In this paper, we propose a novel method for highly efficient follicular segmentation of thyroid cytopathological WSIs. Firstly, we propose a hybrid segmentation architecture, which integrates a classifier into Deeplab V3 by adding a branch. A large amount of the WSI segmentation time is saved by skipping the irrelevant areas using the classification branch. Secondly, we merge the low scale fine features into the original atrous spatial pyramid pooling (ASPP) in Deeplab V3 to accurately represent the details in cytopathological images. Thirdly, our hybrid model is trained by a criterion-oriented adaptive loss function, which leads the model converging much faster. Experimental results on a collection of thyroid patches demonstrate that the proposed model reaches 80.9 on the segmentation accuracy. Besides, 93 time is reduced for the WSI segmentation by using our proposed method, and the WSI-level accuracy achieves 53.4 .
Traditional machine learning @cite_8 @cite_13 methods and deep learning methods @cite_9 @cite_0 greatly improve the accuracy of automatic lesion classification in medical areas. @cite_8 perform support vector machine(SVM) and achieve a diagnostic accuracy of 96.7 Traditional semantic segmentation methods @cite_17 learn the representation from hand-craft features instead of the semantic features. Recently, CNN-based methods largely improve performance. FCN @cite_18 is the pioneering work on semantic segmentation by modifying fully connected layers into convolution layers in classification. DeepLab @cite_6 @cite_5 @cite_2 uses dilated convolutions to provide dense labeling and enlarge the receptive field. Semantic segmentation methods have already been used in the pathological image segmentation. @cite_19 propose a fully automated segmentation framework to identify placental candidate pixels. @cite_4 introduce an image segmentation method based on recurrent neural network.
@cite_18 @cite_4 @cite_8 @cite_9 @cite_6 @cite_0 @cite_19 @cite_2 @cite_5 @cite_13 @cite_17
1903029394 2524644797 2169245092 2739315424 2964288706 2327598497 2476575773 2630837129 2412782625 2072569807 1978085585
Convolutional networks are powerful visual models that yield hierarchies of features. We show that convolutional networks by themselves, trained end-to-end, pixels-to-pixels, exceed the state-of-the-art in semantic segmentation. Our key insight is to build “fully convolutional” networks that take input of arbitrary size and produce correspondingly-sized output with efficient inference and learning. We define and detail the space of fully convolutional networks, explain their application to spatially dense prediction tasks, and draw connections to prior models. We adapt contemporary classification networks (AlexNet [20], the VGG net [31], and GoogLeNet [32]) into fully convolutional networks and transfer their learned representations by fine-tuning [3] to the segmentation task. We then define a skip architecture that combines semantic information from a deep, coarse layer with appearance information from a shallow, fine layer to produce accurate and detailed segmentations. Our fully convolutional network achieves state-of-the-art segmentation of PASCAL VOC (20 relative improvement to 62.2 mean IU on 2012), NYUDv2, and SIFT Flow, while inference takes less than one fifth of a second for a typical image. Deep neural networks have demonstrated very promising performance on accurate segmentation of challenging organs (e.g., pancreas) in abdominal CT and MRI scans. The current deep learning approaches conduct pancreas segmentation by processing sequences of 2D image slices independently through deep, dense per-pixel masking for each image, without explicitly enforcing spatial consistency constraint on segmentation of successive slices. We propose a new convolutional recurrent neural network architecture to address the contextual learning and segmentation consistency problem. A deep convolutional sub-network is first designed and pre-trained from scratch. The output layer of this network module is then connected to recurrent layers and can be fine-tuned for contextual learning, in an end-to-end manner. Our recurrent sub-network is a type of Long short-term memory (LSTM) network that performs segmentation on an image by integrating its neighboring slice segmentation predictions, in the form of a dependent sequence processing. Additionally, a novel segmentation-direct loss function (named Jaccard Loss) is proposed and deep networks are trained to optimize Jaccard Index (JI) directly. Extensive experiments are conducted to validate our proposed deep models, on quantitative pancreas segmentation using both CT and MRI scans. Our method outperforms the state-of-the-art work on CT [11] and MRI pancreas segmentation [1], respectively. Objective: The aim of this study was to develop an automated computer-aided diagnostic system for diagnosis of thyroid cancer pattern in fine needle aspiration cytology (FNAC) microscopic images with high degree of sensitivity and specificity using statistical texture features and a Support Vector Machine classifier (SVM). Materials and Methods: A training set of 40 benign and 40 malignant FNAC images and a testing set of 10 benign and 20 malignant FNAC images were used to perform the diagnosis of thyroid cancer. Initially, segmentation of region of interest (ROI) was performed by region-based morphology segmentation. The developed diagnostic system utilized statistical texture features derived from the segmented images using a Gabor filter bank at various wavelengths and angles. Finally, the SVM was used as a machine learning algorithm to identify benign and malignant states of thyroid nodules. Results: The SVMachieved a diagnostic accuracy of 96.7 with sensitivity and specificity of 95 and 100 , respectively, at a wavelength of 4 and an angle of 45. Conclusion: The results show that the diagnosis of thyroid cancer in FNAC images can be effectively performed using statistical texture information derived with Gabor filters in association with an SVM. Fine needle aspiration cytology is commonly used for diagnosis of breast cancer, with traditional practice being based on the subjective visual assessment of the breast cytopathology cell samples under a microscope to evaluate the state of various cytological features. Therefore, there are many challenges in maintaining consistency and reproducibility of findings. However, digital imaging and computational aid in diagnosis can improve the diagnostic accuracy and reduce the effective workload of pathologists. This paper presents a deep convolutional neural network (CNN) based classification approach for the diagnosis of the cell samples using their microscopic high-magnification multi-views. The proposed approach has been tested using GoogLeNet architecture of CNN on an image dataset of 37 breast cytopathology samples (24 benign and 13 malignant), where the network was trained using images of 54 cell samples and tested on the rest, achieving 89.7 mean accuracy in 8 fold validation. Abstract: Deep Convolutional Neural Networks (DCNNs) have recently shown state of the art performance in high level vision tasks, such as image classification and object detection. This work brings together methods from DCNNs and probabilistic graphical models for addressing the task of pixel-level classification (also called "semantic image segmentation"). We show that responses at the final layer of DCNNs are not sufficiently localized for accurate object segmentation. This is due to the very invariance properties that make DCNNs good for high level tasks. We overcome this poor localization property of deep networks by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF). Qualitatively, our "DeepLab" system is able to localize segment boundaries at a level of accuracy which is beyond previous methods. Quantitatively, our method sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 71.6 IOU accuracy in the test set. We show how these results can be obtained efficiently: Careful network re-purposing and a novel application of the 'hole' algorithm from the wavelet community allow dense computation of neural net responses at 8 frames per second on a modern GPU. Cytopathology is the study of disease at the cellular level and often used as a screening tool for cancer. Thyroid cytopathology is a branch of pathology that studies the diagnosis of thyroid lesions and diseases. A pathologist views cell images that may have high visual variance due to different anatomical structures and pathological characteristics. To assist the physician with identifying and searching through images, we propose a deep semantic mobile application. Our work augments recent advances in the digitization of pathology and machine learning techniques, where there are transformative opportunities for computers to assist pathologists. Our system uses a custom thyroid ontology that can be augmented with multimedia metadata extracted from images using deep machine learning techniques. We describe the utilization of a particular methodology, deep convolutional neural networks, to the application of cytopathology classification. Our method is able to leverage networks that have been trained on millions of generic images, to medical scenarios where only hundreds or thousands of images exist. We demonstrate the benefits of our framework through both quantitative and qualitative results. Recently, magnetic resonance imaging has revealed to be important for the evaluation of placenta’s health during pregnancy. Quantitative assessment of the placenta requires a segmentation, which proves to be challenging because of the high variability of its position, orientation, shape and appearance. Moreover, image acquisition is corrupted by motion artifacts from both fet al and maternal movements. In this paper we propose a fully automatic segmentation framework of the placenta from structural T2-weighted scans of the whole uterus, as well as an extension in order to provide an intuitive pre-natal view into this vital organ. We adopt a 3D multi-scale convolutional neural network to automatically identify placental candidate pixels. The resulting classification is subsequently