Thomas Walter

Publications

Article dans une revue (47)

Identifying Patients With Low Relapse Rate Despite High-Risk Estrogen Receptor–Positive/Human Epidermal Growth Factor Receptor 2–Negative Early Breast Cancer: Development and Validation of a Clinicopathologic Assay François-Clément Bidard,Grégoire Gessain,Thomas Bachelot,Lucie Frechin,Anne Vincent-Salomonet al. Journal of Clinical Oncology, 2025, 43 (28), pp.3090-3101. ⟨10.1200/JCO-25-00742⟩ Article dans une revue hal-05230907v1
Exploring the risks of over-reliance on AI in diagnostic pathology. What lessons can be learned to support the training of young pathologists? Yaëlle Bellahsen-Harrar,Mélanie Lubrano,Charles Lépine,Aurélie Beaufrère,Claire Bocciarelliet al. PLoS ONE, 2025, 20 (8), pp.e0323270. ⟨10.1371/journal.pone.0323270⟩ Article dans une revue inserm-05230192v1
Integration of clinical, pathological, radiological, and transcriptomic data improves prediction for first-line immunotherapy outcome in metastatic non-small cell lung cancer Nicolas Captier,Marvin Lerousseau,Fanny Orlhac,Narinée Hovhannisyan-Baghdasarian,Marie Luporsiet al. Nature Communications, 2025, 16 (1), pp.614. ⟨10.1038/s41467-025-55847-5⟩ Article dans une revue hal-04950400v2
Cell-type deconvolution methods for spatial transcriptomics Lucie Gaspard-Boulinc,Luca Gortana,Thomas Walter,Emmanuel Barillot,Florence Cavalli Nature Reviews Genetics, 2025, ⟨10.1038/s41576-025-00845-y⟩ Article dans une revue hal-05230821v1
A deep learning approach for time-consistent cell cycle phase prediction from microscopy data Thomas Bonte,Oriane Pourcelot,Adham Safieddine,Floric Slimani,Florian Muelleret al. PLoS Computational Biology, 2025, 21 (12), pp.e1013800. ⟨10.1371/journal.pcbi.1013800⟩ Article dans une revue hal-05458920v2
Erratum: Identifying Patients With Low Relapse Rate Despite High-Risk Estrogen Receptor–Positive/Human Epidermal Growth Factor Receptor 2–Negative Early Breast Cancer: Development and Validation of a Clinicopathologic Assay François-Clément Bidard,Grégoire Gessain,Thomas Bachelot,Lucie Frechin,Anne Vincent-Salomonet al. Journal of Clinical Oncology, 2025, 43 (32), pp.3547-3547. ⟨10.1200/JCO-25-02272⟩ Article dans une revue hal-05423679v1
A point cloud segmentation framework for image-based spatial transcriptomics Thomas Defard,Hugo Laporte,Mallick Ayan,Juliette Soulier,Sandra Curras-Alonsoet al. Communications Biology, 2024, 7 (1), pp.823. ⟨10.1038/s42003-024-06480-3⟩ Article dans une revue hal-04874000v1
Trem2-expressing multinucleated giant macrophages are a biomarker of good prognosis in head and neck squamous cell carcinoma Grégoire Gessain,Ahmed-Amine Anzali,Marvin Lerousseau,Kevin Mulder,Mathilde Biedet al. Cancer Discovery, 2024, 14 (12), pp.2352-2366. ⟨10.1158/2159-8290.CD-24-0018⟩ Article dans une revue inserm-04729854v1
Cell-cycle-dependent mRNA localization in P-bodies Adham Safieddine,Marie-Noëlle Benassy,Thomas Bonte,Floric Slimani,Oriane Pourcelotet al. Molecular Cell, 2024, 84 (21), pp.4191-4208.e7. ⟨10.1016/j.molcel.2024.09.011⟩ Article dans une revue hal-04787269v3
pyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging Xavier Devos,Jean-Bernard Fiche,Marion Bardou,Olivier Messina,Christophe Houbronet al. Genome Biology, 2024, 25 (1), pp.47. ⟨10.1186/s13059-024-03178-x⟩ Article dans une revue hal-04762623v1
