Patrick Lemaire

MorphoDeep improves 3D cell segmentation by learning cell interfaces and junctions, achieving higher accuracy and speed than existing methods.

MorphoNet 2.0 improves segmentation accuracy and interpretability for 3D time-lapse imaging datasets through self-evaluation and correction tools.

This paper introduces an automated framework for naming cells in ascidian embryos, revealing consistent and variable features of embryogenesis across species and conditions.

The paper uses single-cell sequencing data and statistical physics methods to identify collective modes of gene expression in early ascidian embryos.

This paper introduces a framework using spectral decomposition to automatically detect and time morphological processes in ascidian embryos from live imaging data.

The paper develops a mechanical atlas for ascidian gastrulation by integrating mathematical models with image data to map spatio-temporal mechanical stresses.

The paper identifies a Nodal/Eph signalling relay that controls the transition from apical constriction to apico-basal shortening during ascidian endoderm invagination, without affecting cell fate specification.

The paper investigates how contact-dependent cell communications maintain morphological invariance during ascidian embryogenesis despite genomic divergence.

This study investigates the evolution of cis-regulatory elements in Phallusia and Ciona ascidians, finding conserved regulatory logic and enhancer structures despite genomic divergence.

The paper shows that spacer sequences between transcription factor binding motifs influence enhancer activity and that randomizing these spacers can awaken dormant genomic clusters of TFBM.