scholarly journals Semantic segmentation of vertebrate microfossils from computed tomography data using a deep learning approach

2021 ◽  
Vol 40 (2) ◽  
pp. 163-173
Author(s):  
Yemao Hou ◽  
Mario Canul-Ku ◽  
Xindong Cui ◽  
Rogelio Hasimoto-Beltran ◽  
Min Zhu
Keyword(s):  
Deep Learning ◽  
Evolutionary Biology ◽  
Semantic Segmentation ◽  
Stratigraphic Correlation ◽  
Segmentation Method ◽  
Research Areas ◽  
Performance Metric ◽  
Segmentation Methods ◽  
Ct Data ◽  
Tomography Data

Abstract. Vertebrate microfossils have broad applications in evolutionary biology and stratigraphy research areas such as the evolution of hard tissues and stratigraphic correlation. Classification is one of the basic tasks of vertebrate microfossil studies. With the development of techniques for virtual paleontology, vertebrate microfossils can be classified efficiently based on 3D volumes. The semantic segmentation of different fossils and their classes from CT data is a crucial step in the reconstruction of their 3D volumes. Traditional segmentation methods adopt thresholding combined with manual labeling, which is a time-consuming process. Our study proposes a deep-learning-based (DL-based) semantic segmentation method for vertebrate microfossils from CT data. To assess the performance of the method, we conducted extensive experiments on nearly 500 fish microfossils. The results show that the intersection over union (IoU) performance metric arrived at least 94.39 %, meeting the semantic segmentation requirements of paleontologists. We expect that the DL-based method could also be applied to other fossils from CT data with good performance.

scholarly journals Self-Attention in Reconstruction Bias U-Net for Semantic Segmentation of Building Rooftops in Optical Remote Sensing Images

2021 ◽  
Vol 13 (13) ◽  
pp. 2524
Author(s):  
Ziyi Chen ◽  
Dilong Li ◽  
Wentao Fan ◽  
Haiyan Guan ◽  
Cheng Wang ◽  
...  
Keyword(s):  
Remote Sensing ◽  
Deep Learning ◽  
Semantic Segmentation ◽  
Extraction Methods ◽  
The Self ◽  
Optical Remote Sensing ◽  
Building Extraction ◽  
Learning Models ◽  
Remote Sensing Images ◽  
Segmentation Methods

Deep learning models have brought great breakthroughs in building extraction from high-resolution optical remote-sensing images. Among recent research, the self-attention module has called up a storm in many fields, including building extraction. However, most current deep learning models loading with the self-attention module still lose sight of the reconstruction bias’s effectiveness. Through tipping the balance between the abilities of encoding and decoding, i.e., making the decoding network be much more complex than the encoding network, the semantic segmentation ability will be reinforced. To remedy the research weakness in combing self-attention and reconstruction-bias modules for building extraction, this paper presents a U-Net architecture that combines self-attention and reconstruction-bias modules. In the encoding part, a self-attention module is added to learn the attention weights of the inputs. Through the self-attention module, the network will pay more attention to positions where there may be salient regions. In the decoding part, multiple large convolutional up-sampling operations are used for increasing the reconstruction ability. We test our model on two open available datasets: the WHU and Massachusetts Building datasets. We achieve IoU scores of 89.39% and 73.49% for the WHU and Massachusetts Building datasets, respectively. Compared with several recently famous semantic segmentation methods and representative building extraction methods, our method’s results are satisfactory.

scholarly journals Real-Time Semantic Segmentation with Dual Encoder and Self-Attention Mechanism for Autonomous Driving

Sensors ◽  
2021 ◽  
Vol 21 (23) ◽  
pp. 8072
Author(s):  
Yu-Bang Chang ◽  
Chieh Tsai ◽  
Chang-Hong Lin ◽  
Poki Chen
Keyword(s):  
Deep Learning ◽  
Real Time ◽  
Network Architecture ◽  
Semantic Segmentation ◽  
Autonomous Driving ◽  
Attention Mechanism ◽  
Trade Off ◽  
Segmentation Methods ◽  
General Semantic ◽  
Deep Learning Model