Diagnosis with confidence: deep learning for reliable classification of laryngeal dysplasia Mélanie Lubrano,Yaëlle Bellahsen-Harrar,Sylvain Berlemont,Sarah Atallah,Emmanuelle Vazet al. Histopathology, 2023, 84 (2), pp.343-355. ⟨10.1111/his.15067⟩ Article dans une revue hal-04396387v1
An interactive murine single-cell atlas of the lung responses to radiation injury Sandra Curras-Alonso,Juliette Soulier,Thomas Defard,Christian Weber,Sophie Heinrichet al. Nature Communications, 2023, 14 (1), pp.2445. ⟨10.1038/s41467-023-38134-z⟩ Article dans une revue hal-04092147v1
Utilisation de l’intelligence artificielle pour prédire le statut tumoral relatif à la recombinaison homologue Tristan Lazard,Guillaume Bataillon,Thomas Walter,Anne Vincent Salomon Médecine/Sciences, 2023, 39 (12), pp.926-928. ⟨10.1051/medsci/2023169⟩ Article dans une revue istex hal-04396381v1
Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer David Page,Glenn Broeckx,Chowdhury Arif Jahangir,Sara Verbandt,Rajarsi Guptaet al. Journal of Pathology, 2023, 260 (5), pp.514-532. ⟨10.1002/path.6165⟩ Article dans une revue hal-04209907v1
Pitfalls in machine learning‐based assessment of tumor‐infiltrating lymphocytes in breast cancer: A report of the International Immuno‐Oncology Biomarker Working Group on Breast Cancer Jeppe Thagaard,Glenn Broeckx,David Page,Chowdhury Arif Jahangir,Sara Verbandtet al. Journal of Pathology, 2023, 260 (5), pp.498-513. ⟨10.1002/path.6155⟩ Article dans une revue hal-04209913v1
HT-smFISH: a cost effective and flexible workflow for high-throughput single molecule RNA imaging Adham Safieddine,Emeline Coleno,Frederic Lionneton,Abdel-Meneem Traboulsi,Soha Salloumet al. Nature Protocols, 2023, 18, pp.157-187. ⟨10.1038/s41596-022-00750-2⟩ Article dans une revue hal-03834928v1
Cell segmentation in images without structural fluorescent labels Daniel Zyss,Susana A Ribeiro,Mary J C Ludlam,Thomas Walter,Amin Fehri Biological Imaging, 2023, 3, pp.e16. ⟨10.1017/S2633903X23000168⟩ Article dans une revue hal-04396484v1
Deep learning identifies morphological patterns of homologous recombination deficiency in luminal breast cancers from whole slide images Tristan Lazard,Guillaume Bataillon,Peter Naylor,Tatiana Popova,François-Clément Bidardet al. Cell Reports Medicine, 2022, 3 (12), pp.100872. ⟨10.1016/j.xcrm.2022.100872⟩ Article dans une revue hal-03936608v1
Prediction of Treatment Response in Triple Negative Breast Cancer From Whole Slide Images Peter Naylor,Tristan Lazard,Guillaume Bataillon,Marick Laé,Anne Vincent-Salomonet al. Frontiers in Signal Processing, 2022, 2, ⟨10.3389/frsip.2022.851809⟩ Article dans une revue hal-03942865v1
Neural network fast‐classifies biological images through features selecting to power automated microscopy Maël Balluet,Florian Sizaire,Youssef El Habouz,Thomas Walter,Jérémy Pontet al. Journal of Microscopy, 2022, 285 (1), pp.3-19. ⟨10.1111/jmi.13062⟩ Article dans une revue hal-03408803v1
FISH-quant v2: a scalable and modular tool for smFISH image analysis Arthur Imbert,Wei Ouyang,Adham Safieddine,Emeline Coleno,Christophe Zimmeret al. RNA, 2022, 28 (6), pp.786-795. ⟨10.1261/rna.079073.121⟩ Article dans une revue hal-03942851v2
Spatial transcriptomics for respiratory research and medicine Sandra Curras-Alonso,Juliette Soulier,Thomas Walter,Florian Mueller,Arturo Londoño-Vallejoet al. European Respiratory Journal, 2021, 58 (1), pp.2004314. ⟨10.1183/13993003.04314-2020⟩ Article dans une revue hal-03376218v1
