Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userContour Transformer Network for One-shot Segmentation of Anatomical Structures
160
0
0.0
(
0
)
Added by
Yuhang Lu
Publication date
2020
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
Accurate segmentation of anatomical structures is vital for medical image analysis. The state-of-the-art accuracy is typically achieved by supervised learning methods, where gathering the requisite expert-labeled image annotations in a scalable manner remains a main obstacle. Therefore, annotation-efficient methods that permit to produce accurate anatomical structure segmentation are highly desirable. In this work, we present Contour Transformer Network (CTN), a one-shot anatomy segmentation method with a naturally built-in human-in-the-loop mechanism. We formulate anatomy segmentation as a contour evolution process and model the evolution behavior by graph convolutional networks (GCNs). Training the CTN model requires only one labeled image exemplar and leverages additional unlabeled data through newly introduced loss functions that measure the global shape and appearance consistency of contours. On segmentation tasks of four different anatomies, we demonstrate that our one-shot learning method significantly outperforms non-learning-based methods and performs competitively to the state-of-the-art fully supervised deep learning methods. With minimal human-in-the-loop editing feedback, the segmentation performance can be further improved to surpass the fully supervised methods.
rate research
Read More
Learning by imitation is one of the most significant abilities of human beings and plays a vital role in humans computational neural system. In medical image analysis, given several exemplars (anchors), experienced radiologist has the ability to delineate unfamiliar organs by imitating the reasoning process learned from existing types of organs. Inspired by this observation, we propose OrganNet which learns a generalized organ concept from a set of annotated organ classes and then transfer this concept to unseen classes. In this paper, we show that such process can be integrated into the one-shot segmentation task which is a very challenging but meaningful topic. We propose pyramid reasoning modules (PRMs) to model the anatomical correlation between anchor and target volumes. In practice, the proposed module first computes a correlation matrix between target and anchor computerized tomography (CT) volumes. Then, this matrix is used to transform the feature representations of both anchor volume and its segmentation mask. Finally, OrganNet learns to fuse the representations from various inputs and predicts segmentation results for target volume. Extensive experiments show that OrganNet can effectively resist the wide variations in organ morphology and produce state-of-the-art results in one-shot segmentation task. Moreover, even when compared with fully-supervised segmentation models, OrganNet is still able to produce satisfying segmentation results.
We introduce one-shot texture segmentation: the task of segmenting an input image containing multiple textures given a patch of a reference texture. This task is designed to turn the problem of texture-based perceptual grouping into an objective benchmark. We show that it is straight-forward to generate large synthetic data sets for this task from a relatively small number of natural textures. In particular, this task can be cast as a self-supervised problem thereby alleviating the need for massive amounts of manually annotated data necessary for traditional segmentation tasks. In this paper we introduce and study two concrete data sets: a dense collage of textures (CollTex) and a cluttered texturized Omniglot data set. We show that a baseline model trained on these synthesized data is able to generalize to natural images and videos without further fine-tuning, suggesting that the learned image representations are useful for higher-level vision tasks.
Few-shot segmentation aims to train a segmentation model that can fast adapt to novel classes with few exemplars. The conventional training paradigm is to learn to make predictions on query images conditioned on the features from support images. Previous methods only utilized the semantic-level prototypes of support images as the conditional information. These methods cannot utilize all pixel-wise support information for the query predictions, which is however critical for the segmentation task. In this paper, we focus on utilizing pixel-wise relationships between support and target images to facilitate the few-shot semantic segmentation task. We design a novel Cycle-Consistent Transformer (CyCTR) module to aggregate pixel-wise support features into query ones. CyCTR performs cross-attention between features from different images, i.e. support and query images. We observe that there may exist unexpected irrelevant pixel-level support features. Directly performing cross-attention may aggregate these features from support to query and bias the query features. Thus, we propose using a novel cycle-consistent attention mechanism to filter out possible harmful support features and encourage query features to attend to the most informative pixels from support images. Experiments on all few-shot segmentation benchmarks demonstrate that our proposed CyCTR leads to remarkable improvement compared to previous state-of-the-art methods. Specifically, on Pascal-$5^i$ and COCO-$20^i$ datasets, we achieve 66.6% and 45.6% mIoU for 5-shot segmentation, outperforming previous state-of-the-art by 4.6% and 7.1% respectively.
Accurate segmentation of critical anatomical structures is at the core of medical image analysis. The main bottleneck lies in gathering the requisite expert-labeled image annotations in a scalable manner. Methods that permit to produce accurate anatomical structure segmentation without using a large amount of fully annotated training images are highly desirable. In this work, we propose a novel contribution of Contour Transformer Network (CTN), a one-shot anatomy segmentor including a naturally built-in human-in-the-loop mechanism. Segmentation is formulated by learning a contour evolution behavior process based on graph convolutional networks (GCNs). Training of our CTN model requires only one labeled image exemplar and leverages additional unlabeled data through newly introduced loss functions that measure the global shape and appearance consistency of contours. We demonstrate that our one-shot learning method significantly outperforms non-learning-based methods and performs competitively to the state-of-the-art fully supervised deep learning approaches. With minimal human-in-the-loop editing feedback, the segmentation performance can be further improved and tailored towards the observer desired outcomes. This can facilitate the clinician designed imaging-based biomarker assessments (to support personalized quantitative clinical diagnosis) and outperforms fully supervised baselines.
Direct contour regression for instance segmentation is a challenging task. Previous works usually achieve it by learning to progressively refine the contour prediction or adopting a shape representation with limited expressiveness. In this work, we argue that the difficulty in regressing the contour points in one pass is mainly due to the ambiguity when discretizing a smooth contour into a polygon. To address the ambiguity, we propose a novel differentiable rendering-based approach named textbf{ContourRender}. During training, it first predicts a contour generated by an invertible shape signature, and then optimizes the contour with the more stable silhouette by converting it to a contour mesh and rendering the mesh to a 2D map. This method significantly improves the quality of contour without iterations or cascaded refinements. Moreover, as optimization is not needed during inference, the inference speed will not be influenced. Experiments show the proposed ContourRender outperforms all the contour-based instance segmentation approaches on COCO, while stays competitive with the iteration-based state-of-the-art on Cityscapes. In addition, we specifically select a subset from COCO val2017 named COCO ContourHard-val to further demonstrate the contour quality improvements. Codes, models, and dataset split will be released.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
