scholarly journals An automatic nuclei segmentation method based on deep convolutional neural networks for histopathology images

2019 ◽  
Vol 1 (1) ◽  
Author(s):  
Hwejin Jung ◽  
Bilal Lodhi ◽  
Jaewoo Kang
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Gaussian Mixture ◽  
Color Variation ◽  
Post Processing ◽  
Segmentation Method ◽  
Deep Convolutional Neural Networks ◽  
Nuclei Segmentation ◽  
Histopathology Images

Abstract Background Since nuclei segmentation in histopathology images can provide key information for identifying the presence or stage of a disease, the images need to be assessed carefully. However, color variation in histopathology images, and various structures of nuclei are two major obstacles in accurately segmenting and analyzing histopathology images. Several machine learning methods heavily rely on hand-crafted features which have limitations due to manual thresholding. Results To obtain robust results, deep learning based methods have been proposed. Deep convolutional neural networks (DCNN) used for automatically extracting features from raw image data have been proven to achieve great performance. Inspired by such achievements, we propose a nuclei segmentation method based on DCNNs. To normalize the color of histopathology images, we use a deep convolutional Gaussian mixture color normalization model which is able to cluster pixels while considering the structures of nuclei. To segment nuclei, we use Mask R-CNN which achieves state-of-the-art object segmentation performance in the field of computer vision. In addition, we perform multiple inference as a post-processing step to boost segmentation performance. We evaluate our segmentation method on two different datasets. The first dataset consists of histopathology images of various organ while the other consists histopathology images of the same organ. Performance of our segmentation method is measured in various experimental setups at the object-level and the pixel-level. In addition, we compare the performance of our method with that of existing state-of-the-art methods. The experimental results show that our nuclei segmentation method outperforms the existing methods. Conclusions We propose a nuclei segmentation method based on DCNNs for histopathology images. The proposed method which uses Mask R-CNN with color normalization and multiple inference post-processing provides robust nuclei segmentation results. Our method also can facilitate downstream nuclei morphological analyses as it provides high-quality features extracted from histopathology images.

scholarly journals Handwritten Bangla Character Recognition Using the State-of-the-Art Deep Convolutional Neural Networks

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Md Zahangir Alom ◽  
Paheding Sidike ◽  
Mahmudul Hasan ◽  
Tarek M. Taha ◽  
Vijayan K. Asari
Keyword(s):  
Neural Networks ◽  
Object Recognition ◽  
Convolutional Neural Networks ◽  
Character Recognition ◽  
State Of The Art ◽  
The State ◽  
Superior Performance ◽  
Deep Convolutional Neural Networks ◽  
Practical Applications ◽  
High Degree

In spite of advances in object recognition technology, handwritten Bangla character recognition (HBCR) remains largely unsolved due to the presence of many ambiguous handwritten characters and excessively cursive Bangla handwritings. Even many advanced existing methods do not lead to satisfactory performance in practice that related to HBCR. In this paper, a set of the state-of-the-art deep convolutional neural networks (DCNNs) is discussed and their performance on the application of HBCR is systematically evaluated. The main advantage of DCNN approaches is that they can extract discriminative features from raw data and represent them with a high degree of invariance to object distortions. The experimental results show the superior performance of DCNN models compared with the other popular object recognition approaches, which implies DCNN can be a good candidate for building an automatic HBCR system for practical applications.

scholarly journals DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout

2019 ◽  
Vol 36 (2) ◽  
pp. 470-477 ◽  
Author(s):  
Badri Adhikari
Keyword(s):  
Neural Networks ◽  
Long Range ◽  
Convolutional Neural Networks ◽  
High Throughput Sequencing ◽  
State Of The Art ◽  
Deep Convolutional Neural Networks ◽  
Contact Prediction ◽  
Learning Techniques ◽  
Medium Range ◽  
Art Methods

Abstract Motivation Exciting new opportunities have arisen to solve the protein contact prediction problem from the progress in neural networks and the availability of a large number of homologous sequences through high-throughput sequencing. In this work, we study how deep convolutional neural networks (ConvNets) may be best designed and developed to solve this long-standing problem. Results With publicly available datasets, we designed and trained various ConvNet architectures. We tested several recent deep learning techniques including wide residual networks, dropouts and dilated convolutions. We studied the improvements in the precision of medium-range and long-range contacts, and compared the performance of our best architectures with the ones used in existing state-of-the-art methods. The proposed ConvNet architectures predict contacts with significantly more precision than the architectures used in several state-of-the-art methods. When trained using the DeepCov dataset consisting of 3456 proteins and tested on PSICOV dataset of 150 proteins, our architectures achieve up to 15% higher precision when L/2 long-range contacts are evaluated. Similarly, when trained using the DNCON2 dataset consisting of 1426 proteins and tested on 84 protein domains in the CASP12 dataset, our single network achieves 4.8% higher precision than the ensembled DNCON2 method when top L long-range contacts are evaluated. Availability and implementation DEEPCON is available at https://github.com/badriadhikari/DEEPCON/.

