Research output per year
Research output per year
- 43 results
Search results
-
2023
Automated large volume sample preparation for vEM
Stempinski, E. S., Pagano, L., Riesterer, J. L., Adamou, S. K., Thibault, G., Song, X., Chang, Y. H. & López, C. S., Jan 2023, Volume Electron Microscopy. Narayan, K., Narayan, K., Collinson, L. & Verkade, P. (eds.). Academic Press Inc., p. 1-32 32 p. (Methods in Cell Biology; vol. 177).Research output: Chapter in Book/Report/Conference proceeding › Chapter
1 Scopus citations -
Efficient semi-supervised semantic segmentation of electron microscopy cancer images with sparse annotations
Pagano, L., Thibault, G., Bousselham, W., Riesterer, J. L., Song, X. & Gray, J., 2023, In: Frontiers in Bioinformatics. 3, 1308707.Research output: Contribution to journal › Article › peer-review
Open Access -
Large-Scale Electron Microscopy to Find Nanoscale Detail in Cancer
Riesterer, J. L., Bueno, C., Stempinski, E. S., Adamou, S. K., López, C. S., Thibault, G., Pagano, L., Grieco, J., Olson, S., Machireddy, A., Chang, Y. H., Song, X. & Gray, J. W., Jul 22 2023, In: Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 29, 1, p. 1078-1079 2 p.Research output: Contribution to journal › Article › peer-review
Open Access -
Segmentation of cellular ultrastructures on sparsely labeled 3D electron microscopy images using deep learning
Machireddy, A., Thibault, G., Loftis, K. G., Stoltz, K., Bueno, C. E., Smith, H. R., Riesterer, J. L., Gray, J. & Song, X., 2023, In: Frontiers in Bioinformatics. 3, 1308708.Research output: Contribution to journal › Article › peer-review
Open Access -
2022
An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer
Johnson, B. E., Creason, A. L., Stommel, J. M., Keck, J. M., Parmar, S., Betts, C. B., Blucher, A., Boniface, C., Bucher, E., Burlingame, E., Camp, T., Chin, K., Eng, J., Estabrook, J., Feiler, H. S., Heskett, M. B., Hu, Z., Kolodzie, A., Kong, B. L., Labrie, M., & 26 others, Feb 15 2022, In: Cell Reports Medicine. 3, 2, 100525.Research output: Contribution to journal › Article › peer-review
Open Access16 Scopus citations -
Efficient Self-Ensemble for Semantic Segmentation
Bousselham, W., Thibault, G., Pagano, L., Machireddy, A., Gray, J., Chang, Y. H. & Song, X., 2022.Research output: Contribution to conference › Paper › peer-review
1 Scopus citations -
2021
Genomic alterations during the in situ to invasive ductal breast carcinoma transition shaped by the immune system
Trinh, A., Gil Del Alcazar, C. R., Shukla, S. A., Chin, K., Chang, Y. H., Thibault, G., Eng, J., Jovanovic, B., Aldaz, C. M., Park, S. Y., Jeong, J., Wu, C., Gray, J. & Polyak, K., Apr 2021, In: Molecular Cancer Research. 19, 4, p. 623-635 13 p.Research output: Contribution to journal › Article › peer-review
Open Access21 Scopus citations -
Spatial Profiles of Intratumoral PD-1+ Helper T Cells Predict Prognosis in Head and Neck Squamous Cell Carcinoma
Yoshimura, K., Tsujikawa, T., Mitsuda, J., Ogi, H., Saburi, S., Ohmura, G., Arai, A., Shibata, S., Thibault, G., Chang, Y. H., Clayburgh, D. R., Yasukawa, S., Miyagawa-Hayashino, A., Konishi, E., Itoh, K., Coussens, L. M. & Hirano, S., Oct 28 2021, In: Frontiers in immunology. 12, 769534.Research output: Contribution to journal › Article › peer-review
Open Access10 Scopus citations -
Toward reproducible, scalable, and robust data analysis across multiplex tissue imaging platforms
Burlingame, E. A., Eng, J., Thibault, G., Chin, K., Gray, J. W. & Chang, Y. H., Aug 23 2021, In: Cell Reports Methods. 1, 4, 100053.Research output: Contribution to journal › Article › peer-review
