Publications de Olivier Burri | EPFL Graph Search

Development of image analysis tool to evaluate Langerhans cell migration after exposure to isothiazolinones

Incidence of allergic contact dermatitis (ACD) is rising worldwide as a consequence of raising chemical exposure, especially from biocides present in common water-based products such as cosmetics and household products. Understanding the biological process ...

SPRINGER HEIDELBERG2025

Injury-induced intestinal stem cell renewal requires capillary morphogenesis gene 2

Béatrice Kunz, Olivier Burri, Françoise Gisou van der Goot Grunberg, Nathalie Brandenberg, Julien Léonard Duc, Romain Guiet, Audrey Geneviève Chuat, Lucie Josepha Marie Bracq

Patients with the rare genetic disorder Hyaline Fibromatosis Syndrome (HFS) often succumb before 18 months of age due to severe diarrhea. As HFS is caused by loss-of-function mutations in the gene encoding capillary morphogenesis gene 2 (CMG2), these sympt ...

Springer Science and Business Media LLC2025

Cellpose training data and scripts from "Inhibition of CERS1 in aging skeletal muscle exacerbates age-related muscle impairments"

Olivier Burri, Johan Auwerx, Martin Rainer Wohlwend

This Workflow contains all the material necessary to reproduce the results of the QuPath analysis performed in the paper "Inhibition of CERS1 in aging skeletal muscle exacerbates age-related muscle impairments" Inside this workflow and dataset, you will f ...

Zenodo2024

Cell density quantification of high resolution Nissl images of the juvenile rat brain

Henry Markram, Olivier Burri, Rodrigo de Campos Perin, Julie Meystre, Daniel Keller, Ying Shi

Copyright © 2024 Meystre, Jacquemier, Burri, Zsolnai, Frank, Vieira, Shi, Perin, Keller and Markram.Nissl histology underpins our understanding of brain anatomy and architecture. Despite its importance, no high-resolution datasets are currently available i ...

2024

Supplementary files for Machine learning for histological annotation and quantification of cortical layers

Olivier Burri, Julie Meystre

Creators Meystre Julie Olivier Burri Contributors Jean Jacquemier Description This dataset contains 7 QuPath projects. The raw data images linked to these projects and located in other Zenodo datasets need to be downloaded as well. The raw data contains im ...

Zenodo2024

Optical imaging of the small intestine immune compartment across scales

Olivier Burri, Aleksandra Radenovic, Arielle Louise Planchette, Alessio Mylonas

The limitations of 2D microscopy constrain our ability to observe and understand tissue-wide networks that are, by nature, 3-dimensional. Optical projection tomography (OPT) enables the acquisition of large volumes (ranging from micrometres to centimetres) ...

NATURE PORTFOLIO2023

Inhibition of CERS1 in skeletal muscle exacerbates age-related muscle dysfunction

Olivier Burri, Johan Auwerx, Giacomo Vincenzo Giorgio Von Alvensleben, Pirkka-Pekka Untamo Laurila, Martin Rainer Wohlwend, Xiaoxu Li, Ludger Jan Elzuë Goeminne, Amélia Lalou, Tanes Imamura de Lima, Barbara Moreira Crisol, Renata Mangione

Age-related muscle wasting and dysfunction render the elderly population vulnerable and incapacitated, while underlying mechanisms are poorly understood. Here, we implicate the CERS1 enzyme of the de novo sphingolipid synthesis pathway in the pathogenesis ...

2023

MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology

Olivier Burri, Giovanna Ambrosini, Bart Deplancke, Arne Seitz, Olaia Maria Naveiras Torres-Quiroga, Frédérica Schyrr, Rita Sarkis, Mariangela Costanza, Martin Weigert

2023

Sphingolipids control dermal fibroblast heterogeneity

Olivier Burri, Sylvia Ho, Romain Guiet, Galina Glousker, Giovanni D'Angelo, Laura Capolupo, Gioele La Manno, Alex Russell Lederer, Irina Khven

Human cells produce thousands of lipids that change during cell differentiation and can vary across individual cells of the same type. However, we are only starting to characterize the function of these cell-to-cell differences in lipid composition. Here, ...

American Association for the Advancement of Science2022

Measuring reporter activity domain in EPI aggregates and Gastruloids.ijm

Matthias Lütolf, Olivier Burri, Romain Guiet, Mehmet Ugur Girgin

This imagej macro analyses the reporter intensity activity and expression domain in EPI aggregates and Gastruloids. ...

