Projects
and research
Our work spans artificial intelligence, quantitative biomedical image analysis, digital pathology, 3D imaging and organoid research.
Our Scientific Collaborations
At QuantaCell, we collaborate across a wide range of research frameworks, including academic and hospital-based collaborations, industrial partnerships, ANR projects (PRC, PRCI and PRCE), regional and national calls, European programmes such as Horizon Europe, EIC and ERC, and international funding schemes such as NIH, NSF and SBIR/STTR.
Working at the interface of life sciences, imaging, data and software, we bring scientific, methodological and operational expertise to help transform complex biological and medical questions into robust, actionable and scientifically valuable analytical workflows.
Do you have a research project in preparation?
We would be delighted to discuss it with you from the earliest stages and explore how QuantaCell could contribute its expertise to your project.
Montpellier University Hospital – Department of Pathology, France
PI: Vanessa Lacheretz Szablewski
Digital pathology & quantitative histology — QuantaCell collaborates with Montpellier University Hospital on clinical research projects involving AI-powered histology image analysis, tissue segmentation, cell classification and spatial analysis. These collaborations combine image analysis expertise with pathological and clinical knowledge to extract robust quantitative information from complex tissue images.
Institut Curie – Paris, France
PI: Matthieu Piel
Quantitative microscopy & biomedical image analysis — QuantaCell collaborates with Institut Curie on the development and application of advanced biomedical image analysis methods. Our expertise in image segmentation, quantitative microscopy and AI helps transform complex microscopy images into reproducible quantitative data for biological research.
Centre Léon Bérard – Lyon, France
PIs: Pierre-Etienne Heudel, Hugo Crochet
Quantitative cancer image analysis — QuantaCell contributes image analysis expertise to oncology research involving tumor tissues, biomarkers and the tumor microenvironment. Quantitative histology and spatial analysis provide objective measurements of tissue architecture, cellular phenotypes and biomarker expression for translational and clinical research.
Discover the project on the Centre Léon Bérard website →
Institute of Mechanobiology — National University of Singapore
PI: Anne Beghin
3D organoid image analysis & phenotyping — QuantaCell collaborates with the National University of Singapore on quantitative 3D image analysis of organoids. Our approaches combine 3D segmentation, multiscale analysis, cellular phenotyping and visualization to extract quantitative information from complex 3D microscopy datasets.
IHU Immun4Cure — Montpellier University Hospital, France
PIs: Jérôme Reboul, Kevin Yauy
Machine learning & multimodal biomedical data analysis — QuantaCell contributes expertise in machine learning and biomedical data analysis to integrate complex biological datasets, including imaging and multi-omics data. These approaches aim to identify quantitative signatures, biomarkers and biological patterns that would be difficult to reveal through individual data sources alone.
Discover the IHU Immun4Cure Annual Report →
ANR FIRE (Pulmonary Fibrosis, 3D Imaging & AI) — Nice France
PI: Chloé Féral (IRCAN)
Pulmonary fibrosis, 3D imaging & AI — Within the ANR FIRE project, QuantaCell develops deep learning methods for quantitative 3D image analysis of light-sheet microscopy images of the lung. The project combines 3D U-Net segmentation, lung branch reconstruction and fibrosis detection and quantification, together with an interactive 3D annotation application to support the characterization of pulmonary fibrosis.
Discover the FIRE project on the ANR website →
IBM × QuantaCell (AI for Medical Imaging) — JFR Data Challenge 2019
PI: Jean Armand Broyelle
AI for medical imaging – QuantaCell collaborated with IBM on the 2019 French Radiology Society (JFR) Data Challenge, developing AI methods for lung nodule detection and classification in 3D CT imaging. The IBM–QuantaCell team achieved the best result among ten participating teams. This work led to the peer-reviewed publication Artificial intelligence solution to classify pulmonary nodules on CT in Diagnostic and Interventional Imaging (2020).