A choreography of centrosomal mRNAs reveals a conserved localization mechanism involving active polysome transport Adham Safieddine,Emeline Coleno,Soha Salloum,Arthur Imbert,Abdel-Meneem Traboulsiet al. Nature Communications, 2021, 12 (1), pp.1352. ⟨10.1038/s41467-021-21585-7⟩ Article dans une revue hal-03014936v2
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions Xavier Pichon,Konstadinos Moissoglu,Emeline Coleno,Tianhong Wang,Arthur Imbertet al. RNA, 2021, pp.rna.078576.120. ⟨10.1261/rna.078576.120⟩ Article dans une revue hal-03371977v1
A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting Racha Chouaib,Adham Safieddine,Xavier Pichon,Arthur Imbert,Oh Sung Kwonet al. Developmental Cell, 2020, 54 (6), pp.773 - 791.e5. ⟨10.1016/j.devcel.2020.07.010⟩ Article dans une revue pasteur-02925687v1
Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen Joseph Boyd,Alice Pinheiro,Elaine Del Nery,Fabien Reyal,Thomas Walter Bioinformatics, 2019, ⟨10.1093/bioinformatics/btz774⟩ Article dans une revue hal-02440603v1
Human lymphoid organ cDC2 and macrophages play complementary roles in T follicular helper responses Mélanie Durand,Thomas Walter,Tiphène Pirnay,Thomas Naessens,Paul Guéguenet al. Journal of Experimental Medicine, 2019, 216 (7), pp.1561-1581. ⟨10.1084/jem.20181994⟩ Article dans une revue hal-02440608v1
Segmentation of Nuclei in Histopathology Images by deep regression of the distance map Peter Naylor,Marick Lae,Fabien Reyal,Thomas Walter IEEE Transactions on Medical Imaging, 2018, pp.1-12 Article dans une revue hal-01984033v1
A computational framework to study sub-cellular RNA localization Aubin Samacoits,Racha Chouaib,Adham Safieddine,Abdel-Meneem Traboulsi,Christophe Zimmeret al. Nature Communications, 2018, 9 (1), pp.4584. ⟨10.1038/s41467-018-06868-w⟩ Article dans une revue hal-01984014v1
Kernel Multitask Regression for Toxicogenetics Elsa Bernard,Yunlong Jiao,Erwan Scornet,Véronique Stoven,Thomas Walteret al. Molecular Informatics, 2017, 36 (10), ⟨10.1002/minf.201700053⟩ Article dans une revue hal-01679030v1
ARHGEF17 is an essential spindle assembly checkpoint factor that targets Mps1 to kinetochores. Mayumi Isokane,Thomas Walter,Robert Mahen,Bianca Nijmeijer,Jean-Karim Hérichéet al. Journal of Cell Biology, 2016, 212 (6), pp.647-59. ⟨10.1083/jcb.201408089⟩ Article dans une revue hal-01427937v1
smiFISH and FISH-quant - a flexible single RNA detection approach with super-resolution capability. Nikolay Tsanov,Aubin Samacoits,Racha Chouaib,Abdel-Meneem Traboulsi,Thierry Gostanet al. Nucleic Acids Research, 2016, ⟨10.1093/nar/gkw784⟩ Article dans une revue pasteur-01375913v1
Waterpixels Vaïa Machairas,Matthieu Faessel,David Cárdenas-Peña,Théodore Chabardes,Thomas Walteret al. IEEE Transactions on Image Processing, 2015, 24 (11), pp.3707 - 3716. ⟨10.1109/TIP.2015.2451011⟩ Article dans une revue hal-01212760v1
A generic methodological framework for studying single cell motility in high-throughput time-lapse data Alice Schoenauer Sebag,Sandra Plancade,Céline Raulet-Tomkiewicz,Robert Barouki,Jean-Philippe Vertet al. Bioinformatics, 2015, 31 (12), pp.i320-i328. ⟨10.1093/bioinformatics/btv225⟩ Article dans une revue hal-01246689v1
Assessment of algorithms for mitosis detection in breast cancer histopathology images Mitko Veta,Paul J. Van Diest,Stefan M. Willems,Haibo Wang,Anant Madabhushiet al. Medical Image Analysis, 2015, 20 (1), pp.237-248. ⟨10.1016/j.media.2014.11.010⟩ Article dans une revue hal-01246695v1
