A large-scale multicenter breast cancer DCE-MRI benchmark dataset with expert segmentations
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arXiv
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| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Preprint |
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2024
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| author | Garrucho, Lidia Kushibar, Kaisar Reidel, Claire-Anne Joshi, Smriti Osuala, Richard Tsirikoglou, Apostolia Bobowicz, Maciej del Riego, Javier Catanese, Alessandro Gwoździewicz, Katarzyna Cosaka, Maria-Laura Abo-Elhoda, Pasant M. Tantawy, Sara W. Sakrana, Shorouq S. Shawky-Abdelfatah, Norhan O. Abdo-Salem, Amr Muhammad Kozana, Androniki Divjak, Eugen Ivanac, Gordana Nikiforaki, Katerina Klontzas, Michail E. García-Dosdá, Rosa Gulsun-Akpinar, Meltem Lafcı, Oğuz Mann, Ritse Martín-Isla, Carlos Prior, Fred Marias, Kostas Starmans, Martijn P. A. Strand, Fredrik Díaz, Oliver Igual, Laura Lekadir, Karim |
| author_facet | Garrucho, Lidia Kushibar, Kaisar Reidel, Claire-Anne Joshi, Smriti Osuala, Richard Tsirikoglou, Apostolia Bobowicz, Maciej del Riego, Javier Catanese, Alessandro Gwoździewicz, Katarzyna Cosaka, Maria-Laura Abo-Elhoda, Pasant M. Tantawy, Sara W. Sakrana, Shorouq S. Shawky-Abdelfatah, Norhan O. Abdo-Salem, Amr Muhammad Kozana, Androniki Divjak, Eugen Ivanac, Gordana Nikiforaki, Katerina Klontzas, Michail E. García-Dosdá, Rosa Gulsun-Akpinar, Meltem Lafcı, Oğuz Mann, Ritse Martín-Isla, Carlos Prior, Fred Marias, Kostas Starmans, Martijn P. A. Strand, Fredrik Díaz, Oliver Igual, Laura Lekadir, Karim |
| contents | Artificial Intelligence (AI) research in breast cancer Magnetic Resonance Imaging (MRI) faces challenges due to limited expert-labeled segmentations. To address this, we present a multicenter dataset of 1506 pre-treatment T1-weighted dynamic contrast-enhanced MRI cases, including expert annotations of primary tumors and non-mass-enhanced regions. The dataset integrates imaging data from four collections in The Cancer Imaging Archive (TCIA), where only 163 cases with expert segmentations were initially available. To facilitate the annotation process, a deep learning model was trained to produce preliminary segmentations for the remaining cases. These were subsequently corrected and verified by 16 breast cancer experts (averaging 9 years of experience), creating a fully annotated dataset. Additionally, the dataset includes 49 harmonized clinical and demographic variables, as well as pre-trained weights for a baseline nnU-Net model trained on the annotated data. This resource addresses a critical gap in publicly available breast cancer datasets, enabling the development, validation, and benchmarking of advanced deep learning models, thus driving progress in breast cancer diagnostics, treatment response prediction, and personalized care. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2406_13844 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | A large-scale multicenter breast cancer DCE-MRI benchmark dataset with expert segmentations Garrucho, Lidia Kushibar, Kaisar Reidel, Claire-Anne Joshi, Smriti Osuala, Richard Tsirikoglou, Apostolia Bobowicz, Maciej del Riego, Javier Catanese, Alessandro Gwoździewicz, Katarzyna Cosaka, Maria-Laura Abo-Elhoda, Pasant M. Tantawy, Sara W. Sakrana, Shorouq S. Shawky-Abdelfatah, Norhan O. Abdo-Salem, Amr Muhammad Kozana, Androniki Divjak, Eugen Ivanac, Gordana Nikiforaki, Katerina Klontzas, Michail E. García-Dosdá, Rosa Gulsun-Akpinar, Meltem Lafcı, Oğuz Mann, Ritse Martín-Isla, Carlos Prior, Fred Marias, Kostas Starmans, Martijn P. A. Strand, Fredrik Díaz, Oliver Igual, Laura Lekadir, Karim Computer Vision and Pattern Recognition Artificial Intelligence Databases Artificial Intelligence (AI) research in breast cancer Magnetic Resonance Imaging (MRI) faces challenges due to limited expert-labeled segmentations. To address this, we present a multicenter dataset of 1506 pre-treatment T1-weighted dynamic contrast-enhanced MRI cases, including expert annotations of primary tumors and non-mass-enhanced regions. The dataset integrates imaging data from four collections in The Cancer Imaging Archive (TCIA), where only 163 cases with expert segmentations were initially available. To facilitate the annotation process, a deep learning model was trained to produce preliminary segmentations for the remaining cases. These were subsequently corrected and verified by 16 breast cancer experts (averaging 9 years of experience), creating a fully annotated dataset. Additionally, the dataset includes 49 harmonized clinical and demographic variables, as well as pre-trained weights for a baseline nnU-Net model trained on the annotated data. This resource addresses a critical gap in publicly available breast cancer datasets, enabling the development, validation, and benchmarking of advanced deep learning models, thus driving progress in breast cancer diagnostics, treatment response prediction, and personalized care. |
| title | A large-scale multicenter breast cancer DCE-MRI benchmark dataset with expert segmentations |
| topic | Computer Vision and Pattern Recognition Artificial Intelligence Databases |
| url | https://arxiv.org/abs/2406.13844 |