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Olivier Vincent

Alumni

Publications

Impact of individual rater style on deep learning uncertainty in medical imaging segmentation
Olivier Vincent
Charley Gros
Julien Cohen-Adad
While multiple studies have explored the relation between inter-rater variability and deep learning model uncertainty in medical segmentatio… (see more)n tasks, little is known about the impact of individual rater style. This study quantifies rater style in the form of bias and consistency and explores their impacts when used to train deep learning models. Two multi-rater public datasets were used, consisting of brain multiple sclerosis lesion and spinal cord grey matter segmentation. On both datasets, results show a correlation (
2021-05-04
ArXiv (preprint)
arxiv.org
arxiv.org
ivadomed: A Medical Imaging Deep Learning Toolbox
Charley Gros
Andréanne Lemay
Olivier Vincent
Lucas Rouhier
Anthime Bucquet
Julien Cohen-Adad
Julien Cohen-Adad
Julien Cohen-Adad
ivadomed is an open-source Python package for designing, end-to-end training, and evaluating deep learning models applied to medical imaging… (see more) data. The package includes APIs, command-line tools, documentation, and tutorials. ivadomed also includes pre-trained models such as spinal tumor segmentation and vertebral labeling. Original features of ivadomed include a data loader that can parse image metadata (e.g., acquisition parameters, image contrast, resolution) and subject metadata (e.g., pathology, age, sex) for custom data splitting or extra information during training and evaluation. Any dataset following the Brain Imaging Data Structure (BIDS) convention will be compatible with ivadomed without the need to manually organize the data, which is typically a tedious task. Beyond the traditional deep learning methods, ivadomed features cutting-edge architectures, such as FiLM and HeMis, as well as various uncertainty estimation methods (aleatoric and epistemic), and losses adapted to imbalanced classes and non-binary predictions. Each step is conveniently configurable via a single file. At the same time, the code is highly modular to allow addition/modification of an architecture or pre/post-processing steps. Example applications of ivadomed include MRI object detection, segmentation, and labeling of anatomical and pathological structures. Overall, ivadomed enables easy and quick exploration of the latest advances in deep learning for medical imaging applications. ivadomed's main project page is available at https://ivadomed.org.
2021-02-11
Journal of Open Source Software (published)
doi.org
arxiv.org