Google Scholar
Research Gate
Thesis
Guillaume THIBAULT. Indices de forme et de texture, de la 2D vers la 3D. Application au classement de noyaux de cellules. Présentation. [bib]
Journal Papers
20 - Archana Machireddy, Guillaume Thibault, Kevin G Loftis, Kevin Stoltz, Cecilia E Bueno, Hannah R Smith, Jessica L. Riesterer, Joe W Gray, Xubo Song. "Segmentation of Cellular Ultrastructure on Sparsely Labeled 3D Electron Microscopy Images using Deep Learning", in Frontiers in Bioinformatics, section Computational Biology vol. 3, 2023. doi.org/10.3389/fbinf.2023.1308708
19 - Lucas Pagano, Guillaume Thibault, Walid Bousselham, Jessica L. Riesterer, Xubo Song, Joe W Gray. "Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations", in Frontiers in Bioinformatics, section Computational Biology vol. 3, 2023. doi.org/10.3389/fbinf.2023.1308707.
18 - Johnson et al. "An OMIC and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer", in Cell Reports Medicine, vol. 3, issue 2, 2022.
17 - Kanako Yoshimura, Takahiro Tsujikawa, Junichi Mitsuda, Hiroshi Ogi, Sumiyo Saburi, Gaku Ohmura, Akihito Arai, Saya Shibata, Guillaume Thibault, Young Hwan Chang, Daniel R. Clayburgh, Satoru Yasukawa, Aya Miyagawa-Hayashino, Eiichi Konishi, Kyoko Itoh, Lisa M. Coussens and Shigeru Hirano. "Spatial Profiles of Intratumoral PD-1+ Helper T Cells Predict Prognosis in Head and Neck Squamous Cell Carcinoma", in Frontiers in Immunology / Cancer Immunity and Immunotherapy, 28/10/2021, https://doi.org/10.3389/fimmu.2021.769534
16 - Erik A. Burlingame, Jennifer Eng, Guillaume Thibault, Koei Chin, Joe W. Gray, and Young Hwan Chang. Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms, in Cell Reports Methods 2021. DOI:https://doi.org/10.1016/j.crmeth.2021.100053.
15 - Anne Trinh, Carlos R. Gil Del Alcazar, Sachet A. Shukla, Koei Chin, Young Hwan Chang, Guillaume Thibault, Jennifer Eng, Bojana Jovanovic, C. Marcelo Aldaz, So Yeon Park, Joon Jeong, Catherine Wu, Joe Gray and Kornelia Polyak. “Genomic alterations during the in situ to invasive ductal breast carcinoma transition shaped by the immune system”, Molecular Cancer Research 2020.
14 - Young Hwan Chang, Koei Chin, Guillaume Thibault, Jennifer Eng, Erik Burlingame, and Joe W. Gray. "RESTORE", in Communication Biology 2020. Doi:10.1038/s42003-020-0828-1
13 - Luke Ternes, Ge Huang, Christian Lanciault, Guillaume Thibault, Rachelle Riggers, Joe W. Gray, John Muschle and Young Hwan Chang, "VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts".
Scientific Reports 2020. doi: 10.1038/s41598-020-78061-3
12 - Erik A. Burlingame, Mary McDonnell, Geoffrey F. Schau, Guillaume Thibault, Christian Lanciault, Terry Morgan, Brett E. Johnson, Christopher Corless, Joe W. Gray and Young Hwan Chang. "SHIFT: speedy histological‐to‐immunofluorescent translation of a tumor signature enabled by deep learning", Scientific Reports 2020, doi: 10.1038/s41598-020-74500-3
11 - Geoffrey F. Schau, Erik A. Burlingame, Guillaume Thibault, Tauangtham Anekpuritanang, Ying Wang, Joe W. Gray, Christopher Corless, and Young H. Chang. "Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin". Journal of Medical Imaging 7(1) 2020. doi: 10.1117/1.JMI.7.1.012706
10 - Archana Machireddy, Guillaume Thibault, Alina Tudorica, Aneela Afzal, May Mishal, Kathleen Kemmer, Arpana Naik, Megan Troxell, Eric Goranson, Karen Oh, Nicole Roy, Neda Jafarian, Megan Holtorf, Wei Huang, Xubo Song. “Early Prediction of Breast Cancer Therapy Response using Multi-Resolution Fractal Analysis of DCE-MRI Parametric Maps", Tomography - A Journal for Imaging Research, special Quantitative Imaging Networks (QIN) issue, 2019 5(1), pp90-98.
