André Ferreira
Publications
++nnU-Net: Scaling nnU-Net with Prefix-Based Data Augmentation
The nnU-Net has demonstrated continuous success in medical segmentation tasks, which heavily rely on the availability and diversity of annotated biomedical data. However, assembling medical imaging cohorts remains challenging due to numerous factors such as privacy regulations and annotation costs. As a result, data augmentation plays a crucial role in increasing data availability while maintaining anatomical feasibility. Hence, we propose the ++nnU-Net, a novel data augmentation module based on image registration that operates prior to preprocessing and training take place. Our framework was evaluated across five different 2D datasets. In this workflow, image data go through a two-stage registration process, generating new warped images. The transformations are then applied to the respective segmentation. In addition, the pipeline computes available disk space, generates supplementary binary synthetic masks and generates checkpoints. We demonstrate that the ++nnU-Net outperforms the nnU-Net baseline, yielding improvements in Dice Similarity Coefficient scores. In the most prominent cases, we observe performance gains of approximately 22\%. These findings highlight the effectiveness of registration-based data augmentation, particularly for 2D medical imaging datasets and suggest that the ++nnU-Net provides a practical and scalable approach for enhancing segmentation performance in data-limited settings. The source code for the ++nnU-Net is available at: https://github.com/sofia-adelie/plusplusnnunet.git
Curated endoscopic retrograde cholangiopancreatography images dataset
Endoscopic Retrograde Cholangiopancreatography (ERCP) is a key procedure in the diagnosis and treatment of biliary and pancreatic diseases. Artificial intelligence has been pointed as one solution to automatize diagnosis. However, public ERCP datasets are scarce, which limits the use of such approach. Therefore, this study aims to help fill this gap by providing a large and curated dataset. The collection is composed of 19.018 raw images and 19.317 processed from 1.602 patients. 5.519 images are labeled, which provides a ready to use dataset. All images were manually inspected and annotated by two gastroenterologist with more than 5 years of experience and reviewed by another gastroenterologist with more than 20 years of experience, all with more than 400 ERCP procedures annually. The utility and validity of the dataset is proven by a classification experiment. This collection aims to provide or contribute for a benchmark in automatic ERCP analysis and diagnosis of biliary and pancreatic diseases.