A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression Veronika Graml,Xenia Studera,Jonathan L.D. Lawson,Anatole Chessel,Marco Geymonatet al. Developmental Cell, 2014, 31 (2), pp.227-239. ⟨10.1016/j.devcel.2014.09.005⟩ Article dans une revue hal-01101880v1
Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation Jean-Karim Hériché,Jon G. Lees,Ian Morilla,Thomas Walter,Boryana Petrovaet al. Molecular Biology of the Cell, 2014, 25 (16), pp.2522-2536. ⟨10.1091/mbc.E13-04-0221⟩ Article dans une revue hal-01101877v1
A community effort to assess and improve drug sensitivity prediction algorithms James C Costello,Laura M Heiser,Elisabeth Georgii,Mehmet Gönen,Michael P Mendenet al. Nature Biotechnology, 2014, 32, pp.1202-1212. ⟨10.1038/nbt.2877⟩ Article dans une revue hal-01101874v1
MAP1S controls microtubule stability throughout the cell cycle in human cells Justus Tegha-Dunghu,Elena Bausch,Beate Neumann,Annelie Wuensche,Thomas Walteret al. Journal of Cell Science, 2014, 127, pp.5007-5013. ⟨10.1242/jcs.136457⟩ Article dans une revue hal-01101879v1
Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay. Gregoire Pau,Thomas Walter,Beate Neumann,Jean-Karim Hériché,Jan Ellenberget al. BMC Bioinformatics, 2013, 14 (1), pp.308. ⟨10.1186/1471-2105-14-308⟩ Article dans une revue inserm-00880889v1
Mitotic lamin disassembly is triggered by lipid-mediated signaling. Moritz Mall,Thomas Walter,Mátyás Gorjánácz,Iain F Davidson,Thi Bach Nga Ly-Hartiget al. Journal of Cell Biology, 2012, 198 (6), pp.981-90 Article dans une revue hal-01428007v1
Micropilot: automation of fluorescence microscopy-based imaging for systems biology. Christian Conrad,Annelie Wünsche,Tze Heng Tan,Jutta Bulkescher,Frank Sieckmannet al. Nature Methods, 2011, 8 (3), pp.246-9 Article dans une revue hal-01430280v1
Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes Beate Neumann,Thomas Walter,Jean-Karim Hériché,Jutta Bulkescher,Holger Erfleet al. Nature, 2010, 464 (7289), pp.721. ⟨10.1038/nature08869⟩ Article dans une revue hal-01144034v1
CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging Michael W Held,Michael W Schmitz,Bernd H Fischer,Thomas Walter,Beate H Neumannet al. Nature Methods, 2010, 7, pp.747 - 754. ⟨10.1038/nmeth.1486⟩ Article dans une revue hal-01431427v1
Automatic identification and clustering of chromosome phenotypes in a genome wide RNAi screen by time-lapse imaging. Thomas Walter,Michael Held,Beate Neumann,Jean-Karim Hériché,Christian Conradet al. Journal of Structural Biology, 2010, 170 (1), pp.1-9 Article dans une revue hal-01427996v1
Evaluation of automated fundus photograph analysis algorithms for detecting microaneurysms, haemorrhages and exudates, and of a computer-assisted diagnostic system for grading diabetic retinopathy Bénédicte Dupas,Thomas R. Walter,Ali Erginay,Richard Ordonez,Nilanjana Deb-Joardaret al. Diabetes & Metabolism, 2010, 36 (3), pp.213-220. ⟨10.1016/j.diabet.2010.01.002⟩ Article dans une revue istex hal-00836043v1
Anti-angiogenic properties of myo-inositol trispyrophosphate in ovo and growth reduction of implanted glioma J.-M. Lehn,G. Sihn,T. Walter,J.-C. Klein,I. Queguineret al. FEBS Letters, 2007, 581, pp.962-966. ⟨10.1016/j.febslet.2007.01.079⟩ Article dans une revue hal-00166409v1

