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Register a new userConvPath: A Software Tool for Lung Adenocarcinoma Digital Pathological Image Analysis Aided by Convolutional Neural Network
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Added by
Guanghua Xiao
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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The spatial distributions of different types of cells could reveal a cancer cell growth pattern, its relationships with the tumor microenvironment and the immune response of the body, all of which represent key hallmarks of cancer. However, manually recognizing and localizing all the cells in pathology slides are almost impossible. In this study, we developed an automated cell type classification pipeline, ConvPath, which includes nuclei segmentation, convolutional neural network-based tumor, stromal and lymphocytes classification, and extraction of tumor microenvironment related features for lung cancer pathology images. The overall classification accuracy is 92.9% and 90.1% in training and independent testing datasets, respectively. By identifying cells and classifying cell types, this pipeline can convert a pathology image into a spatial map of tumor, stromal and lymphocyte cells. From this spatial map, we can extracted features that characterize the tumor micro-environment. Based on these features, we developed an image feature-based prognostic model and validated the model in two independent cohorts. The predicted risk group serves as an independent prognostic factor, after adjusting for clinical variables that include age, gender, smoking status, and stage.
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In this paper, we present a novel approach that uses deep learning techniques for colorizing grayscale images. By utilizing a pre-trained convolutional neural network, which is originally designed for image classification, we are able to separate content and style of different images and recombine them into a single image. We then propose a method that can add colors to a grayscale image by combining its content with style of a color image having semantic similarity with the grayscale one. As an application, to our knowledge the first of its kind, we use the proposed method to colorize images of ukiyo-e a genre of Japanese painting?and obtain interesting results, showing the potential of this method in the growing field of computer assisted art.
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.
With the development of the super-resolution convolutional neural network (SRCNN), deep learning technique has been widely applied in the field of image super-resolution. Previous works mainly focus on optimizing the structure of SRCNN, which have been achieved well performance in speed and restoration quality for image super-resolution. However, most of these approaches only consider a specific scale image during the training process, while ignoring the relationship between different scales of images. Motivated by this concern, in this paper, we propose a cascaded convolution neural network for image super-resolution (CSRCNN), which includes three cascaded Fast SRCNNs and each Fast SRCNN can process a specific scale image. Images of different scales can be trained simultaneously and the learned network can make full use of the information resided in different scales of images. Extensive experiments show that our network can achieve well performance for image SR.
The conventional spatial convolution layers in the Convolutional Neural Networks (CNNs) are computationally expensive at the point where the training time could take days unless the number of layers, the number of training images or the size of the training images are reduced. The image size of 256x256 pixels is commonly used for most of the applications of CNN, but this image size is too small for applications like Diabetic Retinopathy (DR) classification where the image details are important for accurate classification. This research proposed Frequency Domain Convolution (FDC) and Frequency Domain Pooling (FDP) layers which were built with RFFT, kernel initialization strategy, convolution artifact removal and Channel Independent Convolution (CIC) to replace the conventional convolution and pooling layers. The FDC and FDP layers are used to build a Frequency Domain Convolutional Neural Network (FDCNN) to accelerate the training of large images for DR classification. The Full FDC layer is an extension of the FDC layer to allow direct use in conventional CNNs, it is also used to modify the VGG16 architecture. FDCNN is shown to be at least 54.21% faster and 70.74% more memory efficient compared to an equivalent CNN architecture. The modified VGG16 architecture with Full FDC layer is reported to achieve a shorter training time and a higher accuracy at 95.63% compared to the original VGG16 architecture for DR classification.
Early diagnosis of interstitial lung diseases is crucial for their treatment, but even experienced physicians find it difficult, as their clinical manifestations are similar. In order to assist with the diagnosis, computer-aided diagnosis (CAD) systems have been developed. These commonly rely on a fixed scale classifier that scans CT images, recognizes textural lung patterns and generates a map of pathologies. In a previous study, we proposed a method for classifying lung tissue patterns using a deep convolutional neural network (CNN), with an architecture designed for the specific problem. In this study, we present an improved method for training the proposed network by transferring knowledge from the similar domain of general texture classification. Six publicly available texture databases are used to pretrain networks with the proposed architecture, which are then fine-tuned on the lung tissue data. The resulting CNNs are combined in an ensemble and their fused knowledge is compressed back to a network with the original architecture. The proposed approach resulted in an absolute increase of about 2% in the performance of the proposed CNN. The results demonstrate the potential of transfer learning in the field of medical image analysis, indicate the textural nature of the problem and show that the method used for training a network can be as important as designing its architecture.
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