scholarly journals A review and comparison of breast tumor cell nuclei segmentation performances using deep convolutional neural networks

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Andrew Lagree ◽  
Majidreza Mohebpour ◽  
Nicholas Meti ◽  
Khadijeh Saednia ◽  
Fang-I. Lu ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Breast Tissue ◽  
Superior Performance ◽  
Histopathological Analysis ◽  
Cell Nuclei ◽  
Deep Convolutional Neural Networks ◽  
Nuclei Segmentation ◽  
Histopathological Images ◽  
Biopsy Examination

AbstractBreast cancer is currently the second most common cause of cancer-related death in women. Presently, the clinical benchmark in cancer diagnosis is tissue biopsy examination. However, the manual process of histopathological analysis is laborious, time-consuming, and limited by the quality of the specimen and the experience of the pathologist. This study's objective was to determine if deep convolutional neural networks can be trained, with transfer learning, on a set of histopathological images independent of breast tissue to segment tumor nuclei of the breast. Various deep convolutional neural networks were evaluated for the study, including U-Net, Mask R-CNN, and a novel network (GB U-Net). The networks were trained on a set of Hematoxylin and Eosin (H&E)-stained images of eight diverse types of tissues. GB U-Net demonstrated superior performance in segmenting sites of invasive diseases (AJI = 0.53, mAP = 0.39 & AJI = 0.54, mAP = 0.38), validated on two hold-out datasets exclusively containing breast tissue images of approximately 7,582 annotated cells. The results of the networks, trained on images independent of breast tissue, demonstrated that tumor nuclei of the breast could be accurately segmented.

scholarly journals Artificial Intelligence-based Segmentation of Nuclei in Multi-organ Histopathology Images: Model Development and Validation (Preprint)

2020 ◽  
Author(s):  
Tahir Mahmood ◽  
Muhammad Owais ◽  
Kyoung Jun Noh ◽  
Hyo Sik Yoon ◽  
Adnan Haider ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
State Of The Art ◽  
Computational Cost ◽  
The State ◽  
Segmentation Method ◽  
Dice Coefficient ◽  
Nuclei Segmentation ◽  
Art Methods ◽  
Histopathology Images ◽  
Computational Pathology

BACKGROUND Accurate nuclei segmentation in histopathology images plays a key role in digital pathology. It is considered a prerequisite for the determination of cell phenotype, nuclear morphometrics, cell classification, and the grading and prognosis of cancer. However, it is a very challenging task because of the different types of nuclei, large intra-class variations, and diverse cell morphologies. Consequently, the manual inspection of such images under high-resolution microscopes is tedious and time-consuming. Alternatively, artificial intelligence (AI)-based automated techniques, which are fast, robust, and require less human effort, can be used. Recently, several AI-based nuclei segmentation techniques have been proposed. They have shown a significant performance improvement for this task, but there is room for further improvement. Thus, we propose an AI-based nuclei segmentation technique in which we adopt a new nuclei segmentation network empowered by residual skip connections to address this issue. OBJECTIVE The aim of this study was to develop an AI-based nuclei segmentation method for histopathology images of multiple organs. METHODS Our proposed residual-skip-connections-based nuclei segmentation network (R-NSN) is comprised of two main stages: Stain normalization and nuclei segmentation as shown in Figure 2. In the 1st stage, a histopathology image is stain normalized to balance the color and intensity variation. Subsequently, it is used as an input to the R-NSN in stage 2, which outputs a segmented image. RESULTS Experiments were performed on two publicly available datasets: 1) The Cancer Genomic Atlas (TCGA), and 2) Triple-negative Breast Cancer (TNBC). The results show that our proposed technique achieves an aggregated Jaccard index (AJI) of 0.6794, Dice coefficient of 0.8084, and F1-measure of 0.8547 on the TCGA dataset, and an AJI of 0.7332, Dice coefficient of 0.8441, precision of 0.8352, recall of 0.8306, and F1-measure of 0.8329 on the TNBC dataset. These values are higher than those of the state-of-the-art methods. CONCLUSIONS The proposed R-NSN has the potential to maintain crucial features by using the residual connectivity from the encoder to the decoder and uses only a few layers, which reduces the computational cost of the model. The selection of a good stain normalization technique, the effective use of residual connections to avoid information loss, and the use of only a few layers to reduce the computational cost yielded outstanding results. Thus, our nuclei segmentation method is robust and is superior to the state-of-the-art methods. We expect that this study will contribute to the development of computational pathology software for research and clinical use and enhance the impact of computational pathology.