As the techniques of autonomous driving become increasingly valued and universal, real-time semantic segmentation has become very popular and challenging in the field of deep learning and computer vision in recent years. However, in order to apply the deep learning model to edge devices accompanying sensors on vehicles, we need to design a structure that has the best trade-off between accuracy and inference time. In previous works, several methods sacrificed accuracy to obtain a faster inference time, while others aimed to find the best accuracy under the condition of real time. Nevertheless, the accuracies of previous real-time semantic segmentation methods still have a large gap compared to general semantic segmentation methods. As a result, we propose a network architecture based on a dual encoder and a self-attention mechanism. Compared with preceding works, we achieved a 78.6% mIoU with a speed of 39.4 FPS with a 1024 × 2048 resolution on a Cityscapes test submission.

scholarly journals Skin lesion segmentation method for dermoscopic images with convolutional neural networks and semantic segmentation

2021 ◽  
Vol 45 (1) ◽  
pp. 122-129
Author(s):  
Dang N.H. Thanh ◽  
Nguyen Hoang Hai ◽  
Le Minh Hieu ◽  
Prayag Tiwari ◽  
V.B. Surya Prasath
Keyword(s):  
Skin Cancer ◽  
Skin Lesion ◽  
Semantic Segmentation ◽  
Segmentation Method ◽  
Lesion Segmentation ◽  
Computing Systems ◽  
Segmentation Methods ◽  
Dermoscopic Image ◽  
Better Than

Melanoma skin cancer is one of the most dangerous forms of skin cancer because it grows fast and causes most of the skin cancer deaths. Hence, early detection is a very important task to treat melanoma. In this article, we propose a skin lesion segmentation method for dermoscopic images based on the U-Net architecture with VGG-16 encoder and the semantic segmentation. Base on the segmented skin lesion, diagnostic imaging systems can evaluate skin lesion features to classify them. The proposed method requires fewer resources for training, and it is suitable for computing systems without powerful GPUs, but the training accuracy is still high enough (above 95 %). In the experiments, we train the model on the ISIC dataset – a common dermoscopic image dataset. To assess the performance of the proposed skin lesion segmentation method, we evaluate the Sorensen-Dice and the Jaccard scores and compare to other deep learning-based skin lesion segmentation methods. Experimental results showed that skin lesion segmentation quality of the proposed method are better than ones of the compared methods.

scholarly journals Efficient Multi-Organ Multi-Center Cell Nuclei Segmentation Method Based on Deep Learnable Aggregation Network

2021 ◽  
Vol 38 (3) ◽  
pp. 653-661
Author(s):  
Loay Hassan ◽  
Adel Saleh ◽  
Mohamed Abdel-Nasser ◽  
Osama A. Omer ◽  
Domenec Puig
Keyword(s):  
Deep Learning ◽  
Color Variation ◽  
Segmentation Method ◽  
Cell Nuclei ◽  
Nuclei Segmentation ◽  
Segmentation Methods ◽  
Cancer Subtype ◽  
Center Cell ◽  
Cancer Grading ◽  
Segmentation Models

Automated cell nuclei delineation in whole-slide imaging (WSI) is a fundamental step for many tasks like cancer cell recognition, cancer grading, and cancer subtype classification. Although numerous computational methods have been proposed for segmenting nuclei in WSI images based on image processing and deep learning, existing approaches face major challenges such as color variation due to the use of different stains, the various structures of cell nuclei, and the overlapping and clumped cell nuclei. To circumvent these challenges in this article, we propose an efficient and accurate cell nuclei segmentation method based on deep learning, in which a set of accurate individual cell nuclei segmentation models are developed to predict rough segmentation masks, and then a learnable aggregation network (LANet) is used to predict the final nuclei masks. Besides, we develop cell nuclei segmentation software (with a graphical user interface—GUI) that includes the proposed method and other deep-learning-based cell nuclei segmentation methods. A challenging WSI dataset collected from different centers and organs is used to demonstrate the efficiency of our method. The experimental results reveal that our method obtains a competitive performance compared to the existing approaches in terms of the aggregated Jaccard index (AJI=89.25%) and F1-score (F1=73.02%). The developed nuclei segmentation software can be downloaded from https://github.com/loaysh2010/Cell-Nuclei-Segmentation-GUI-Application.

