Fields of expertise
Tools & Software:
ImageJ/Fiji, CellProfiler, ilastik, Imaris, Arivis, Matlab, RStudio, IntelliJ, Eclipse, Jupyter Notebooks
- 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.
Measuring reporter activity domain in EPI aggregates and Gastruloids.ijm2022-12-07.
Sphingolipids control dermal fibroblast heterogeneityScience. 2022-04-15. DOI : 10.1126/science.abh1623.
T Cell-Mediated Transport of Polymer Nanoparticles across the Blood-Brain BarrierAdvanced 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 Sections2020-11-01. Annual Meeting of the American-Society-for-Bone-and Mineral Research (ASBMR), ELECTR NETWORK, Sep 11-15, 2020. p. 95-95.
An optimized and validated 384-well plate assay to test platelet function in a high-throughput screening formatPlatelets. 2019-01-01. DOI : 10.1080/09537104.2018.1514106.
Automated analysis of single stem cells in microfluidic trapsLab On A Chip. 2012. DOI : 10.1039/c2lc40317j.
A Stochastic Translation Algorithm: The View Of The Ribosome2009
Réception par des psychiatres d'un reportage télévisuel sur la folie2007
Teaching & PhD
MOOC: Image Processing & Analysis for Life ScientiSince 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!