9 - Takahiro Tsujikawa*, Guillaume Thibault*, Vahid Azimi, Sam Sivagnanam, Grace Banik, Casey Means, Rie Kawashima, Daniel R. Clayburgh, Joe W. Gray, Lisa M. Coussens, Young Hwan Chang. "Robust cell detection and segmentation for image cytometry reveal Th17 cell heterogeneity", Cytometry Part A, 2019.
8 - Langer EM*, Allen-Petersen BL*, King SM, Kendsersky ND, Turnidge MA, Kuziel GM, Riggers R, Samatham R, Amery TS, Jacques SL, Sheppard BC, Korkola JE, Muschler JL, Thibault G, Chang YH, Gray JW, Presnell SC, Nguyen DG, Sears RC. "Modeling tumor phenotypes in vitro with three-dimensional bioprinting", Cell Reports, 2019, 26: 608-623, PMID: 30650355. *Equal contribution.
7 - Ryan S. Lane, Julia Femel, Alec P. Breazeale, Christopher P. Loo, Guillaume Thibault, Andy Kaempf, Motomi Mori, Takahiro Tsujikawa, Young Hwan Chang, Amanda W. Lund. "IFNγ-activated dermal lymphatic vessels inhibit cytotoxic T cells in melanoma and inflamed skin", Journal of Experimental Medicine, October 2018. DOI 10.1084/jem.20180654
6 - Takahiro Tsujikawa, Sushil Kumar, Rohan N. Borkar, Vahid Azimi, Guillaume Thibault, Young Hwan Chang, Ariel Balter, Rie Kawashima, Gina Choe, David Sauer, Edward El Rassi, Daniel R. Clayburgh, Molly F. Kulesz-Martin, Eric R. Lutz, Lei Zheng, Elizabeth M. Jaffee, Patrick Leyshock, Adam A. Margolin, Motomi Mori, Joe W. Gray, Paul W. Flint, and Lisa M. Coussen. "Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis", in Cell Reports, April 2017. DOI https://doi.org/10.1016/j.celrep.2017.03.037
5 - Guillaume Thibault, A. Tudorica, A. Afzal, S. Chui, A. Naik, M. Troxell, K. Kemmer, K. Oh, N. Roy, N. Jafarian, M. Holtorf, Wei Huang and Xubo Song. "DCE-MRI Texture Features for Early Prediction of Breast Cancer Therapy Response", in Tomography, vol. 3, n° 1, March 2017. https://www.ncbi.nlm.nih.gov/pubmed/28691102 [bib]
4 - Xiwei Zhang, Guillaume Thibault, Etienne Decencière, Beatriz Marcotegui, Bruno Laÿ, Ronan Danno, Guy Cazuguel, Gwénolé Quellec, Mathieu Lamard, Pascale Massin and Ali Erginay. "Exudate detection in color retinal images for mass screening of diabetic retinopathy", in Medical Image Analysis, vol. 18, n° 7, pp. 1026-1043, 2014. [bib]
3 - Guillaume Thibault, Jesus Angulo and Fernand Meyer. "Advanced Statistical Matrices for Texture Characterization: Application to Cell Classification", in IEEE Transaction on Biomedical Engineering, vol. 61, n° 3, pp. 630-637, 2014. [bib]
2 - Etienne Decencière, Guy Cazuguel, Xiwei Zhang, Guillaume Thibault, Jean-Claude Klein, Fernand Meyer, Beatriz Marcotegui, Gwénolé Quellec, Mathieu Lamard, Ronan Danno, Damien Eli, Pascale Massin, Ali Erginay, Bruno Laÿ and Agnès Chabouis. "TeleOphta: Machine Learning and image processing methods for teleophthalmology", in IRBM, vol. 34, n° 2, pp. 196-203, 2013. [bib]
1 - Guillaume Thibault, Bernard Fertil, Claire Navarro, Sandrine Pereira, Pierre Cau, Nicolas Levy, Jean Sequeira and Jean-Luc Mari. "Shape and Texture Indexes, Application to Cell Nuclei Classification", in International Journal of Pattern Recognition and Artificial Intelligence (IJPRAI), vol. 27, n° 1, 2013. [bib]
arXiv
1 - Guillaume Thibault and Izhak Shafran. "Fuzzy Statistical Matrices for Cell Classification", November 2016.
