Olivier Burri
Engineer
olivier.burri@epfl.ch +41 21 693 96 29 https://www.epfl.ch/research/facilities/ptbiop/
Citizenship: Swiss / Venezuelan
Birth date: 30.04.1984
EPFL SV PTECH PTBIOP
AI 0140 (Bâtiment AI)
Station 15
1015 Lausanne
Web site: Web site: https://biop.epfl.ch/
EPFL > VPA-AVP-PGE > AVP-PGE-EDOC > EDMS-ENS
Web site: Web site: https://go.epfl.ch/edms
Fields of expertise
Development of bioimage analysis workflows and algorithms to extract quantitative data from microscopy images
Tools & Software:
ImageJ/Fiji, CellProfiler, ilastik, Imaris, Arivis, Matlab, RStudio, IntelliJ, Eclipse, Jupyter Notebooks
Programming languages:
Java, Groovy, JavaScript, TypeScript, PHP, Python, R, C, C , Matlab, Bash
Tools & Software:
ImageJ/Fiji, CellProfiler, ilastik, Imaris, Arivis, Matlab, RStudio, IntelliJ, Eclipse, Jupyter Notebooks
Programming languages:
Java, Groovy, JavaScript, TypeScript, PHP, Python, R, C, C , Matlab, Bash
Mission
- Provide bioimage analysis tools and training to EPFL collaborators through the BioImaging and Optics Core Facility (BIOP).
- Assist in teaching courses on image formation, image acquisition and image analysis.
- Provide support and advice in the development of meaningful biological experiments where the output relies on image analysis.
- Develop tools and algorithms using open source tools and promote Open Science whenever possible.
- Disseminate SOPs on FAIR data practices.
- Maintain the BIOP's IT infrastructure through software maintenance and backup.
- Assist in the acquisition of new equipments and services related to IT and image analysis (Website, Servers, GPUs, ...)
- Provide support to the greater imaging community through activity on the Image.sc forum.
Publications
Infoscience publications
Infoscience
2024
Cellpose training data and scripts from "Inhibition of CERS1 in aging skeletal muscle exacerbates age-related muscle impairments"
2024.2023
Inhibition of CERS1 in skeletal muscle exacerbates age-related muscle dysfunction
eLife. 2023-09-28. DOI : 10.7554/eLife.90522.1.Optical imaging of the small intestine immune compartment across scales
Communications Biology. 2023-03-31. DOI : 10.1038/s42003-023-04642-3.Thermo-Responsive Hyaluronan-Based Hydrogels Combined with Allogeneic Cytotherapeutics for the Treatment of Osteoarthritis
Pharmaceutics. 2023-05-18. DOI : 10.3390/pharmaceutics15051528.MarrowQuant 2.0: A Digital Pathology Workflow Assisting Bone Marrow Evaluation in Experimental and Clinical Hematology
Modern Pathology. 2023. DOI : 10.1016/j.modpat.2022.100088.2022
Measuring reporter activity domain in EPI aggregates and Gastruloids.ijm
2022-12-07.Sphingolipids control dermal fibroblast heterogeneity
Science. 2022-04-15. DOI : 10.1126/science.abh1623.An Open-Source Whole Slide Image Registration Workflow at Cellular Precision Using Fiji, QuPath and Elastix
Frontiers In Computer Science. 2022-01-05. DOI : 10.3389/fcomp.2021.780026.2021
Miniature neurotransmission is required to maintain Drosophila synaptic structures during ageing
Nature Communications. 2021-07-20. DOI : 10.1038/s41467-021-24490-1.Deep Learning Enables Individual Xenograft Cell Classification in Histological Images by Analysis of Contextual Features
Journal of Mammary Gland Biology and Neoplasia. 2021-05-17. DOI : 10.1007/s10911-021-09485-4.Biotin-NeutrAvidin Mediated Immobilization of Polymer Micro- and Nanoparticles on T Lymphocytes
Bioconjugate Chemistry. 2021-03-17. DOI : 10.1021/acs.bioconjchem.1c00026.2020
T Cell-Mediated Transport of Polymer Nanoparticles across the Blood-Brain Barrier
Advanced Healthcare Materials. 2020-11-25. DOI : 10.1002/adhm.202001375.MarrowQuant across Aging and Aplasia: A Digital Pathology Tool for Quantification of Bone Marrow Compartments in Histological Sections
2020-11-01. Annual Meeting of the American-Society-for-Bone-and Mineral Research (ASBMR), ELECTR NETWORK, Sep 11-15, 2020. p. 95-95.MarrowQuantAcross Aging and Aplasia: A Digital Pathology Workflow for Quantification of Bone Marrow Compartments in Histological Sections
Frontiers In Endocrinology. 2020-09-24. DOI : 10.3389/fendo.2020.00480.2019
A Derived Positional Mapping of Inhibitory Subtypes in the Somatosensory Cortex
Frontiers In Neuroanatomy. 2019-08-06. DOI : 10.3389/fnana.2019.00078.Development of Sample-Adaptable Holders for Lightsheet Microscopy
Frontiers In Neuroanatomy. 2019-03-08. DOI : 10.3389/fnana.2019.00026.Open Source Tools for Biological Image Analysis
Computer Optimized Microscopy; Humana Press, 2019. p. 460.An optimized and validated 384-well plate assay to test platelet function in a high-throughput screening format
Platelets. 2019-01-01. DOI : 10.1080/09537104.2018.1514106.Cellular Uptake and Intracellular Trafficking of Poly(N-(2-Hydroxypropyl) Methacrylamide)
Biomacromolecules. 2019. DOI : 10.1021/acs.biomac.8b01372.2017
TRACMIT: An effective pipeline for tracking and analyzing cells on micropatterns through mitosis
Plos One. 2017. DOI : 10.1371/journal.pone.0179752.Advances in pancreatic islet monolayer culture on glass surfaces enable super-resolution microscopy and insights into beta cell ciliogenesis and proliferation
Scientific Reports. 2017. DOI : 10.1038/srep45961.2015
The Nimrod transmembrane receptor Eater is required for hemocyte attachment to the sessile compartment in Drosophila melanogaster
Biology Open. 2015. DOI : 10.1242/bio.201410595.2012
Automated analysis of single stem cells in microfluidic traps
Lab On A Chip. 2012. DOI : 10.1039/c2lc40317j.2009
A Stochastic Translation Algorithm: The View Of The Ribosome
20092007
Réception par des psychiatres d'un reportage télévisuel sur la folie
2007Teaching & PhD
MOOC: Image Processing & Analysis for Life Scienti
Since 2017, Romain Guiet, Nicolas Chiaruttini, Arne Seitz and myself have created and maintain the course Image Processing and Analysis for Life Scientists, which is available on EdX and Courseware for EPFL members.It is a basic image analysis for life scientists with a non-engineering background. The main goal is to teach how to address and solve scientific questions by state of the art image analysis strategies. It is self-paced and open to everyone!
Courses
Image Processing for Life Science
Registration details will be announced via email. It takes place yearly from Sept./October to December & intends to teach image processing with a strong emphasis of applications in life sciences. The idea is to enable the participants to solve image-processing questions via workflows independently.