Romain Guiet
EPFL SV PTECH PTBIOP
AI 0140 (Bâtiment AI)
Station 15
CH-1015 Lausanne
Web site: Web site: https://biop.epfl.ch/
EPFL > VPA > 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.
- BioSample Preparation : in vitro cell, organoid, time-lapse, fixation, staining strategies, actin, mitochondria, fluorescent protein expression
- BioImage Acquisition : Widefield, Confocal, Whole Slide Imaging, Super-resolution (SIM, STORM, STED), FRET, FRAP, FLIM
- BioImage Analysis: Co-localization analysis, Deconvolution, Time-lapse , Whole Slide Imaging
- Tools & Software: ImageJ/Fiji, QuPath, ilastik CellProfiler, Imaris, Arivis, Matlab, Rstudio, Jupyter Notebooks, Renku
- Programming languages: ImageJ macro language, Groovy, Java, Python, (R, Matlab)
Biography
Romain has been working at the BIOP since 2011 after a Ph.D. in Biology. He is responsible, along with Olivier Burri and Nicolas Chiaruttini, for the advice and follow up of student projects involving microscopy and quantification.His expertise with in vitro cell culture and imaging is also beneficial to help users with their staining strategies and experiment design/optimization.
Background: Bioengineering, Ph.D. Immunology & Cancer (3D cell migration , organoid , cell-cytoskeleton)
Mission
- Development of BioImage Analysis workflows and training to EPFL collaborators
- Teaching during 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.
- Provide support to the greater imaging community through activity on the forum.image.sc .
Current work
PTBIOP - BioImaging and Optics Core FacilityPublications
Selected publications
| Giger S, Hofer M, Miljkovic-Licina M, Hoehnel S, Brandenberg N, Guiet R, Ehrbar M, Kleiner E, Gegenschatz-Schmid K, Matthes T, Lutolf MP. APL Bioeng . 2022 Jul 8;6(3):036101. doi: 10.1063/5.0092860. eCollection 2022 Sep. |
Microarrayed human bone marrow organoids for modeling blood stem cell dynamics |
| Esmaeili V, Oryshchuk A, Asri R, Tamura K, Foustoukos G, Liu Y, Guiet R, Crochet S, Petersen CCH. PLoS Biol . 2022 May 31;20(5):e3001667. doi: 10.1371/journal.pbio.3001667. |
Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas |
| Laura Capolupo , Irina Khven , Alex R Lederer , Luigi Mazzeo , Galina Glousker , Sylvia Ho , Francesco Russo , Jonathan Paz Montoya , Dhaka R Bhandari , Andrew P Bowman , Shane R Ellis, Romain Guiet , Olivier Burri , Johanna Detzner , Johannes Muthing , Krisztian Homicsko , François Kuonen , Michel Gilliet , Bernhard Spengler , Ron M A Heeren , G Paolo Dotto , Gioele La Manno , Giovanni D'Angelo Science . 2022 Apr 15;376(6590):eabh1623. doi: 10.1126/science.abh1623. Epub 2022 Apr 15. |
Sphingolipids control dermal fibroblast heterogeneity |
| Gabriel G Martins , Fabrice P Cordelières , Julien Colombelli , Rocco D'Antuono , Ofra Golani , Romain Guiet , Robert Haase , Anna H Klemm, Marion Louveaux, Perrine Paul-Gilloteaux , Jean-Yves Tinevez, Kota Miura F1000Res . 2021 Apr 30;10:334. doi: 10.12688/f1000research.25485.1. eCollection 2021. |
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists |
| Ayer M, Burri O, Guiet R, Seitz A, Kaba E, Engelhardt B, Klok HA. Bioconjug Chem. 2021 Mar 17;32(3):541-552 |
Biotin-NeutrAvidin Mediated Immobilization of Polymer Micro- and Nanoparticles on T Lymphocytes. |
| Rossi G, Broguiere N, Miyamoto M, Boni A, Guiet R, Girgin M, Kelly RG, Kwon C, Lutolf MP Cell Stem Cell. 2021 Feb 4;28(2):230-240.e6 |
Capturing Cardiogenesis in Gastruloids. |
| Guiet R, Burri O, Chiaruttini N, Hagens O, Seitz A. F1000Res. 2020 Nov 27;9:1380 |
DEVILS: a tool for the visualization of large datasets with a high dynamic range. |
Teaching & PhD
Courses
Image Processing for Life Science
Registration details will be announced via email. It takes place from September 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.