bioRxiv
4 - Geoffrey F. Schau, Hassan Ghani, Erik A. Burlingame, Guillaume Thibault, Joe W. Gray, Christopher Corless, and Young Hwan Chang. “Transfer Learning for Infer- ence of Metastatic Origin from Whole Slide Histology”. In: bioRxiv (2021). DOI: 10.1101/2021.04.21.440864
3 - Erik A. Burlingame, Jennifer Eng, Guillaume Thibault, Koei Chin, Joe W. Gray, and Young Hwan Chang. “Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms”. In: bioRxiv 2020, p. 2020.12.11.422048. DOI: 10.1101/2020.12.11.422048
2 - Johnson, B. E., Creason, A. L., Stommel, J. M., Keck, J., Parmar, S., Betts, C. B., Blucher, A., Boniface, C., Bucher, E., Burlingame, E. A., Chin, K., Eng, J., Feiler, H. S., Kolodzie, A., Kong, B., Labrie, M., Leyshock, P., Mitri, S., Patterson, J., Riesterer, J. L., Sivagnanam, S., Sudar, D., Thibault, G., Zheng, C., Nan, X., Heiser, L. M., Spellman, P. T., Thomas, G. V., Demir, E., Chang, Y. H., Coussens, L. M., Guimaraes, A. R., Corless, C., Goecks, J., Bergan, R., Mitri, Z., Mills, G. B., Gray, J. W. "An Integrated Clinical, Omic, and Image Atlas of an Evolving Metastatic Breast Cancer." bioRxiv 2020.12.03.408500; doi: https://doi.org/10.1101/2020.12.03.408500
1 - Young Hwan Chang, Koei Chin, Guillaume Thibault, Jennifer Eng, Lydia Grace, Erik Burlingame, and Joe W. Gray. "RESTORE: Robust intEnSiTy nORmalization mEthod for Multiplex Imaging", 2019.
National Journal Paper
1 - Guillaume Thibault, Bernard Fertil, Jean Sequeira et Jean-Luc Mari. « Indices de forme et de texture, de la 2D vers la 3D. Application au classement de noyaux de cellules », dans Revue des Sciences et Technologies de l’Information (RSTI) 2/2010. [bib]
Book Chapter
3 - Jessica L. Riesterer, Claudia S. López, Erin S. Stempinski, Melissa Williams, Kevin Loftis, Kevin Stoltz, Guillaume Thibault, Christian Lanicault, Todd Williams, and Joe W. Gray. "A workflow for visualizing human cancer biopsies using large-format electron microscopy", in Methods in Cell Biology, vol. 158, https://doi.org/10.1016/bs.mcb.2020.01.005
2 - Jennifer Eng, Guillaume Thibault, Shiuh-Wen Luoh, Joe W. Gray, Young Hwan Chang, and Koei Chin, "Cyclic Multiplexed-Immunofluorescence (cmIF), a Highly Multiplexed Method for Single-Cell Analysis", in Methods Molecular Biology, vol. 2055 "Biomarkers for Immunotherapy of Cancer", "Methods and Protocols", ISBN: 978-1-4939-9772-5, 2019.
1 - Claudia S. Lòpez, Cédric Bouchet-Marquis, Christopher P. Arthur, Jessica L. Riesterer, Gregor Heiss, Guillaume Thibault, Lee Pullan, Sunjong Kwon, and Joe W. Gray. “A fully integrated three-dimensional fluorescence to electron microscopy correlative workflow”, in Methods in Cell Biology, 2017.
National Book
1 - Guillaume Thibault. « Indices de forme et de texture ». Aux Editions Universitaires Européennes, ISBN 978-613-1-53989-3. [bib]
Patents
2 - Young Hwan Chang and Guillaume Thibault. "Automatic Nuclei Segmentation in Histopathology Images", US20190042826A1, 2018/08. Google.
