Virginie Uhlmann

Shield-4i: A Whole-mount Multiplexed Imaging Platform for Studying Multiscale Information Flow in 3D Multicellular Systems

Shield-4i enables high-throughput, subcellular-resolution imaging of whole-mount structures to study multiscale information flow in multicellular systems.

Spatial atlas of the ovary identifies molecular events in primordial follicle activation in humans

This study creates a comprehensive spatial atlas of the human ovarian cortex, revealing molecular mechanisms of primordial follicle activation and follicle niche organization.

Topology-aware reconstruction of cellular state landscapes from microscopy using self-supervised learning

The paper introduces SI-SimCLR, a self-supervised learning framework for reconstructing cellular phenotypic landscapes from microscopy data without segmentation or annotation, revealing substate organization and connections in astrocytes.

Fractal: Towards FAIR bioimage analysis at scale with OME-Zarr-native workflows

Fractal introduces a task specification and platform for scalable, reproducible OME-Zarr-native bioimage analysis workflows, demonstrating reproducibility across diverse imaging data and clinical settings.

Residual ellipticity in waveplate-compensated polarization-resolved SHG microscopy may arise from femtosecond laser spectral bandwidth

This study investigates residual polarization ellipticity in waveplate-compensated polarization-resolved SHG microscopy and identifies femtosecond laser spectral bandwidth as a potential cause.

An improved neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens

DeepTangleCrawl, DeepTangle retrained for crawling C. elegans, skeletonises more coiled and overlapping worms than Tierpsy, Omnipose or a PAF tracker, with longer tracks and larger screen effect sizes than Tierpsy.

Temporal variability and cell mechanics control robustness in mammalian embryogenesis

The paper shows that stochastic division timing and cell mechanics contribute to robust embryo patterning and morphogenesis in mammals.

Simulating structurally variable Nuclear Pore Complexes for Microscopy

The paper introduces a simulation pipeline to generate structurally variable synthetic NPCs for benchmarking image analysis methods and understanding NPC variability in SMLM data.

COORDINATION BETWEEN EMBRYO GROWTH AND TROPHOBLAST MIGRATION UPON IMPLANTATION DELINEATES MOUSE EMBRYOGENESIS

This study develops an engineered uterus-like microenvironment to study mouse embryo implantation, revealing coordination between trophoblast migration and embryo growth.

MorphoFeatures: unsupervised exploration of cell types, tissues and organs in volume electron microscopy

The paper introduces an unsupervised method to extract morphological features from 3D EM data, enabling cell type and tissue organization analysis in a segmented worm.

SplineDist: Automated Cell Segmentation with Spline Curves

SplineDist improves cell segmentation by using spline curves instead of star-convex polygons, achieving comparable quality with a smaller network and better handling of complex shapes.

A Learning-Based Formulation of Parametric Curve Fitting for Bioimage Analysis

This paper introduces a convolutional neural network to predict continuous parametric representations of biological object outlines, tested on cell nucleus images from a public dataset.

FlyLimbTracker: an active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila

The paper introduces FlyLimbTracker, a method for semi-automatically tracking leg segments in unmarked Drosophila, showing robustness across video resolutions and behaviors.