Accurate multi-organ abdominal CT segmentation is essential to many clinical applications such as computer-aided intervention. As data annotation requires massive human labor from experienced radiologists, it is common that training data are partially labeled, e.g., pancreas datasets only have the pancreas labeled while leaving the rest marked as background. However, these background labels can be misleading in multi-organ segmentation since the "background" usually contains some other organs of interest. To address the background ambiguity in these partially-labeled datasets, we propose Prior-aware Neural Network (PaNN) via explicitly incorporating anatomical priors on abdominal organ sizes, guiding the training process with domain-specific knowledge. More specifically, PaNN assumes that the average organ size distributions in the abdomen should approximate their empirical distributions, a prior statistics obtained from the fully-labeled dataset. As our training objective is difficult to be directly optimized using stochastic gradient descent [20], we propose to reformulate it in a min-max form and optimize it via the stochastic primal-dual gradient algorithm. PaNN achieves state-of-the-art performance on the MICCAI2015 challenge "Multi-Atlas Labeling Beyond the Cranial Vault", a competition on organ segmentation in the abdomen. We report an average Dice score of 84.97 , surpassing the prior art by a large margin of 3.27 .
However, these methods fail to capture the anatomical priors @cite_44 . Inclusion of priors in medical imaging could potentially have much more impact compared with their usage in natural images since anatomical objects in medical images are naturally more constrained in terms of shape, location, size, . Some recent works @cite_14 @cite_51 demonstrate that these priors can be learnt by a generative model. But these methods will induce heavy computational overhead. Kervadec al @cite_47 proposed that directly imposing inequality constraints on sizes is also an effective way of incorporating anatomical priors. Unlike these methods, we propose to learn from partial annotations by embedding the abdominal region statistics in the training objective, which requires no additional training budget.
@cite_44 @cite_47 @cite_14 @cite_51
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Abstract Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks. Concise overviews are provided of studies per application area: neuro, retinal, pulmonary, digital pathology, breast, cardiac, abdominal, musculoskelet al. We end with a summary of the current state-of-the-art, a critical discussion of open challenges and directions for future research. Abstract Weakly-supervised learning based on, e.g., partially labelled images or image-tags, is currently attracting significant attention in CNN segmentation as it can mitigate the need for full and laborious pixel voxel annotations. Enforcing high-order (global) inequality constraints on the network output (for instance, to constrain the size of the target region) can leverage unlabeled data, guiding the training process with domain-specific knowledge. Inequality constraints are very flexible because they do not assume exact prior knowledge. However, constrained Lagrangian dual optimization has been largely avoided in deep networks, mainly for computational tractability reasons. To the best of our knowledge, the method of (2015a) is the only prior work that addresses deep CNNs with linear constraints in weakly supervised segmentation. It uses the constraints to synthesize fully-labeled training masks (proposals) from weak labels, mimicking full supervision and facilitating dual optimization. We propose to introduce a differentiable penalty, which enforces inequality constraints directly in the loss function, avoiding expensive Lagrangian dual iterates and proposal generation. From constrained-optimization perspective, our simple penalty-based approach is not optimal as there is no guarantee that the constraints are satisfied. However, surprisingly, it yields substantially better results than the Lagrangian-based constrained CNNs in (2015a) , while reducing the computational demand for training. By annotating only a small fraction of the pixels, the proposed approach can reach a level of segmentation performance that is comparable to full supervision on three separate tasks. While our experiments focused on basic linear constraints such as the target-region size and image tags, our framework can be easily extended to other non-linear constraints, e.g., invariant shape moments (Klodt and Cremers, 2011) and other region statistics (, 2014). Therefore, it has the potential to close the gap between weakly and fully supervised learning in semantic medical image segmentation. Our code is publicly available. We consider the problem of segmenting a biomedical image into anatomical regions of interest. We specifically address the frequent scenario where we have no paired training data that contains images and their manual segmentations. Instead, we employ unpaired segmentation images that we use to build an anatomical prior. Critically these segmentations can be derived from imaging data from a different dataset and imaging modality than the current task. We introduce a generative probabilistic model that employs the learned prior through a convolutional neural network to compute segmentations in an unsupervised setting. We conducted an empirical analysis of the proposed approach in the context of structural brain MRI segmentation, using a multi-study dataset of more than 14,000 scans. Our results show that an anatomical prior enables fast unsupervised segmentation which is typically not possible using standard convolutional networks. The integration of anatomical priors can facilitate CNN-based anatomical segmentation in a range of novel clinical problems, where few or no annotations are available and thus standard networks are not trainable. The code, model definitions and model weights are freely available at http: github.com adalca neuron.