1 - Xiwei Zhang, Guillaume Thibault, Etienne Decencière. "Method for analyzing a photograph of the retina or a bank of photographs of the retina", WO2013160619 (A1), 2013/10. Google, Espacenet. [bib]
Conferences
25 - Walid Bousselham, Guillaume Thibault, Lucas Pagano, Archana Machireddy, Joe Gray, Young Hwan Chang, Xubo Song. "Efficient Self-Ensemble Framework for Semantic Segmentation", British Machine Vision Conference (BMCV) 2022.
24 - Gray E, Liudahl S, Sivagnanam S, Betts C, Link J, Sheppard B, Sears R, Thibault G, Gray JW, Coussens LM, Chang YH. Activation vs. Organization: Prognostic Implications of T and B Cell Features of the PDAC Microenvironment. In International Symposium on Mathematical and Computational Oncology 2020 Oct 8 (p44-55). Springer, Cham.
23 - Ternes L, Thibault G, Gray JW, Chang YH. Iterative deep learning-based segmentation on cyclic immunofluorescence imaging by using recursive refinement, IEEE International Symposium on Biomedical Imaging (ISBI2020), the Marriott CoralVille, Iowa City, April 3-7, 2020.
22 - Erik A.Burlingame,JenniferEng,GuillaumeThibault,GeoffreyF.Schau,KoeiChin, Joe W. Gray and Young Hwan Chang, "Balanced learning of cellstate representa- tions," poster presentation at the Learning Meaningful Representations of Life work- shop at the Neural Information Processing Systems 2019.
21 - Nathan McMahon, Jocelyn Jones, Jennifer Eng, Sunjong Kwon, Young Hwan Chang, Guillaume Thibault, Koei Chin, Michel Nederlof, Joe W. Gray, Summer Gibbs, "Signal removal methods for highly multiplexed immunofluorescent staining using antibody conjugated oligonucleotides", in Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII, March 2019, DOI: 10.1117/12.2510573.
20 - Geoffrey F. Schau, Guillaume Thibault, Mark A. Dane, Joe W. Gray, Laura M. Heiser, and Young Hwan Chang. "Variational autoencoding tissue response to microenvironment perturbation", Proc. SPIE 10949, Medical Imaging 2019: Image Processing, 109491M, doi: 10.1117/12.2512660.
19 - Archana Machireddy, Guillaume THIBAULT, Xubo SONG, and Wei Huang. "Analysis of DCE-MRI for Early Prediction of Breast Cancer Therapy Response", in 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS), 2018.
18 - Young Hwan Chang, Guillaume Thibault, Brett Johnson, Owen Madin, Cole Meyers, Vahid Azimi, Danielle Jorgens, Christoper Corless, Adam Margolin, and Joe W. Gray. « Deep Leaning based Nucleus Classification in Histological Tissue Image », in EMBS 2017.
17 - Vahid Azimi, Young Hwan Chang, Guillaume Thibault, Jaclyn Smith, Takahiro Tsujikana, Christoper Corless, Adam Margolin, and Joe W. Gray. « Quantitative Image Analysis Pipeline for Tumor Purity Estimation », in IEEE ISBI 2017.
16 - Young Hwan Chang, Guillaume Thibault, Brett Johnson, Adam Margolin, Joe W. Gray. "Integrative Analysis on Histopathological Image for Identifying Cellular Heterogeneity", in SPIE Medical Imaging (Digital Pathology), 2017 (Accepted).
15 - Guillaume Thibault, A. Tudorica, A. Afzal, S. Chui, A. Naik, M. Troxell, K. Kemmer, K. Oh, N. Roy, M. Holtorf, Wei Huang, and Xubo Song. « Texture Feature Analysis of Quantitative and Semi-Quantitative DCE-MRI Metrics for Early Prediction of Breast Cancer Therapy Response », in International Society for Magnetic Resonance in Medicine (ISMRM) 2016. [bib]
14 - Young Hwan Chang, Guillaume Thibault, Vahid Azimi, Brett Johnson, Danielle Jorgens, Jason Link, Adam Margolin and Joe Gray. « Quantitative Analysis of Histological Tissue Image based on Cytological Profiles ans Spatial Statistics », in the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS) 2016.