Zenodo2022

An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix

Olivier Burri, Jessica Sordet, Arne Seitz, Romain Guiet, Nicolas René Chiaruttini

Image analysis workflows for Histology increasingly require the correlation and combination of measurements across several whole slide images. Indeed, for multiplexing, as well as multimodal imaging, it is indispensable that the same sample is imaged multi ...

FRONTIERS MEDIA SA2022

Miniature neurotransmission is required to maintain Drosophila synaptic structures during ageing

Olivier Burri, Evelyne Ruchti, Brian Donal McCabe, Wei Jiao, Soumya Banerjee, Samuel William Vernon

The decline of neuronal synapses is an established feature of ageing accompanied by the diminishment of neuronal function, and in the motor system at least, a reduction of behavioural capacity. Here, we have investigated Drosophila motor neuron synaptic te ...

Nature Research2021

Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features

Michaël Unser, Daniel Sage, Olivier Burri, Cathrin Brisken, Quentin Juppet, Fabio De Martino, Martin Weigert

Patient-Derived Xenografts (PDXs) are the preclinical models which best recapitulate inter- and intra-patient complexity of human breast malignancies, and are also emerging as useful tools to study the normal breast epithelium. However, data analysis gener ...

2021

Biotin-NeutrAvidin Mediated Immobilization of Polymer Micro- and Nanoparticles on T Lymphocytes

Harm-Anton Klok, Olivier Burri, Maxime Ayer, Arne Seitz, Romain Guiet

Cells are powerful carriers that can help to improve the delivery of nanomedicines. One approach to use cells as carriers is to immobilize the nanoparticulate cargo on the cell surface. While a plethora of chemical conjugation strategies are available to b ...

2021

Cellpose training data and scripts from "Machine learning for histological annotation and quantification of cortical layers"

Olivier Burri, Julie Meystre

This Workflow contains all the material necessary to reproduce the cells detection, thanks to the QuPath performed in the paper "Machine learning for histological annotation and quantification of cortical layers" Inside this workflow and dataset, you wi ...

Zenodo2021

T Cell-Mediated Transport of Polymer Nanoparticles across the Blood-Brain Barrier

Harm-Anton Klok, Olivier Burri, Maxime Ayer, Arne Seitz, Romain Guiet, Markus Schuster

Delivery of therapeutics to the central nervous system (CNS) is challenging due to the presence of the blood-brain barrier (BBB). Amongst various approaches that have been explored to facilitate drug delivery to the CNS, the use of cells that have the intr ...

WILEY2020

MarrowQuantAcross Aging and Aplasia: A Digital Pathology Workflow for Quantification of Bone Marrow Compartments in Histological Sections

Nicolas Kunz, Olivier Burri, Olaia Maria Naveiras Torres-Quiroga, Vasco Ledebur de Antas de Campos, Chiheb Boussema, Frédérica Schyrr, Josefine Catharina Pedersen Tratwal, Shanti Rojas-Sutterlin, Rita Sarkis, Daniel Naveed Tavakol

The bone marrow (BM) exists heterogeneously as hematopoietic/red or adipocytic/yellow marrow depending on skeletal location, age, and physiological condition. Mouse models and patients undergoing radio/chemotherapy or suffering acute BM failure endure rapi ...

2020

MarrowQuant across Aging and Aplasia: A Digital Pathology Tool for Quantification of Bone Marrow Compartments in Histological Sections

Nicolas Kunz, Olivier Burri, Olaia Maria Naveiras Torres-Quiroga, Vasco Ledebur de Antas de Campos, Frédérica Schyrr, Josefine Catharina Pedersen Tratwal, Shanti Rojas-Sutterlin, Rita Sarkis

WILEY2020

Cellular Uptake and Intracellular Trafficking of Poly(N-(2-Hydroxypropyl) Methacrylamide)

Harm-Anton Klok, Olivier Burri, Graham Knott, Arne Seitz, Claudia Battistella, Anders Meibom, Romain Guiet, Stéphane Laurent Escrig

Cellular uptake and intracellular trafficking of polymer conjugates or polymer nanoparticles is typically monitored using fluorescence-based techniques such as confocal microscopy. While these methods have provided a wealth of insight into the internalizat ...

American Chemical Society2019

Development of Sample-Adaptable Holders for Lightsheet Microscopy

Olivier Burri, Thierry Laroche, Arne Seitz, Lalit Kumar Dubey

Multi-user core microscopy facilities are often faced with the challenge to adapt or modify existing instruments. This is essential in order to fulfill the requirements of the user community, who wants to image a wide range of model organisms with varying ...

2019