Our scientific
publications
iScience - January 2026
Human iPSC-derived airway models enable comparative analysis of SARS-CoV-2 infection in healthy and COPD bronchial epithelium
Lisa Morichon, Jitendriya Swain, Nathalie Gros, Amel Nasri, Florent Foisset, Gaetan Galisot, Victor Racine, Said Assou, Arnaud Bourdin, John De Vos, Delphine Muriaux
PMID: 41782833 PMCID: PMC12955582 DOI: 10.1016/j.isci.2026.114741
Keywords: Quantitative image analysis · Airway models · Cell quantification · Fluorescence microscopy · Biomedical image analysis
Nature Methods - May 2025
Digitalized organoids: integrated pipeline for high-speed 3D analysis of organoid structures using multilevel segmentation and cellular topology
Nat Methods.2025 May;22, 1343–1354. doi: 10.1038/s41592-025-02685-4. Epub 2025 May 14. Autors : Hui Ting Ong, Esra Karatas, Titouan Poquillon, Gianluca Grenci, Alessandro Furlan, Florian Dilasser, Saburnisha Binte Mohamad Raffi, Damien Blanc, Elise Drimaracci, Dimitri Mikec, Gaetan Galisot, Blake A. Johnson, Albert Zou Liu, Cora Thiel, Oliver Ullrich, OrgaRES Consortium, Victor Racine & Anne Beghin. Keywords : Organoids, Morphology, Biomedical Research
Parasites & Vectors - March 2025
Computational histology reveals that concomitant application of insect repellent with sunscreen impairs UV protection in an ex vivo human skin model
Sophie Charrasse, Titouan Poquillon, Charlotte Saint-Omer, Audrey Schunemann, Mylène Weill, Victor Racine, Abdel Aouacheria
PMID: 40038831 PMCID: PMC11881410 DOI: 10.1186/s13071-025-06712-3. Keywords: Computational histology · Histology image analysis · Deep learning · Nuclear morphometry · Skin image analysis · Quantitative pathology
J Clin Invest - April 2024
Human NLRC4 expression promotes cancer survival and associates with type I interferon signaling and immune infiltration
23,134(11):e166085. doi: 10.1172/JCI166085. Authors : Charlotte Domblides, Steven Crampton, Hong Liu, Juliet M Bartleson, Annie Nguyen, Claudia Champagne, Emily E Landy, Lindsey Spiker, Christopher Proffitt, Sunil Bhattarai, Anissa P Grawe, Matias Fuentealba Valenzuela, Lydia Lartigue, Isabelle Mahouche, Jeremy Dupaul-Chicoine, Kazuho Nishimura, Félix Lefort, Marie Decraecker, Valérie Velasco, Sonia Netzer, Vincent Pitard, Christian Roy, Isabelle Soubeyran, Victor Racine, Patrick Blanco, Julie Déchanet-Merville, Maya Saleh, Scott W Canna, David Furman, Benjamin Faustin. Keywords: Cancer immunotherapy, Cellular immune response, Immunology, Innate immunity, Oncology.
PLOS ONE, - March 2024
Quantitative imaging and semiotic phenotyping of mitochondrial network morphology in live human cells
Sophie Charrasse, Victor Racine, Charlotte Saint-Omer, Titouan Poquillon, Loïc Lionnard, Marine Ledru, Christophe Gonindard, Sandrine Delaunois, Karima Kissa, Richard E Frye, Manuela Pastore, Christelle Reynes, Mathilde Frechet, Hanane Chajra, Abdel Aouacheria
Keywords: Quantitative imaging · Automated image analysis · Live-cell imaging · Morphological profiling · Confocal microscopy · Cellular phenotyping
Front nucl med - January 2024
Automatic deep learning method for third lumbar selection and body composition evaluation on CT scans of cancer patients
10,3:1292676. doi: 10.3389/fnume.2023.1292676. eCollection 2023. Authors : Lidia Delrieu, Damien Blanc, Amine Bouhamama, Fabien Reyal, Frank Pilleul, Victor Racine, Anne Sophie Hamy, Hugo Crochet, Timothée Marchal, Pierre Etienne Heudel. Keywords: body composition, cancer; computed tomography, deep learning, sarcopenia.