scholarly journals Semantic Segmentation Deep Learning for Extracting Surface Mine Extents from Historic Topographic Maps

2020 ◽  
Vol 12 (24) ◽  
pp. 4145
Author(s):  
Aaron E. Maxwell ◽  
Michelle S. Bester ◽  
Luis A. Guillen ◽  
Christopher A. Ramezan ◽  
Dennis J. Carpinello ◽  
...  
Keyword(s):  
United States ◽  
Deep Learning ◽  
Model Performance ◽  
Semantic Segmentation ◽  
Topographic Maps ◽  
Commission Error ◽  
Dice Coefficient ◽  
Surface Mine ◽  
Segmentation Methods ◽  
Historic Record

Historic topographic maps, which are georeferenced and made publicly available by the United States Geological Survey (USGS) and the National Map’s Historical Topographic Map Collection (HTMC), are a valuable source of historic land cover and land use (LCLU) information that could be used to expand the historic record when combined with data from moderate spatial resolution Earth observation missions. This is especially true for landscape disturbances that have a long and complex historic record, such as surface coal mining in the Appalachian region of the eastern United States. In this study, we investigate this specific mapping problem using modified UNet semantic segmentation deep learning (DL), which is based on convolutional neural networks (CNNs), and a large example dataset of historic surface mine disturbance extents from the USGS Geology, Geophysics, and Geochemistry Science Center (GGGSC). The primary objectives of this study are to (1) evaluate model generalization to new geographic extents and topographic maps and (2) to assess the impact of training sample size, or the number of manually interpreted topographic maps, on model performance. Using data from the state of Kentucky, our findings suggest that DL semantic segmentation can detect surface mine disturbance features from topographic maps with a high level of accuracy (Dice coefficient = 0.902) and relatively balanced omission and commission error rates (Precision = 0.891, Recall = 0.917). When the model is applied to new topographic maps in Ohio and Virginia to assess generalization, model performance decreases; however, performance is still strong (Ohio Dice coefficient = 0.837 and Virginia Dice coefficient = 0.763). Further, when reducing the number of topographic maps used to derive training image chips from 84 to 15, model performance was only slightly reduced, suggesting that models that generalize well to new data and geographic extents may not require a large training set. We suggest the incorporation of DL semantic segmentation methods into applied workflows to decrease manual digitizing labor requirements and call for additional research associated with applying semantic segmentation methods to alternative cartographic representations to supplement research focused on multispectral image analysis and classification.

scholarly journals Deep learning-based segmentation of high-resolution computed tomography image data outperforms commonly used automatic bone segmentation methods

2021 ◽  
Author(s):  
Daniella M. Patton ◽  
Emilie N. Henning ◽  
Rob W. Goulet ◽  
Sean K. Carroll ◽  
Erin M.R. Bigelow ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Deep Learning ◽  
Femoral Neck ◽  
Vertebral Body ◽  
Automatic Segmentation ◽  
Image Data ◽  
Segmentation Methods ◽  
Unseen Data ◽  
Vertebral Bodies ◽  
Ct Data

