In the medical sector, three-dimensional (3D) images are commonly used like computed tomography (CT) and magnetic resonance imaging (MRI). The 3D MRI is a non-invasive method of studying the soft-tissue structures in a knee joint for osteoarthritis studies. It can greatly improve the accuracy of segmenting structures such as cartilage, bone marrow lesion, and meniscus by identifying the bone structure first. U-net is a convolutional neural network that was originally designed to segment the biological images with limited training data. The input of the original U-net is a single 2D image and the output is a binary 2D image. In this study, we modified the U-net model to identify the knee bone structures using 3D MRI, which is a sequence of 2D slices. A fully automatic model has been proposed to detect and segment knee bones. The proposed model was trained, tested, and validated using 99 knee MRI cases where each case consists of 160 2D slices for a single knee scan. To evaluate the model’s performance, the similarity, dice coefficient (DICE), and area error metrics were calculated. Separate models were trained using different knee bone components including tibia, femur, patella, as well as a combined model for segmenting all the knee bones. Using the whole MRI sequence (160 slices), the method was able to detect the beginning and ending bone slices first, and then segment the bone structures for all the slices in between. On the testing set, the detection model accomplished 98.79% accuracy and the segmentation model achieved DICE 96.94% and similarity 93.98%. The proposed method outperforms several state-of-the-art methods, i.e., it outperforms U-net by 3.68%, SegNet by 14.45%, and FCN-8 by 2.34%, in terms of DICE score using the same dataset.
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This content will become publicly available on June 27, 2024
Joint Self-Supervised Image-Volume Representation Learning with Intra-inter Contrastive Clustering
Collecting large-scale medical datasets with fully annotated samples for training of deep networks is prohibitively expensive, especially for 3D volume data. Recent breakthroughs in self-supervised learning (SSL) offer the ability to overcome the lack of labeled training samples by learning feature representations from unlabeled data. However, most current SSL techniques in the medical field have been designed for either 2D images or 3D volumes. In practice, this restricts the capability to fully leverage unlabeled data from numerous sources, which may include both 2D and 3D data. Additionally, the use of these pre-trained networks is constrained to downstream tasks with compatible data dimensions.In this paper, we propose a novel framework for unsupervised joint learning on 2D and 3D data modalities. Given a set of 2D images or 2D slices extracted from 3D volumes, we construct an SSL task based on a 2D contrastive clustering problem for distinct classes. The 3D volumes are exploited by computing vectored embedding at each slice and then assembling a holistic feature through deformable self-attention mechanisms in Transformer, allowing incorporating long-range dependencies between slices inside 3D volumes. These holistic features are further utilized to define a novel 3D clustering agreement-based SSL task and masking embedding prediction inspired by pre-trained language models. Experiments on downstream tasks, such as 3D brain segmentation, lung nodule detection, 3D heart structures segmentation, and abnormal chest X-ray detection, demonstrate the effectiveness of our joint 2D and 3D SSL approach. We improve plain 2D Deep-ClusterV2 and SwAV by a significant margin and also surpass various modern 2D and 3D SSL approaches.
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- Award ID(s):
- 2100237
- NSF-PAR ID:
- 10431877
- Date Published:
- Journal Name:
- Proceedings of the AAAI Conference on Artificial Intelligence
- Volume:
- 37
- Issue:
- 12
- ISSN:
- 2159-5399
- Page Range / eLocation ID:
- 14426 to 14435
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Methods Here, we implement the popular self-supervised contrastive learning methods of NNCLR Nearest neighbor Contrastive Learning of visual Representations) and SimCLR (Simple framework for Contrastive Learning of visual Representations) for the classification of spatial orientation and segmentation of embryos of maize kernels. Maize kernels are imaged using a commercial high-throughput imaging system. This image data is often used in multiple downstream applications across both production and breeding applications, for instance, sorting for oil content based on segmenting and quantifying the scutellum’s size and for classifying haploid and diploid kernels.
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