Communication dans un congrès (11)

Light My Cells : Bright Field to Fluorescence Imaging Challenge 2024 Dorian Kauffmann,Emmanuel Faure,Guillaume Gay,Edouard Bertrand,Thomas Walteret al. ISBI 2024 - 21st IEEE International Symposium on Biomedical Imaging, May 2024, Athenes, Greece. ⟨10.5281/zenodo.10687569⟩ Communication dans un congrès lirmm-04796737v1
Giga-SSL: Self-Supervised Learning for Gigapixel Images Tristan Lazard,Marvin Lerousseau,Etienne Decencière,Thomas Walter IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR) Workshops, Jun 2023, Vancouver (CA), Canada. ⟨10.1109/CVPRW59228.2023.00453⟩ Communication dans un congrès hal-04396498v1
EXPERIMENTALLY-GENERATED GROUND TRUTH FOR DETECTING CELL TYPES IN AN IMAGE-BASED IMMUNOTHERAPY SCREEN Joseph Boyd,Zelia Gouveia,Franck Perez,Thomas Walter 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI), Apr 2020, Iowa City, United States. pp.886-890, ⟨10.1109/ISBI45749.2020.9098696⟩ Communication dans un congrès hal-02976141v1
A Deep Learning Approach To Identify MRNA Localization Patterns Rémy Dubois,Arthur Imbert,Aubin Samacoits,Marion Peter,Edouard Bertrandet al. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, France. pp.1386-1390, ⟨10.1109/ISBI.2019.8759235⟩ Communication dans un congrès hal-02343547v1
Predicting Residual Cancer Burden in a triple negative breast cancer cohort Peter Naylor,Joseph Boyd,Marick Lae,Fabien Reyal,Thomas Walter 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI), Apr 2019, Venice, Italy. pp.933-937, ⟨10.1109/ISBI.2019.8759205⟩ Communication dans un congrès hal-02440647v1
ANALYSING DOUBLE-STRAND BREAKS IN CULTURED CELLS FOR DRUG SCREENING APPLICATIONS BY CAUSAL INFERENCE Joseph Boyd,Alice Pinhiero,Elaine Del Nery,Fabien Reyal,Thomas Walter IEEE International Symposium on Biomedical Imaging, Apr 2018, Washington, United States Communication dans un congrès hal-01984323v1
Nuclei segmentation in histopathology images using deep neural networks Peter Naylor,Marik Laé,Fabien Reyal,Thomas Walter 2017 IEEE 14th International Symposium on Biomedical Imaging (ISBI 2017), 2017, Melbourne, Australia Communication dans un congrès hal-01683969v1
NEW GENERAL FEATURES BASED ON SUPERPIXELS FOR IMAGE SEGMENTATION LEARNING V Machairas,T Baldeweck,T Walter,Etienne Decencière International Symposium on Biomedical Imaging, Apr 2016, Prague, Czech Republic Communication dans un congrès hal-01276132v1
Spatial Repulsion Between Markers Improves Watershed Performance Vaïa Machairas,Etienne Decencière,Thomas Walter 12th International Symposium, ISMM 2015, Reykjavik, Iceland, May 27-29, 2015, May 2015, Reykjavik, Iceland. pp.194-202, ⟨10.1007/978-3-319-18720-4_17⟩ Communication dans un congrès hal-01246692v1
Infering an ontology of single cell motions from high-throughput microscopy data Alice Schoenauer Sebag,Sandra Plancade,Céline Raulet-Tomkiewicz,Robert Barouki,Jean-Philippe Vertet al. IEEE 12th International Symposium on Biomedical Imaging, Apr 2015, New York, United States. pp.4, ⟨10.1109/ISBI.2015.7163840⟩ Communication dans un congrès hal-02742630v1
Waterpixels: Superpixels based on the watershed transformation Vaïa Machairas,Etienne Decencière,Thomas Walter IEEE International Conference On Image Processing, Oct 2014, Paris, France. ⟨10.1109/ICIP.2014.7025882⟩ Communication dans un congrès hal-01139797v1