Segmenting bone from background is required to quantify bone architecture in computed tomography (CT) image data. A deep learning approach using convolutional neural networks (CNN) is a promising alternative method for automatic segmentation. The study objectives were to evaluate the performance of CNNs in automatic segmentation of human vertebral body (micro-CT) and femoral neck (nano-CT) data and to investigate the performance of CNNs to segment data across scanners. Scans of human L1 vertebral bodies (microCT [North Star Imaging], n=28, 53μm3) and femoral necks (nano-CT [GE], n=28, 27μm3) were used for evaluation. Six slices were selected for each scan and then manually segmented to create ground truth masks (Dragonfly 4.0, ORS). Two-dimensional U-Net CNNs were trained in Dragonfly 4.0 with images of the [FN] femoral necks only, [VB] vertebral bodies only, and [F+V] combined CT data. Global (i.e., Otsu and Yen) and local (i.e., Otsu r = 100) thresholding methods were applied to each dataset. Segmentation performance was evaluated using the Dice index, a similarity metric of overlap. Kruskal-Wallis and Tukey-Kramer post-hoc tests were used to test for significant differences in the accuracy of segmentation methods. The FN U-Net had significantly higher Dice indices (i.e., better performance) than the global (Otsu: p=0.001; Yen: p=0.001) and local (Otsu [r=100]: p=0.001) thresholding methods and the VB U-Net (p=0.001) but there was no significant difference in model performance compared to the FN + VB U-net (p=0.783) on femoral neck image data. The VB U-net had significantly higher Dice coefficients than the global and local Otsu (p=0.001 for both) and FN U-Net (p=0.001) but not compared to the Yen (p=0.462) threshold or FN + VB U-net (p=0.783) on vertebral body image data. The results demonstrate that the U-net architecture outperforms common thresholding methods. Further, a network trained with bone data from a different system (i.e., different image acquisition parameters and voxel size) and a different anatomical site can perform well on unseen data. Finally, a network trained with combined datasets performed well on both datasets, indicating that a network can feasibly be trained with multiple datasets and perform well on varied image data.

scholarly journals Deep learning models for COVID-19 infected area segmentation in CT images

2020 ◽  
Author(s):  
Athanasios Voulodimos ◽  
Eftychios Protopapadakis ◽  
Iason Katsamenis ◽  
Anastasios Doulamis ◽  
Nikolaos Doulamis
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Networks ◽  
Class Imbalance ◽  
Semantic Segmentation ◽  
Ct Images ◽  
Learning Models ◽  
Fully Convolutional Neural Networks ◽  
Infected Area ◽  
Ct Data

Recent studies indicated that detecting radiographic patterns on CT chest scans could in some cases yield higher sensitivity and specificity for COVID-19 detection compared to other methods such as RTPCR. In this work, we scrutinize the effectiveness of deep learning models for semantic segmentation of pneumonia infected area segmentation in CT images for the detection of COVID-19. We explore the efficacy of U-Nets and Fully Convolutional Neural Networks in this task using real-world CT data from COVID-19 patients. The results indicate that Fully Convolutional Neural Networks are capable of accurate segmentation despite the class imbalance on the dataset and the man-made annotation errors on the boundaries of symptom manifestation areas, and can be a promising method for further analysis of COVID-19 induced pneumonia symptoms in CT images.

scholarly journals A Semantic Segmentation Method for Early Forest Fire Smoke Based on Concentration Weighting

Electronics ◽  
2021 ◽  
Vol 10 (21) ◽  
pp. 2675
Author(s):  
Zewei Wang ◽  
Change Zheng ◽  
Jiyan Yin ◽  
Ye Tian ◽  
Wenbin Cui
Keyword(s):  
Deep Learning ◽  
Target Detection ◽  
Forest Fire ◽  
Semantic Segmentation ◽  
Segmentation Method ◽  
Smoke Detection ◽  
Fire Smoke ◽  
First Time ◽  
Deep Learning Model ◽  
Selection Of

Forest fire smoke detection based on deep learning has been widely studied. Labeling the smoke image is a necessity when building datasets of target detection and semantic segmentation. The uncertainty in labeling the forest fire smoke pixels caused by the non-uniform diffusion of smoke particles will affect the recognition accuracy of the deep learning model. To overcome the labeling ambiguity, the weighted idea was proposed in this paper for the first time. First, the pixel-concentration relationship between the gray value and the concentration of forest fire smoke pixels in the image was established. Second, the loss function of the semantic segmentation method based on concentration weighting was built and improved; thus, the network could pay attention to the smoke pixels differently, an effort to better segment smoke by weighting the loss calculation of smoke pixels. Finally, based on the established forest fire smoke dataset, selection of the optimum weighted factors was made through experiments. mIoU based on the weighted method increased by 1.52% than the unweighted method. The weighted method cannot only be applied to the semantic segmentation and target detection of forest fire smoke, but also has a certain significance to other dispersive target recognition.

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