Comput Struct Biotechnol J - November 2023
Quantitative assessment of mitochondrial morphology relevant for studies on cellular health and environmental toxicity
Sophie Charrasse, Titouan Poquillon, Charlotte Saint-Omer, Manuela Pastore, Benoit Bordignon, Richard E Frye, Christelle Reynes, Victor Racine, Abdel Aouacheria
Keywords: High-content screening · Quantitative imaging · Automated image analysis · Morphological profiling · Live-cell imaging · Toxicology
Nature Methods - July 2022
Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification
19(7):881-892. doi: 10.1038/s41592-022-01508-0. Epub 2022 Jun 13.Autors : Anne Beghin, Gianluca Grenci, Geetika Sahni, Su Guo, Harini Rajendiran, Tom Delaire, Saburnisha Binte Mohamad Raffi, Damien Blanc, Richard de Mets, Hui Ting Ong, Xareni Galindo, Anais Monet, Vidhyalakshmi Acharya, Victor Racine, Florian Levet, Remi Galland, Jean-Baptiste Sibarita, Virgile Viasnoff. Keywords : 3D imaging, Deep Learning, Quantification.
Diagn Interv Imaging - December 2020
Artificial intelligence solution to classify pulmonary nodules on CT
101(12):803-810. Autors : D Blanc, V Racine, A Khalil, M Deloche, J-A Broyelle, I Hammouamri, E Sinitambirivoutin, M Fiammante, E Verdier, T Besson, A Sadate, M Lederlin, F Laurent, G Chassagnon, G Ferretti, Y Diascorn, P-Y Brillet, Lucie Cassagnes, C Caramella, A Loubet, N Abassebay, P Cuingnet, M Ohana, J Behr, A Ginzac, H Veyssiere, X Durando, I Bousaïd, N Lassau, J Brehant. Keywords : Deep learning, Retina-UNET, 3D U-Net, PyTorch
Transl Psychiatry - October 2020
Mitochondrial morphology is associated with respiratory chain uncoupling in autism spectrum disorder
11(1):527. Autors : RE Frye, L Lionnard, I Singh, MA Karim, H Chajra, M Frechet, K Kissa, V Racine, A Ammanamanchi, PJ McCarty, L Delhey, M Tippett, S Rose, A Aouacheria. Keywords : Cell segmentation, nuclei segmentation, statistics, AssayScope
Methods Cell Biol - January 2017
Fluorescence eXclusion Measurement of volume in live cell
Auteurs : Cadart C, Zlotek-Zlotkiewicz E, Venkova L, Thouvenin O, Racine V, Le Berre M, Monnier S, Piel M. Keywords : Mass analysis. Biophysics, Microfluidcs
Nature Commun - June 2014
Synaptic recruitment of gephyrin regulates surface GABAA receptor dynamics for the expression of inhibitory LTP
Auteurs :Petrini EM, Ravasenga T, Hausrat TJ, Iurilli G, Olcese U, Racine V, Sibarita JB, Jacob TC, Moss SJ, Benfenati F, Medini P, Kneussel M, Barberis A. Keywords : Neuroscience, dynamique des récepteurs, suivi dans le temps, segmentation
Optics Express - January 2012
Wavelet analysis for single molecule localization microscopy
20(3):2081-95. PDF Auteurs :Izeddin I, Boulanger J, Racine V, Specht CG, Kechkar A, Nair D, Triller A, Choquet D, Dahan M, Sibarita JB. Keywords : TIRF/PALM, SPT, détection moléculaire, imagerie avancée, ondelettes, fit gaussien, traitement des images
Molecular Systems Biology - January 2012
RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells
Auteurs :Chia J, Goh G, Racine V, Ng S, Kumar P, Bard F. Keywords : Criblage phénotypique, structure cellulaire, siRNA, machine learning, statistiques
Nature - May 2007
Experimental and theoretical study of mitotic spindle orientation
447(7143):493-6. Auteurs :Théry M, Jiménez-Dalmaroni A, Racine V, Bornens M, Jülicher F. Keywords : Cellule unique, détection et segmentation de compartiments, adhésion, microscopie automatisée, visualisation des données, modèle théorique, cytosquelette
From Research to Real-World Image Analysis
Our scientific work directly contributes to the development of QuantaCell’s image analysis methods and technologies. From histology and digital pathology to 3D organoids, quantitative microscopy and AI, this research expertise enables us to develop robust image analysis workflows for complex biological questions.
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