13 - Guillaume Thibault, A. Tudorica, A. Afzal, S. Chui, A. Naik, M. Troxell, K. Kemmer, K. Oh, N. Roy, M. Holtorf, Wei Huang, and Xubo Song. « Early Prediction of Breast Cancer Therapy Response to Neoadjuvant Chemotherapy through Texture Analysis of DCE-MRI », in MICCAI-BIA 2015, 3rd MICCAI workshop on Breast Image Analysis, p145-152.[bib]
12 - Guillaume Thibault, A. Tudorica, A. Afzal, S. Chui, A. Naik, M. Troxell, K. Kemmer, K. Oh, N. Roy, M. Holtorf, Wei Huang, and Xubo Song. « DCE-MRI Texture Analysis for Early Prediction of Breast Cancer Therapy Response », in International Society for Magnetic Resonance in Medicine (ISMRM) 2015. [bib]
11 - Nastaran Ghadar, Xikang Zhang, Kang Li, Deniz Erdogmus, Guillaume Thibault, Alireza Bayestehtashk, Izhak Shafran, Kris Coleman, and Kathleen Grant. « Visual hull reconstruction for automated primate behavior observation », in IEEE International Workshop on Machine Learning for Signal Processing (MLSP), 2013.
10 - Guillaume Thibault, Kristiina Iljin, Christopher Arthur, Izhak Shafran, and Joe Gray. « Adaptive H-Extrema for Automatic Immunogold Particle Detection », in CIARP 2013. [bib]
9 - Guillaume Thibault, Jesùs Angulo. « Efficient Statistical/Morphological Cell Texture Characterization and Classification », in ICPR 2012. Poster. [bib]
8 - Xiwei Zhang, Guillaume Thibault, Etienne Decencière, Guy Cazuguel, Gwénolé Quellec, Ronan Danno, Bruno Laÿ, Ali Erginay, Pascale Massin, Zeynep Guvenli-Victor, and Agnes Chabouis. « Automatic Detection of Exudates in Retinal Images », in ARVO 2012. Poster. [bib]
7 - Xiwei Zhang, Guillaume Thibault, Etienne Decencière, Guy Cazuguel, Gwénolé Quellec, Ronan Danno, Bruno Laÿ, Ali Erginay, Pascale Massin, Zeynep Guvenli-Victor, and Agnes Chabouis. « Spatial Normalization of Eye Fundus Images », in ISBI 2012. Poster. [bib]
6 - Jesùs Angulo, Delphine Reberioux, Guillaume Thibault, Chantal Etievant, and Fernand Meyer. « Self-normalization of cell images in multifocus quantitative fluorescence », in International Congress for Stereology (ICS) 2011, October, Beijing, China. [bib]
5 - Xiwei Zhang, Guillaume Thibault, and Etienne Decencière. «Application of the Morphological Ultimate Opening to the Detection of Microaneurysms on Eye Fundus Images from Clinical Databases», in International Congress for Stereology (ICS) 2011. [bib]
4 - Guillaume Thibault, Jesùs Angulo, and Fernand Meyer. «Advanced Statistical Matrices for Texture Characterization: Application to DNA Chromatin and Microtubule Netwok Classification», in International Conference on Image Processing (ICIP) 2011. [bib]
3 - Guillaume Thibault, Bernard Fertil, Claire Navarro, Sandrine Pereira, Pierre Cau, Nicolas Levy, Jean Sequeira, and Jean-Luc Mari. « Texture Indexes and Gray Level Size Zone Matrix. Application to Cell Nuclei Classification », in Pattern Recognition and Information Processing (PRIP) 2009. [bib]
2 - Guillaume Thibault, Bernard Fertil, Jean Sequeira, and Jean-Luc Mari. « Cell Nuclei Classification Using Shape And Texture Indexes » in WSCG 2008. Poster. [bib]
1 - Romain Raffin, Guillaume Thibault, and Gilles Gesquiere. « Simple And Efficient Tools For VirSculpt », in GRAPP 2006. [bib]
National Conferences
2 - Guillaume Thibault, Bernard Fertil, Jean Sequeira et Jean-Luc Mari. « Indices de textures : application au classement de noyaux de cellules », dans MajecSTIC 2008. [bib]
1 - Guillaume Thibault, Bernard Fertil, Jean Sequeira et Jean-Luc Mari. « Indices de formes : de la 2D vers la 3D. Application au classement de noyaux de cellules », dans AFIG 2007. [bib]
Master
Stage de master.