refined by a 3D dense conditional random field, so that a high resolution placental volume can be reconstructed from multiple overlapping stacks of slices. Our segmentation framework has been tested on 66 subjects at gestational ages 20–38 weeks achieving a Dice score of (71.95 19.79 , ) for healthy fetuses with a fixed scan sequence and (66.89 15.35 , ) for a cohort mixed with cases of intrauterine fet al growth restriction using varying scan parameters. In this work, we revisit atrous convolution, a powerful tool to explicitly adjust filter's field-of-view as well as control the resolution of feature responses computed by Deep Convolutional Neural Networks, in the application of semantic image segmentation. To handle the problem of segmenting objects at multiple scales, we design modules which employ atrous convolution in cascade or in parallel to capture multi-scale context by adopting multiple atrous rates. Furthermore, we propose to augment our previously proposed Atrous Spatial Pyramid Pooling module, which probes convolutional features at multiple scales, with image-level features encoding global context and further boost performance. We also elaborate on implementation details and share our experience on training our system. The proposed DeepLabv3' system significantly improves over our previous DeepLab versions without DenseCRF post-processing and attains comparable performance with other state-of-art models on the PASCAL VOC 2012 semantic image segmentation benchmark. In this work we address the task of semantic image segmentation with Deep Learning and make three main contributions that are experimentally shown to have substantial practical merit. First , we highlight convolution with upsampled filters, or ‘atrous convolution’, as a powerful tool in dense prediction tasks. Atrous convolution allows us to explicitly control the resolution at which feature responses are computed within Deep Convolutional Neural Networks. It also allows us to effectively enlarge the field of view of filters to incorporate larger context without increasing the number of parameters or the amount of computation. Second , we propose atrous spatial pyramid pooling (ASPP) to robustly segment objects at multiple scales. ASPP probes an incoming convolutional feature layer with filters at multiple sampling rates and effective fields-of-views, thus capturing objects as well as image context at multiple scales. Third , we improve the localization of object boundaries by combining methods from DCNNs and probabilistic graphical models. The commonly deployed combination of max-pooling and downsampling in DCNNs achieves invariance but has a toll on localization accuracy. We overcome this by combining the responses at the final DCNN layer with a fully connected Conditional Random Field (CRF), which is shown both qualitatively and quantitatively to improve localization performance. Our proposed “DeepLab” system sets the new state-of-art at the PASCAL VOC-2012 semantic image segmentation task, reaching 79.7 percent mIOU in the test set, and advances the results on three other datasets: PASCAL-Context, PASCAL-Person-Part, and Cityscapes. All of our code is made publicly available online. An automated medical diagnosis system has been developed to discriminate benign and malignant thyroid nodules in multi-stained fine needle aspiration biopsy (FNAB) images using multiple classifier fusion and presented in this paper. First, thyroid cell regions are extracted from the auto-cropped sub-image by implementing mathematical morphology segmentation method. Subsequently, statistical features are extracted by two-level wavelet decomposition based on texture characteristics of the thyroid cells. After that, decision tree (DT), k-nearest neighbor (k-NN), Elman neural network (ENN) and support vector machine (SVM) classifiers are used separately to classify thyroid nodules into benign and malignant. The four individual classifier outputs are then fused together using majority voting rule and linear combination rules to improve the performance of the diagnostic system. The classification results of ENN and SVM classifiers show an overall diagnostic accuracy (DA) of 90 , sensitivity (Se) of 85 and 100 ... Image segmentation is the process of clustering pixels into salient image regions (i.e) regions corresponding to individual surfaces, objects or natural parts of objects. Image segmentation plays a vital role in image analysis and computer vision applications. Several general-purpose algorithms and techniques have been developed for image segmentation. Segmentation process should be stopped when region of interest is separated from the input image. Based on the application, region of interest may differ and hence none of the segmentation algorithm satisfies the global applications. Thus segmentation still remains a challenging area for researchers. This paper presents a comparison of some literature on color image segmentation based on region growing and merging algorithm. Finally an automatic seeded region growing algorithm is proposed for segmenting color images.