Brevet (1)

Prediction of BRCAness/Homologous Recombination Deficiency of Breast Tumors on Digitalized Slides Anne Vincent-Salomon,Thomas Walter,Etienne Decencière,Tristan Lazard,Guillaume Bataillon France, Patent n° : 18292903. 2024 Brevet hal-04842499v1

Pré-publication, Document de travail (23)

Robust Pan-Cancer Mitotic Figure Detection with YOLOv12 Raphaël Bourgade,Guillaume Balezo,Hana Feki,Lily Monier,Matthieu Blonset al. 2026 Pré-publication, Document de travail hal-05463492v1
Efficient Fine-Tuning of DINOv3 Pretrained on Natural Images for Atypical Mitotic Figure Classification (MIDOG 2025 Task 2 Winner) Guillaume Balezo,Hana Feki,Raphaël Bourgade,Lily Monnier,Matthieu Blonset al. 2026 Pré-publication, Document de travail hal-05463481v1
RNA2seg: a generalist model for cell segmentation in image-based spatial transcriptomics Thomas Defard,Alice Blondel,Sebastien Bellow,Anthony Coleon,Guilherme Dias de Meloet al. 2025 Pré-publication, Document de travail hal-05230880v1
MIPHEI-ViT: Multiplex Immunofluorescence Prediction from H&E Images using ViT Foundation Models Guillaume Balezo,Roger Trullo,Albert Pla Planas,Etienne Decencière,Thomas Walter 2025 Pré-publication, Document de travail hal-05230838v1
Cut-Detector: A Tool for Automated Temporal Analysis of Late Cytokinetic Events Thomas Bonte,Lucas Dubois,Paul Gagna,Rayane Dibsy,Anđela Petrovićet al. 2025 Pré-publication, Document de travail hal-05230503v1
Deep Learning Bridges Histology and Transcriptomics to Predict Molecular Subtypes and Outcomes in Muscle-Invasive Bladder Cancer Alice Blondel,Clémentine Krucker,Valentin Harter,Melissa da Silva,Clarice S Groeneveldet al. 2026 Pré-publication, Document de travail hal-05463469v1
sCellST: a Multiple Instance Learning approach to predict single-cell gene expression from H&E images using spatial transcriptomics Loïc Chadoutaud,Marvin Lerousseau,Daniel Herrero-Saboya,Julian Ostermaier,Jacqueline Fontugneet al. 2025 Pré-publication, Document de travail hal-04887129v1
Interpretable Embeddings for Segmentation-Free Single-Cell Analysis in Multiplex Imaging Simon Gutwein,Daria Lazic,Thomas Walter,Sabine Taschner-Mandl,Roxane Licandro 2025 Pré-publication, Document de travail hal-04984593v1
Self-supervised learning to predict intrahepatic cholangiocarcinoma transcriptomic classes on routine histology Aurélie Beaufrère,Tristan Lazard,Rémy Nicolle,Gwladys Lubuela,Jérémy Augustinet al. 2025 Pré-publication, Document de travail hal-04887163v1
PointFISH -- learning point cloud representations for RNA localization patterns Arthur Imbert,Florian Mueller,Thomas Walter 2023 Pré-publication, Document de travail hal-04029994v1
A point cloud segmentation framework for image-based spatial transcriptomics Thomas Defard,Hugo Laporte,Mallick Ayan,Soulier Juliette,Sandra Curras-Alonsoet al. 2024 Pré-publication, Document de travail hal-04396330v1
AI-Augmented Pathology for Head and Neck Squamous Lesions Improves Non-HN Pathologist Agreement to Expert Level Yaëlle Bellahsen-Harrar,Mélanie Lubrano,Charles Lépine,Aurélie Beaufrère,Claire Bocciarelliet al. 2024 Pré-publication, Document de travail hal-04396487v1
Democratizing computational pathology: optimized Whole Slide Image representations for The Cancer Genome Atlas Tristan Lazard,Marvin Lerousseau,Sophie Gardrat,Anne Vincent-Salomon,Marc-Henri Sternet al. 2024 Pré-publication, Document de travail hal-04396311v1
Learning with minimal effort: leveraging in silico labeling for cell and nucleus segmentation Thomas Bonte,Maxence Philbert,Emeline Coleno,Edouard Bertrand,Arthur Imbertet al. 2024 Pré-publication, Document de travail hal-04396531v1
Simple and Efficient Confidence Score for Grading Whole Slide Images Mélanie Lubrano,Yaëlle Bellahsen-Harrar,Rutger Fick,Cécile Badoual,Thomas Walter 2023 Pré-publication, Document de travail hal-04030031v1
Giga-SSL: Self-Supervised Learning for Gigapixel Images Tristan Lazard,Marvin Lerousseau,Etienne Decencière,Thomas Walter 2023 Pré-publication, Document de travail hal-04030020v1
Diagnosis with Confidence: Deep Learning for Reliable Classification of Squamous Lesions of the Upper Aerodigestive Tract Mélanie Lubrano,Yaëlle Bellahsen-Harrar,Sylvain Berlemont,Sarah Atallah,Emmanuelle Vazet al. 2023 Pré-publication, Document de travail hal-03942781v1
Automatic grading of cervical biopsies by combining full and self-supervision Melanie Lubrano Di Scandalea,Tristan Lazard,Guillaume Balezo,Yaëlle Bellahsen-Harrar,Cécile Badoualet al. 2022 Pré-publication, Document de travail hal-03533712v1
Neural network for the prediction of treatment response in Triple Negative Breast Cancer * Peter Naylor,Tristan Lazard,Guillaume Bataillon,Marick Lae,Anne Vincent-Salomonet al. 2022 Pré-publication, Document de travail hal-03633354v1
The kinesin KIF1C transports APC-dependent mRNAs to cell protrusions Xavier Pichon,Konstadinos Moissoglu,Emeline Coleno,Tianhong Wang,Arthur Imbertet al. 2021 Pré-publication, Document de travail hal-03116720v1
Deep Learning identifies new morphological patterns of Homologous Recombination Deficiency in luminal breast cancers from whole slide images Tristan Lazard,Guillaume Bataillon,Peter Naylor,Tatiana Popova,François-Clément Bidardet al. 2021 Pré-publication, Document de travail hal-03533688v1
Neural network fast-classifies biological images using features selected after their random-forests-importance to power smart microscopy Maël Balluet,Florian Sizaire,Thomas Walter,Jérémy Pont,Baptiste Girouxet al. 2020 Pré-publication, Document de travail hal-03065051v1
A localization screen reveals translation factories and widespread co-translational RNA targeting Racha Chouaib,Adham Safieddine,Xavier Pichon,Arthur Imbert,Oh Sung Kwonet al. 2020 Pré-publication, Document de travail pasteur-02873144v1