Open Access14 Scopus citations -
2020
Activation vs. Organization: Prognostic Implications of T and B Cell Features of the PDAC Microenvironment
Gray, E., Liudahl, S., Sivagnanam, S., Betts, C., Link, J., Keith, D., Sheppard, B., Sears, R., Thibault, G., Gray, J. W., Coussens, L. M. & Chang, Y. H., 2020, Mathematical and Computational Oncology - Second International Symposium, ISMCO 2020, 2020, Proceedings. Bebis, G., Alekseyev, M., Cho, H., Gevertz, J. & Rodriguez Martinez, M. (eds.). Springer Science and Business Media Deutschland GmbH, p. 44-55 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 12508 LNBI).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access -
A workflow for visualizing human cancer biopsies using large-format electron microscopy
Riesterer, J. L., López, C. S., Stempinski, E. S., Williams, M., Loftis, K., Stoltz, K., Thibault, G., Lanicault, C., Williams, T. & Gray, J. W., 2020, Methods in Cell Biology. Tran, P. (ed.). Academic Press Inc., p. 163-181 19 p. (Methods in Cell Biology; vol. 158).Research output: Chapter in Book/Report/Conference proceeding › Chapter
Open Access10 Scopus citations -
Cyclic Multiplexed-Immunofluorescence (cmIF), a Highly Multiplexed Method for Single-Cell Analysis
Eng, J., Thibault, G., Luoh, S. W., Gray, J. W., Chang, Y. H. & Chin, K., 2020, Methods in Molecular Biology. Humana Press Inc., p. 521-562 42 p. (Methods in Molecular Biology; vol. 2055).Research output: Chapter in Book/Report/Conference proceeding › Chapter
24 Scopus citations -
Predicting primary site of secondary liver cancer with a neural estimator of metastatic origin
Schau, G. F., Burlingame, E. A., Thibault, G., Anekpuritanang, T., Wang, Y., Gray, J. W., Corless, C. & Chang, Y. H., Jan 1 2020, In: Journal of Medical Imaging. 7, 1, 012706.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
Quantification of fluorophore distribution and therapeutic response in matched in vivo and ex vivo pancreatic cancer model systems
Solanki, A., King, D., Thibault, G., Wang, L. & Gibbs, S. L., 2020, In: PloS one. 15, 2, e0229407.Research output: Contribution to journal › Article › peer-review
Open Access1 Scopus citations -
RESTORE: Robust intEnSiTy nORmalization mEthod for multiplexed imaging
Chang, Y. H., Chin, K., Thibault, G., Eng, J., Burlingame, E. & Gray, J. W., Dec 1 2020, In: Communications Biology. 3, 1, 111.Research output: Contribution to journal › Article › peer-review
Open Access20 Scopus citations -
SHIFT: speedy histological-to-immunofluorescent translation of a tumor signature enabled by deep learning
Burlingame, E. A., McDonnell, M., Schau, G. F., Thibault, G., Lanciault, C., Morgan, T., Johnson, B. E., Corless, C., Gray, J. W. & Chang, Y. H., Dec 1 2020, In: Scientific Reports. 10, 1, 17507.Research output: Contribution to journal › Article › peer-review
Open Access22 Scopus citations -
The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
Human Tumor Atlas Network, Apr 16 2020, In: Cell. 181, 2, p. 236-249 14 p.Research output: Contribution to journal › Review article › peer-review
Open Access246 Scopus citations -
VISTA: VIsual Semantic Tissue Analysis for pancreatic disease quantification in murine cohorts
Ternes, L., Huang, G., Lanciault, C., Thibault, G., Riggers, R., Gray, J. W., Muschler, J. & Chang, Y. H., Dec 2020, In: Scientific Reports. 10, 1, 20904.Research output: Contribution to journal › Article › peer-review
Open Access5 Scopus citations -
2019
cmIF: A Python Library for Scalable Multiplex Imaging Pipelines
