Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks

Cytoarchitectonic parcellations of the human brain serve as anatomical references in multimodal atlas frameworks. They are based on analysis of cell-body stained histological sections and the identification of borders between brain areas. The de-facto standard involves a semi-automatic, reproducible border detection, but does not scale with high-throughput imaging in large series of sections at microscopical resolution. Automatic parcellation, however, is extremely challenging due to high variation in the data, and the need for a large field of view at microscopic resolution. The performance of a recently proposed Convolutional Neural Network model that addresses this problem especially suffers from the naturally limited amount of expert annotations for training. To circumvent this limitation, we propose to pre-train neural networks on a self-supervised auxiliary task, predicting the 3D distance between two patches sampled from the same brain. Compared to a random initialization, fine-tuning from these networks results in significantly better segmentations. We show that the self-supervised model has implicitly learned to distinguish several cortical brain areas -- a strong indicator that the proposed auxiliary task is appropriate for cytoarchitectonic mapping.Comment: Accepted at MICCAI 201

Self-supervised Contrastive Video-Speech Representation Learning for Ultrasound

In medical imaging, manual annotations can be expensive to acquire and sometimes infeasible to access, making conventional deep learning-based models difficult to scale. As a result, it would be beneficial if useful representations could be derived from raw data without the need for manual annotations. In this paper, we propose to address the problem of self-supervised representation learning with multi-modal ultrasound video-speech raw data. For this case, we assume that there is a high correlation between the ultrasound video and the corresponding narrative speech audio of the sonographer. In order to learn meaningful representations, the model needs to identify such correlation and at the same time understand the underlying anatomical features. We designed a framework to model the correspondence between video and audio without any kind of human annotations. Within this framework, we introduce cross-modal contrastive learning and an affinity-aware self-paced learning scheme to enhance correlation modelling. Experimental evaluations on multi-modal fetal ultrasound video and audio show that the proposed approach is able to learn strong representations and transfers well to downstream tasks of standard plane detection and eye-gaze prediction.Comment: MICCAI 2020 (early acceptance

Revisiting Rubik's Cube: Self-supervised Learning with Volume-wise Transformation for 3D Medical Image Segmentation

Deep learning highly relies on the quantity of annotated data. However, the annotations for 3D volumetric medical data require experienced physicians to spend hours or even days for investigation. Self-supervised learning is a potential solution to get rid of the strong requirement of training data by deeply exploiting raw data information. In this paper, we propose a novel self-supervised learning framework for volumetric medical images. Specifically, we propose a context restoration task, i.e., Rubik's cube++, to pre-train 3D neural networks. Different from the existing context-restoration-based approaches, we adopt a volume-wise transformation for context permutation, which encourages network to better exploit the inherent 3D anatomical information of organs. Compared to the strategy of training from scratch, fine-tuning from the Rubik's cube++ pre-trained weight can achieve better performance in various tasks such as pancreas segmentation and brain tissue segmentation. The experimental results show that our self-supervised learning method can significantly improve the accuracy of 3D deep learning networks on volumetric medical datasets without the use of extra data.Comment: Accepted by MICCAI 202

Improving Cytoarchitectonic Segmentation of Human Brain Areas with Self-supervised Siamese Networks

Cytoarchitectonic parcellations of the human brain serve as anatomical references in multimodal atlas frameworks. They are based on analysis of cell-body stained histological sections and the identification of borders between brain areas. The de-facto standard involves a semi-automatic, reproducible border detection, but does not scale with high-throughput imaging in large series of sections at microscopical resolution. Automatic parcellation, however, is extremely challenging due to high variation in the data, and the need for a large field of view at microscopic resolution. The performance of a recently proposed Convolutional Neural Network model that addresses this problem especially suffers from the naturally limited amount of expert annotations for training. To circumvent this limitation, we propose to pre-train neural networks on a self-supervised auxiliary task, predicting the 3D distance between two patches sampled from the same brain. Compared to a random initialization, fine-tuning from these networks results in significantly better segmentations. We show that the self-supervised model has implicitly learned to distinguish several cortical brain areas -- a strong indicator that the proposed auxiliary task is appropriate for cytoarchitectonic mapping.Comment: Accepted at MICCAI 201