcased the potential of such complex dataset, modern acquisition systems, such as fluorescence light-sheet imaging, now generate terabyte-scale datasets for intricate organisms like zebrafish, mice, and Drosophila.
Recent years have seen major advances in algorithms for automatically or semi-automatically reconstructing cell lineages, producing highly complex spatio-temporal datasets. Yet, what has remained elusive are effective tools for manipulating, querying, and characterizing these datasets.
In his presentation, he will introduce lineagetree and napari-ReLAX (Reconstructed Lineages Analysis and eXploration), two open-source Python libraries designed for seamless, hassle-free exploration of any tracking dataset. He will then introduce the unordered constrained tree edit distance which allows to measure in an agnostic manner any two cell lineage trees (or tree-like structures). Finally, he will showcase the usefulness of this metric across multiple example in C. elegans, P. hawaiensis and other systems.