Eng, J., Bucher, E., Gray, E., Campbell, L. G., Thibault, G., Heiser, L., Gibbs, S., Gray, J. W., Chin, K. & Chang, Y. H., 2019, Mathematical and Computational Oncology - 1st International Symposium, ISMCO 2019, Proceedings. Bebis, G., Benos, T., Chen, K., Jahn, K. & Lima, E. (eds.). Springer, p. 37-43 7 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11826 LNCS).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
1 Scopus citations -
Early Prediction of Breast Cancer Therapy Response using Multiresolution Fractal Analysis of DCE-MRI Parametric Maps
Machireddy, A., Thibault, G., Tudorica, L., Afzal, A., Mishal, M., Kemmer, K., Naik, A., Troxell, M., Goranson, E., Oh, K., Roy, N., Jafarian, N., Holtorf, M., Huang, W. & Song, X., Mar 1 2019, In: Tomography (Ann Arbor, Mich.). 5, 1, p. 90-98 9 p.Research output: Contribution to journal › Article › peer-review
Open Access23 Scopus citations -
Modeling Tumor Phenotypes In Vitro with Three-Dimensional Bioprinting
Langer, E. M., Allen-Petersen, B. L., King, S. M., Kendsersky, N. D., Turnidge, M. A., Kuziel, G. M., Riggers, R., Samatham, R., Amery, T. S., Jacques, S., Sheppard, B. C., Korkola, J. E., Muschler, J. L., Thibault, G., Chang, Y. H., Gray, J. W., Presnell, S. C., Nguyen, D. G. & Sears, R. C., Jan 15 2019, In: Cell Reports. 26, 3, p. 608-623.e6Research output: Contribution to journal › Article › peer-review
Open Access157 Scopus citations -
Robust Cell Detection and Segmentation for Image Cytometry Reveal Th17 Cell Heterogeneity
Tsujikawa, T., Thibault, G., Azimi, V., Sivagnanam, S., Banik, G., Means, C., Kawashima, R., Clayburgh, D. R., Gray, J. W., Coussens, L. M. & Chang, Y. H., Apr 2019, In: Cytometry Part A. 95, 4, p. 389-398 10 p.Research output: Contribution to journal › Article › peer-review
Open Access13 Scopus citations -
Signal removal methods for highly multiplexed immunofluorescent staining using antibody conjugated oligonucleotides
McMahon, N., Jones, J., Eng, J., Kwon, S., Chang, Y. H., Thibault, G., Chin, K., Nederlof, M., Gray, J. & Gibbs, S. L., 2019, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XVII. Leary, J. F., Tarnok, A. & Farkas, D. L. (eds.). SPIE, 108810X. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10881).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access -
Variational autoencoding tissue response to microenvironment perturbation
Schau, G. F., Thibault, G., Dane, M. A., Gray, J. W., Heiser, L. M. & Chang, Y. H., 2019, Medical Imaging 2019: Image Processing. Angelini, E. D., Angelini, E. D., Angelini, E. D. & Landman, B. A. (eds.). SPIE, 109491M. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10949).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access1 Scopus citations -
2018
Analysis of DCE-MRI for Early Prediction of Breast Cancer Therapy Response
Machireddy, A., Thibault, G., Huang, W. & Song, X., Oct 26 2018, 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2018. Institute of Electrical and Electronics Engineers Inc., p. 682-685 4 p. 8512301. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS; vol. 2018-July).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
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IFNγ-activated dermal lymphatic vessels inhibit cytotoxic T cells in melanoma and inflamed skin
Lane, R. S., Femel, J., Breazeale, A. P., Loo, C. P., Thibault, G., Kaempf, A., Mori, M., Tsujikawa, T., Chang, Y. H. & Lund, A., Dec 1 2018, In: Journal of Experimental Medicine. 215, 12, p. 3057-3074 18 p.Research output: Contribution to journal › Article › peer-review
Open Access107 Scopus citations -
2017
