Guillaume Jacquemet

PhenoMe: An interactive AI framework for interpretable, microscopy-driven phenotyping

PhenoMe provides an open-source framework for analyzing microscopy images using foundation model-derived embeddings and experimental metadata to enable phenotyping and data exploration.

Mapping bioimage-analysis software adoption in microscopy

The paper tracks the adoption of bioimage-analysis software across 1.7 million microscopy papers from 2010 to 2025, finding increased usage and concentration on general-purpose platforms like ImageJ/Fiji.

Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction

This study identifies two distinct mechanisms by which pancreatic cancer cells extravasate: protrusion-driven invasion and endothelial retraction, with implications for anti-metastatic strategies.

NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations

NucleiSky registers microscopy images across scales and modalities by aligning nuclei constellations, achieving accurate localization with minimal landmarks.

Scaffold protein SHANK3 regulates endothelial cell motility and tissue mechanics

This study shows SHANK3 regulates endothelial cell motility and tissue mechanics, affecting vascular development in zebrafish and mice.

Filopodia-mediated trans-endocytosis

The paper shows filopodia can penetrate neighboring cells to form impact sites that initiate trans-endocytosis, with internalized tips often being double-membraned and associated with endoplasmic reticulum.

Fast label-free live imaging reveals key roles of flow dynamics and CD44-HA interaction in cancer cell arrest on endothelial monolayers

This study uses fast label-free live imaging and deep learning to analyze cancer cell arrest on endothelial monolayers, finding CD44-HA interactions and flow dynamics are key factors.

PhotoFiTT: A Quantitative Framework for Assessing Phototoxicity in Live-Cell Microscopy Experiments

PhotoFiTT quantifies phototoxicity in live-cell microscopy by analyzing mitotic timing, cell size, and activity, showing near-UV light causes significant mitotic delays at low doses.

Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions

The paper identifies CCT8 as a MYO10 interactor critical for filopodia functions through proteomics and functional studies in cancer cells.

Customizable FDM-based zebrafish embryo mold for live imaging

The paper introduces a 3D-printed mold for zebrafish embryos to enable consistent live imaging by maintaining dorsoventral orientation.

Structural Repetition Detector: multi-scale quantitative mapping of molecular complexes through microscopy

The paper introduces SReD, an unsupervised framework for detecting repetitive biological structures in microscopy images, demonstrating its use on three datasets.

LSD1 serine 166 is a phosphorylation switch for chromatinlandscaping, gene activation, and tissue remodeling

This paper identifies S166 phosphorylation on LSD1 as a regulatory switch that controls gene activation, chromatin remodeling, and tumor microenvironment in non-hormonal cancer cells.

A subpopulation of Talin 1 resides in the nucleus and regulates gene expression

This study identifies a nuclear subpopulation of Talin 1 that regulates gene expression in human breast epithelial cells.

NanoPyx: super-fast bioimage analysis powered by adaptive machine learning

NanoPyx improves bioimage analysis speed using adaptive machine learning to optimize algorithm selection and execution.

CellTracksColab--A platform for compiling, analyzing, and exploring tracking data

CellTracksColab is a platform for compiling, analyzing, and exploring tracking data from biological movies, enabling holistic dataset analysis and identification of behavioral patterns.

Fast4DReg: Fast registration of 4D microscopy datasets

Fast4DReg corrects drift in 3D microscopy datasets using 2D cross-correlations, outperforming existing tools in speed and accuracy.

BioImage Model Zoo: A Community-Driven Resource for Accessible Deep Learning in BioImage Analysis

The BioImage Model Zoo provides a community standard, infrastructure, and open repository for sharing, testing, and deploying pre-trained deep learning microscopy models across multiple bioimage analysis tools.

Bringing TrackMate into the era of machine-learning and deep-learning.

Rewritten Fiji plugin TrackMate now uses StarDist, ilastik, Weka, MorphoLibJ or imported label images as detectors, stores 2D object contours, and tracks shape and intensity over time.

ZeroCostDL4Mic: an open platform to use Deep-Learning in Microscopy

ZeroCostDL4Mic provides a platform to use deep learning in microscopy, enabling tasks like segmentation and denoising through Google Colab.

Superresolution architecture of pluripotency guarding adhesions

The paper investigates the three-dimensional architecture of unique focal adhesions in human pluripotent stem cells and identifies structural features linked to pluripotency maintenance.