HDR (1)

Bioimage Informatics for Phenomics Thomas Walter Bioinformatics [q-bio.QM]. Sorbonne Université, 2020 HDR tel-02981391v1

Proceedings/Recueil des communications (4)

Learning with minimal effort: leveraging in silico labeling for cell and nucleus segmentation Thomas Bonte,Maxence Philbert,Emeline Coleno,Edouard Bertrand,Arthur Imbertet al. ECCV 2022 proceedings (Bio-image computing workshop), ECCV 2022 proceedings (Bio-image computing workshop), 2023 Proceedings/Recueil des communications hal-03935104v1
Learning with Minimal Effort: Leveraging in Silico Labeling for Cell and Nucleus Segmentation Thomas Bonte,Maxence Philbert,Emeline Coleno,Edouard Bertrand,Arthur Imbertet al. ECCV 2022 Workshops. Lecture Notes in Computer Science, 13804, Springer Nature Switzerland, pp.423-436, 2023, Lecture Notes in Computer Science, 978-3-031-25068-2. ⟨10.1007/978-3-031-25069-9_28⟩ Proceedings/Recueil des communications hal-04029154v1
PointFISH: Learning Point Cloud Representations for RNA Localization Patterns Arthur Imbert,Florian Mueller,Thomas Walter European Conference on Computer Vision, ECCV 2022 Workshops. Lecture Notes in Computer Science, 13804, Springer Nature, pp.487-502, 2023, Lecture Notes in Computer Science, 978-3-031-25069-9. ⟨10.1007/978-3-031-25069-9_32⟩ Proceedings/Recueil des communications hal-04029169v1
Automatic Grading of Cervical Biopsies by Combining Full and Self-supervision Mélanie Lubrano,Tristan Lazard,Guillaume Balezo,Yaëlle Bellahsen-Harrar,Cécile Badoualet al. 13807, Springer Nature Switzerland, pp.408-423, 2023, Lecture Notes in Computer Science, ⟨10.1007/978-3-031-25082-8_27⟩ Proceedings/Recueil des communications hal-04029228v1