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Paper · 2406.13844 · 2024

A large-scale multicenter breast cancer DCE-MRI benchmark dataset with expert segmentations

arXiv · PDF · Open in the Atlas

Code that ran

We lifted 3 functions out of this paper's own repositories and ran 3 of them in a sandbox. "Ran" means the function executed on a synthesized input and returned a value. It is not a reproduction of the paper's results.

RepositoryRoleRan
lidiagarrucho/mama-mia canonical 3 of 3
FunctionStatusWhere it lives
filter_clinical_data Ran lidiagarrucho/mama-mia/src/clinical_data.py
pointer only (licence: NOASSERTION) · get_code("7ea3ef0e6f9fddf4")
filter_patient_info Ran lidiagarrucho/mama-mia/src/clinical_data.py
pointer only (licence: NOASSERTION) · get_code("492419b818aa283d")
region_or_label_to_mask Ran lidiagarrucho/mama-mia/src/challenge/metrics.py
pointer only (licence: NOASSERTION) · get_code("be711f3c68679d28")

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Abstract

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.

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