Segmentation of wood cell in cross-section using deep convolutional neural networks

2021 ◽  
pp. 1-10
Author(s):  
Halime Ergun
Keyword(s):  
Neural Networks ◽  
Cross Section ◽  
Convolutional Neural Networks ◽  
Optimization Algorithm ◽  
Cell Types ◽  
Anatomical Structure ◽  
Automatic Identification ◽  
Segmentation Method ◽  
Deep Convolutional Neural Networks ◽  
Anatomical Features

Fiber and vessel structures located in the cross-section are anatomical features that play an important role in identifying tree species. In order to determine the microscopic anatomical structure of these cell types, each cell must be accurately segmented. In this study, a segmentation method is proposed for wood cell images based on deep convolutional neural networks. The network, which was developed by combining two-stage CNN structures, was trained using the Adam optimization algorithm. For evaluation, the method was compared with SegNet and U-Net architectures, trained with the same dataset. The losses in these models trained were compared using IoU (Intersection over Union), accuracy, and BF-score measurements on the test data. The automatic identification of the cells in the wood images obtained using a microscope will provide a fast, inexpensive, and reliable tool for those working in this field.

Early and Late Level Fusion of Deep Convolutional Neural Networks for Visual Concept Recognition

2016 ◽  
Vol 10 (03) ◽  
pp. 379-397 ◽  
Author(s):  
Hilal Ergun ◽  
Yusuf Caglar Akyuz ◽  
Mustafa Sert ◽  
Jianquan Liu
Keyword(s):  
Neural Networks ◽  
Best Practices ◽  
Convolutional Neural Networks ◽  
Network Architecture ◽  
Data Augmentation ◽  
State Of The Art ◽  
Great Promise ◽  
Visual Concept ◽  
Deep Convolutional Neural Networks ◽  
Concept Recognition

Visual concept recognition is an active research field in the last decade. Related to this attention, deep learning architectures are showing great promise in various computer vision domains including image classification, object detection, event detection and action recognition in videos. In this study, we investigate various aspects of convolutional neural networks for visual concept recognition. We analyze recent studies and different network architectures both in terms of running time and accuracy. In our proposed visual concept recognition system, we first discuss various important properties of popular convolutional network architecture under consideration. Then we describe our method for feature extraction at different levels of abstraction. We present extensive empirical information along with best practices for big data practitioners. Using these best practices we propose efficient fusion mechanisms both for single and multiple network models. We present state-of-the-art results on benchmark datasets while keeping computational costs at low level. Our results show that these state-of-the-art results can be reached without using extensive data augmentation techniques.

scholarly journals Direct Quantization for Training Highly Accurate Low Bit-width Deep Neural Networks

2020 ◽  
Author(s):  
Tuan Hoang ◽  
Thanh-Toan Do ◽  
Tam V. Nguyen ◽  
Ngai-Man Cheung
Keyword(s):  
Neural Networks ◽  
Cost Function ◽  
Image Classification ◽  
Convolutional Neural Networks ◽  
Gradient Descent ◽  
Deep Neural Networks ◽  
State Of The Art ◽  
Deep Convolutional Neural Networks ◽  
Novel Method ◽  
The Cost

This paper proposes two novel techniques to train deep convolutional neural networks with low bit-width weights and activations. First, to obtain low bit-width weights, most existing methods obtain the quantized weights by performing quantization on the full-precision network weights. However, this approach would result in some mismatch: the gradient descent updates full-precision weights, but it does not update the quantized weights. To address this issue, we propose a novel method that enables direct updating of quantized weights with learnable quantization levels to minimize the cost function using gradient descent. Second, to obtain low bit-width activations, existing works consider all channels equally. However, the activation quantizers could be biased toward a few channels with high-variance. To address this issue, we propose a method to take into account the quantization errors of individual channels. With this approach, we can learn activation quantizers that minimize the quantization errors in the majority of channels. Experimental results demonstrate that our proposed method achieves state-of-the-art performance on the image classification task, using AlexNet, ResNet and MobileNetV2 architectures on CIFAR-100 and ImageNet datasets.

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