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Register a new userSemantic Segmentation of Pathological Lung Tissue with Dilated Fully Convolutional Networks
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Stergios Christodoulidis Mr.
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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Early and accurate diagnosis of interstitial lung diseases (ILDs) is crucial for making treatment decisions, but can be challenging even for experienced radiologists. The diagnostic procedure is based on the detection and recognition of the different ILD pathologies in thoracic CT scans, yet their manifestation often appears similar. In this study, we propose the use of a deep purely convolutional neural network for the semantic segmentation of ILD patterns, as the basic component of a computer aided diagnosis (CAD) system for ILDs. The proposed CNN, which consists of convolutional layers with dilated filters, takes as input a lung CT image of arbitrary size and outputs the corresponding label map. We trained and tested the network on a dataset of 172 sparsely annotated CT scans, within a cross-validation scheme. The training was performed in an end-to-end and semi-supervised fashion, utilizing both labeled and non-labeled image regions. The experimental results show significant performance improvement with respect to the state of the art.
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In this paper, we present a conceptually simple, strong, and efficient framework for panoptic segmentation, called Panoptic FCN. Our approach aims to represent and predict foreground things and background stuff in a unified fully convolutional pipeline. In particular, Panoptic FCN encodes each object instance or stuff category into a specific kernel weight with the proposed kernel generator and produces the prediction by convolving the high-resolution feature directly. With this approach, instance-aware and semantically consistent properties for things and stuff can be respectively satisfied in a simple generate-kernel-then-segment workflow. Without extra boxes for localization or instance separation, the proposed approach outperforms previous box-based and -free models with high efficiency on COCO, Cityscapes, and Mapillary Vistas datasets with single scale input. Our code is made publicly available at https://github.com/Jia-Research-Lab/PanopticFCN.
Purpose: An approach for the automated segmentation of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) in multicenter water-fat MRI scans of the abdomen was investigated, using two different neural network architectures. Methods: The two fully convolutional network architectures U-Net and V-Net were trained, evaluated and compared on the water-fat MRI data. Data of the study Tellus with 90 scans from a single center was used for a 10-fold cross-validation in which the most successful configuration for both networks was determined. These configurations were then tested on 20 scans of the multicenter study beta-cell function in JUvenile Diabetes and Obesity (BetaJudo), which involved a different study population and scanning device. Results: The U-Net outperformed the used implementation of the V-Net in both cross-validation and testing. In cross-validation, the U-Net reached average dice scores of 0.988 (VAT) and 0.992 (SAT). The average of the absolute quantification errors amount to 0.67% (VAT) and 0.39% (SAT). On the multi-center test data, the U-Net performs only slightly worse, with average dice scores of 0.970 (VAT) and 0.987 (SAT) and quantification errors of 2.80% (VAT) and 1.65% (SAT). Conclusion: The segmentations generated by the U-Net allow for reliable quantification and could therefore be viable for high-quality automated measurements of VAT and SAT in large-scale studies with minimal need for human intervention. The high performance on the multicenter test data furthermore shows the robustness of this approach for data of different patient demographics and imaging centers, as long as a consistent imaging protocol is used.
Transformers have shown impressive performance in various natural language processing and computer vision tasks, due to the capability of modeling long-range dependencies. Recent progress has demonstrated to combine such transformers with CNN-based semantic image segmentation models is very promising. However, it is not well studied yet on how well a pure transformer based approach can achieve for image segmentation. In this work, we explore a novel framework for semantic image segmentation, which is encoder-decoder based Fully Transformer Networks (FTN). Specifically, we first propose a Pyramid Group Transformer (PGT) as the encoder for progressively learning hierarchical features, while reducing the computation complexity of the standard visual transformer(ViT). Then, we propose a Feature Pyramid Transformer (FPT) to fuse semantic-level and spatial-level information from multiple levels of the PGT encoder for semantic image segmentation. Surprisingly, this simple baseline can achieve new state-of-the-art results on multiple challenging semantic segmentation benchmarks, including PASCAL Context, ADE20K and COCO-Stuff. The source code will be released upon the publication of this work.
Fully convolutional neural networks give accurate, per-pixel prediction for input images and have applications like semantic segmentation. However, a typical FCN usually requires lots of floating point computation and large run-time memory, which effectively limits its usability. We propose a method to train Bit Fully Convolution Network (BFCN), a fully convolutional neural network that has low bit-width weights and activations. Because most of its computation-intensive convolutions are accomplished between low bit-width numbers, a BFCN can be accelerated by an efficient bit-convolution implementation. On CPU, the dot product operation between two bit vectors can be reduced to bitwise operations and popcounts, which can offer much higher throughput than 32-bit multiplications and additions. To validate the effectiveness of BFCN, we conduct experiments on the PASCAL VOC 2012 semantic segmentation task and Cityscapes. Our BFCN with 1-bit weights and 2-bit activations, which runs 7.8x faster on CPU or requires less than 1% resources on FPGA, can achieve comparable performance as the 32-bit counterpart.
Introducing explicit constraints on the structural predictions has been an effective way to improve the performance of semantic segmentation models. Existing methods are mainly based on insufficient hand-crafted rules that only partially capture the image structure, and some methods can also suffer from the efficiency issue. As a result, most of the state-of-the-art fully convolutional networks did not adopt these techniques. In this work, we propose a simple, fast yet effective method that exploits structural information through direct supervision with minor additional expense. To be specific, our method explicitly requires the network to predict semantic segmentation as well as dilated affinity, which is a sparse version of pair-wise pixel affinity. The capability of telling the relationships between pixels are directly built into the model and enhance the quality of segmentation in two stages. 1) Joint training with dilated affinity can provide robust feature representations and thus lead to finer segmentation results. 2) The extra output of affinity information can be further utilized to refine the original segmentation with a fast propagation process. Consistent improvements are observed on various benchmark datasets when applying our framework to the existing state-of-the-art model. Codes will be released soon.
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