A fully integrated, three-dimensional fluorescence to electron microscopy correlative workflow
López, C. S., Bouchet-Marquis, C., Arthur, C. P., Riesterer, J. L., Heiss, G., Thibault, G., Pullan, L., Kwon, S. & Gray, J. W., 2017, In: Methods in cell biology. 140, p. 149-164 16 p.Research output: Contribution to journal › Article › peer-review
13 Scopus citations -
Breast cancer histopathology image analysis pipeline for tumor purity estimation
Azimi, V., Chang, Y. H., Thibault, G., Smith, J., Tsujikawa, T., Kukull, B., Jensen, B., Corless, C., Margolin, A. & Gray, J. W., Jun 15 2017, 2017 IEEE 14th International Symposium on Biomedical Imaging, ISBI 2017. IEEE Computer Society, p. 1137-1140 4 p. 7950717. (Proceedings - International Symposium on Biomedical Imaging).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access9 Scopus citations -
DCE-MRI Texture Features for Early Prediction of Breast Cancer Therapy Response
Thibault, G., Tudorica, A., Afzal, A., Chui, S. Y. C., Naik, A., Troxell, M. L., Kemmer, K. A., Oh, K. Y., Roy, N., Jafarian, N., Holtorf, M. L., Huang, W. & Song, X., Mar 1 2017, In: Tomography (Ann Arbor, Mich.). 3, 1, p. 23-32 10 p.Research output: Contribution to journal › Article › peer-review
Open Access55 Scopus citations -
Deep learning based Nucleus Classification in pancreas histological images
Chang, Y. H., Thibault, G., Madin, O., Azimi, V., Meyers, C., Johnson, B., Link, J., Margolin, A. & Gray, J. W., Sep 13 2017, 2017 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Smarter Technology for a Healthier World, EMBC 2017 - Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 672-675 4 p. 8036914. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
42 Scopus citations -
Integrative analysis on histopathological image for identifying cellular heterogeneity
Chang, Y. H., Thibault, G., Johnson, B., Margolin, A. & Gray, J. W., 2017, Medical Imaging 2017: Digital Pathology. Gurcan, M. N. & Tomaszewski, J. E. (eds.). SPIE, 101400T. (Progress in Biomedical Optics and Imaging - Proceedings of SPIE; vol. 10140).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access -
Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis
Tsujikawa, T., Kumar, S., Borkar, R. N., Azimi, V., Thibault, G., Chang, Y. H., Balter, A., Kawashima, R., Choe, G., Sauer, D., El Rassi, E., Clayburgh, D. R., Kulesz-Martin, M. F., Lutz, E. R., Zheng, L., Jaffee, E. M., Leyshock, P., Margolin, A. A., Mori, M., Gray, J. W., & 2 others, Apr 4 2017, In: Cell Reports. 19, 1, p. 203-217 15 p.Research output: Contribution to journal › Article › peer-review
Open Access364 Scopus citations -
2016
Quantitative analysis of histological tissue image based on cytological profiles and spatial statistics
Chang, Y. H., Thibault, G., Azimi, V., Johnson, B., Jorgens, D., Link, J., Margolin, A. & Gray, J. W., Oct 13 2016, 2016 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2016. Institute of Electrical and Electronics Engineers Inc., p. 1175-1178 4 p. 7590914. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS; vol. 2016-October).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
7 Scopus citations -
2014
Advanced statistical matrices for texture characterization: Application to cell classification
Thibault, G., Angulo, J. & Meyer, F., Mar 2014, In: IEEE Transactions on Biomedical Engineering. 61, 3, p. 630-637 8 p., 6621011.Research output: Contribution to journal › Article › peer-review
192 Scopus citations -
Exudate detection in color retinal images for mass screening of diabetic retinopathy
