Romain Guiet
Nationality: French
EPFL SV PTECH PTBIOP
AI 0140 (Bâtiment AI)
Station 15
1015 Lausanne
+41 21 693 77 31
+41 21 693 96 29
Office: AI 0140
EPFL › SV › PTECH › PTBIOP
Website: https://biop.epfl.ch/
+41 21 693 77 31
EPFL › VPA › VPA-AVP-DLE › AVP-DLE-EDOC › EDMS-ENS
Website: https://go.epfl.ch/edms
+41 21 693 77 31
EPFL › SV › SV-DEC › CF-SV
Website: https://sv.epfl.ch/Council
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: Colocalisation analysis, Deconvolution, Time-lapse , Whole Slide Imaging
- Tools & Software: ImageJ/Fiji, QuPath, ilastik, CellProfiler, Imaris, Arivis, Napari, Jupyter Notebooks
- Programming languages: ImageJ macro language, Groovy, Java, Python, (R, Matlab)
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 .
CoPe candidacy
Current work
His expertise with in vitro cell culture and imaging is also beneficial to help BIOP users with their staining strategies and experiment design/optimization.
Background: Bioengineering, Ph.D. Immunology & Cancer (3D cell migration , organoid , cell-cytoskeleton)
Education
PhD
| Immunology & Cancer
2007 – 2011
University Paul Sabatier-Toulouse III, Toulouse, FRANCE
Directed by
Advisor: PhD. I. Maridonneau-Parini
IPBS-UMR5089.
205 route de Narbonne
Toulouse, France
M2R (eq. Research Master Degree)
| Molecular and cellular biology2006 – 2007 University Paul Sabatier-Toulouse III, Toulouse, FRANCE
Biological Engineer (eq. Master Degree)
| Protein Engineering2003 – 2006 Polytech Clermont-Ferrand, Clermont-Ferrand, France
Preparatory classes
| (2-year intensive program preparing for the national competitive exam for entry to French engineering schools). Specialty: Biology2001 – 2003 High School Louis Barthou, Pau, France
Baccalauréat (eq. high school degree)
| Scientific Grade2000 – 2001 High School St John Perse, Pau, France
Selected publications
Injury-induced intestinal stem cell renewal requires capillary morphogenesis gene 2.
Bracq L, Chuat A, Kunz B, Burri O, Guiet R, Duc J, Brandenberg N, van der Goot FG.
Published in EMBO Mol Med. 2025 Oct;17(10):2612-2631. doi: 10.1038/s44321-025-00295-3. Epub 2025 Aug 22. in 2025
Structural and molecular characterization of astrocyte and vasculature connectivity in the mouse hippocampus and cortex.
Lorin C, Guiet R, Chiaruttini N, Ambrosini G, Boci E, Abdellah M, Markram H, Keller D.
Published in Glia. 2024 Nov;72(11):2001-2021. doi: 10.1002/glia.24594. Epub 2024 Jul 15. in 2024
Microarrayed human bone marrow organoids for modeling blood stem cell dynamics
Giger S, Hofer M, Miljkovic-Licina M, Hoehnel S, Brandenberg N, Guiet R, Ehrbar M, Kleiner E, Gegenschatz-Schmid K, Matthes T, Lutolf MP.
Published in APL Bioeng . 2022 Jul 8;6(3):036101. doi: 10.1063/5.0092860. eCollection 2022 Sep. in
Learning-related congruent and incongruent changes of excitation and inhibition in distinct cortical areas
Esmaeili V, Oryshchuk A, Asri R, Tamura K, Foustoukos G, Liu Y, Guiet R, Crochet S, Petersen CCH.
Published in PLoS Biol . 2022 May 31;20(5):e3001667. doi: 10.1371/journal.pbio.3001667. in
Sphingolipids control dermal fibroblast heterogeneity
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
Published in Science . 2022 Apr 15;376(6590):eabh1623. doi: 10.1126/science.abh1623. Epub 2022 Apr 15. in
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists
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
Published in F1000Res . 2021 Apr 30;10:334. doi: 10.12688/f1000research.25485.1. eCollection 2021. in
Biotin-NeutrAvidin Mediated Immobilization of Polymer Micro- and Nanoparticles on T Lymphocytes.
Ayer M, Burri O, Guiet R, Seitz A, Kaba E, Engelhardt B, Klok HA.
Published in Bioconjug Chem. 2021 Mar 17;32(3):541-552 in
Capturing Cardiogenesis in Gastruloids.
Rossi G, Broguiere N, Miyamoto M, Boni A, Guiet R, Girgin M, Kelly RG, Kwon C, Lutolf MP
Published in Cell Stem Cell. 2021 Feb 4;28(2):230-240.e6 in
DEVILS: a tool for the visualization of large datasets with a high dynamic range.
Guiet R, Burri O, Chiaruttini N, Hagens O, Seitz A.
Published in F1000Res. 2020 Nov 27;9:1380 in
Teaching & PhD
Courses
Image Processing for Life Science
BIO-695
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.