Zhang, X., Thibault, G., Decencière, E., Marcotegui, B., Laÿ, B., Danno, R., Cazuguel, G., Quellec, G., Lamard, M., Massin, P., Chabouis, A., Victor, Z. & Erginay, A., Oct 2014, In: Medical Image Analysis. 18, 7, p. 1026-1043 18 p.Research output: Contribution to journal › Article › peer-review
Open Access228 Scopus citations -
2013
Adaptive H-extrema for automatic immunogold particle detection
Thibault, G., Iljin, K., Arthur, C., Shafran, I. & Gray, J., 2013, Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications - 18th Iberoamerican Congress, CIARP 2013, Proceedings. PART 2 ed. p. 238-245 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8259 LNCS, no. PART 2).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
Open Access -
Shape and texture indexes application to cell nuclei classification
Thibault, G., Fertil, B., Navarro, C., Pereira, S., Cau, P., Levy, N., Sequeira, J. & Mari, J. L., Feb 2013, In: International Journal of Pattern Recognition and Artificial Intelligence. 27, 1, 1357002.Research output: Contribution to journal › Article › peer-review
144 Scopus citations -
TeleOphta: Machine learning and image processing methods for teleophthalmology
Decencière, E., Cazuguel, G., Zhang, X., Thibault, G., Klein, J. C., Meyer, F., Marcotegui, B., Quellec, G., Lamard, M., Danno, R., Elie, D., Massin, P., Viktor, Z., Erginay, A., Laÿ, B. & Chabouis, A., Apr 2013, In: IRBM. 34, 2, p. 196-203 8 p.Research output: Contribution to journal › Article › peer-review
365 Scopus citations -
Visual hull reconstruction for automated primate behavior observation
Ghadar, N., Zhang, X., Li, K., Erdogmus, D., Thibault, G., Bayestehtashk, A., Coleman, I. S. K. & Grant, K. A., 2013, 2013 IEEE International Workshop on Machine Learning for Signal Processing - Proceedings of MLSP 2013. 6661922. (IEEE International Workshop on Machine Learning for Signal Processing, MLSP).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
1 Scopus citations -
2012
Efficient statistical/morphological cell texture characterization and classification
Thibault, G. & Angulo, J., 2012, ICPR 2012 - 21st International Conference on Pattern Recognition. p. 2440-2443 4 p. 6460660. (Proceedings - International Conference on Pattern Recognition).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
18 Scopus citations -
2011
Advanced statistical matrices for texture characterization: Application to DNA chromatin and microtubule network classification
Thibault, G., Angulo, J. & Meyer, F., 2011, ICIP 2011: 2011 18th IEEE International Conference on Image Processing. p. 53-56 4 p. 6116401. (Proceedings - International Conference on Image Processing, ICIP).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
12 Scopus citations -
2008
Poster: Classification of cell nuclei using shape and texture indexes
Thibault, G., Devic, C., Horn, J. F., Fertil, B., Sequeira, J. & Mari, J. L., 2008, 16th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision, WSCG'2008 - In Co-operation with EUROGRAPHICS, Full Papers. p. 25-28 4 p. (16th International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision, WSCG'2008 - In Co-operation with EUROGRAPHICS, Full Papers).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
3 Scopus citations -
2006
Simple and efficient tools for virsculpt
Raffin, R., Thibault, G. & Gesquière, G., 2006, GRAPP 2006 - Proceedings of the 1st International Conference on Computer Graphics Theory and Applications. p. 436-440 5 p. (GRAPP 2006 - Proceedings of the 1st International Conference on Computer Graphics Theory and Applications).Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
1 Scopus citations