scholarly journals Convolutional Neural Network-Based Instance Segmentation Algorithm to Acquire Quantitative Criteria of Early Mouse Development

2018 ◽  
Author(s):  
Yuta Tokuoka ◽  
Takahiro G Yamada ◽  
Noriko F Hiroi ◽  
Tetsuya J Kobayashi ◽  
Kazuo Yamagata ◽  
...  
Keyword(s):  
Neural Network ◽  
Image Processing ◽  
Deep Learning ◽  
Three Dimensional ◽  
Semantic Segmentation ◽  
Critical Issue ◽  
Segmentation Algorithm ◽  
Embryonic Cells ◽  
Mouse Development ◽  
Instance Segmentation

AbstractIn embryology, image processing methods such as segmentation are applied to acquiring quantitative criteria from time-series three-dimensional microscopic images. When used to segment cells or intracellular organelles, several current deep learning techniques outperform traditional image processing algorithms. However, segmentation algorithms still have unsolved problems, especially in bioimage processing. The most critical issue is that the existing deep learning-based algorithms for bioimages can perform only semantic segmentation, which distinguishes whether a pixel is within an object (for example, nucleus) or not. In this study, we implemented a novel segmentation algorithm, based on deep learning, which segments each nucleus and adds different labels to the detected objects. This segmentation algorithm is called instance segmentation. Our instance segmentation algorithm, implemented as a neural network, which we named QCA Net, substantially outperformed 3D U-Net, which is the best semantic segmentation algorithm that uses deep learning. Using QCA Net, we quantified the nuclear number, volume, surface area, and center of gravity coordinates during the development of mouse embryos. In particular, QCA Net distinguished nuclei of embryonic cells from those of polar bodies formed in meiosis. We consider that QCA Net can greatly contribute to bioimage segmentation in embryology by generating quantitative criteria from segmented images.

scholarly journals Convolutional Neural Network for the Semantic Segmentation of Remote Sensing Images

2021 ◽  
Vol 26 (1) ◽  
pp. 200-215
Author(s):  
Muhammad Alam ◽  
Jian-Feng Wang ◽  
Cong Guangpei ◽  
LV Yunrong ◽  
Yuanfang Chen
Keyword(s):  
Neural Network ◽  
Remote Sensing ◽  
Neural Networks ◽  
Image Processing ◽  
Deep Learning ◽  
Semantic Segmentation ◽  
Natural Scene ◽  
Remote Sensing Images ◽  
Advantages And Disadvantages ◽  
Target Segmentation

AbstractIn recent years, the success of deep learning in natural scene image processing boosted its application in the analysis of remote sensing images. In this paper, we applied Convolutional Neural Networks (CNN) on the semantic segmentation of remote sensing images. We improve the Encoder- Decoder CNN structure SegNet with index pooling and U-net to make them suitable for multi-targets semantic segmentation of remote sensing images. The results show that these two models have their own advantages and disadvantages on the segmentation of different objects. In addition, we propose an integrated algorithm that integrates these two models. Experimental results show that the presented integrated algorithm can exploite the advantages of both the models for multi-target segmentation and achieve a better segmentation compared to these two models.

scholarly journals InstantDL: an easy-to-use deep learning pipeline for image segmentation and classification

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dominik Jens Elias Waibel ◽  
Sayedali Shetab Boushehri ◽  
Carsten Marr
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Specific Problem ◽  
State Of The Art ◽  
Image Data ◽  
Semantic Segmentation ◽  
Parameter Tuning ◽  
Cellular Processes ◽  
Minimal Effort ◽  
Instance Segmentation

Abstract Background Deep learning contributes to uncovering molecular and cellular processes with highly performant algorithms. Convolutional neural networks have become the state-of-the-art tool to provide accurate and fast image data processing. However, published algorithms mostly solve only one specific problem and they typically require a considerable coding effort and machine learning background for their application. Results We have thus developed InstantDL, a deep learning pipeline for four common image processing tasks: semantic segmentation, instance segmentation, pixel-wise regression and classification. InstantDL enables researchers with a basic computational background to apply debugged and benchmarked state-of-the-art deep learning algorithms to their own data with minimal effort. To make the pipeline robust, we have automated and standardized workflows and extensively tested it in different scenarios. Moreover, it allows assessing the uncertainty of predictions. We have benchmarked InstantDL on seven publicly available datasets achieving competitive performance without any parameter tuning. For customization of the pipeline to specific tasks, all code is easily accessible and well documented. Conclusions With InstantDL, we hope to empower biomedical researchers to conduct reproducible image processing with a convenient and easy-to-use pipeline.

scholarly journals Multiclass semantic segmentation for digitisation of movable heritage using deep learning techniques

2021 ◽  
Vol 12 (25) ◽  
pp. 85
Author(s):  
Giacomo Patrucco ◽  
Francesco Setragno
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Three Dimensional ◽  
Semantic Segmentation ◽  
Semantic Classification ◽  
Object Categories ◽  
Network Training ◽  
Acquisition Strategies ◽  
Learning Techniques ◽  
High Degree

<p class="VARAbstract">Digitisation processes of movable heritage are becoming increasingly popular to document the artworks stored in our museums. A growing number of strategies for the three-dimensional (3D) acquisition and modelling of these invaluable assets have been developed in the last few years. Their objective is to efficiently respond to this documentation need and contribute to deepening the knowledge of the masterpieces investigated constantly by researchers operating in many fieldworks. Nowadays, one of the most effective solutions is represented by the development of image-based techniques, usually connected to a Structure-from-Motion (SfM) photogrammetric approach. However, while images acquisition is relatively rapid, the processes connected to data processing are very time-consuming and require the operator’s substantial manual involvement. Developing deep learning-based strategies can be an effective solution to enhance the automatism level. In this research, which has been carried out in the framework of the digitisation of a wooden maquettes collection stored in the ‘Museo Egizio di Torino’, using a photogrammetric approach, an automatic masking strategy using deep learning techniques is proposed, to increase the level of automatism and therefore, optimise the photogrammetric pipeline. Starting from a manually annotated dataset, a neural network was trained to automatically perform a semantic classification to isolate the maquettes from the background. The proposed methodology allowed the researchers to obtain automatically segmented masks with a high degree of accuracy. The workflow is described (as regards acquisition strategies, dataset processing, and neural network training). In addition, the accuracy of the results is evaluated and discussed. Finally, the researchers proposed the possibility of performing a multiclass segmentation on the digital images to recognise different object categories in the images, as well as to define a semantic hierarchy to perform automatic classification of different elements in the acquired images.</p><p><strong>Highlights:</strong></p><ul><li><p>In the framework of movable heritage digitisation processes, many procedures are very time-consuming, and they still require the operator’s substantial manual involvement.</p></li><li><p>This research proposes using deep learning techniques to enhance the automatism level in the generation of exclusion masks, improving the optimisation of the photogrammetric procedures.</p></li><li><p>Following this strategy, the possibility of performing a multiclass semantic segmentation (on the 2D images and, consequently, on the 3D point cloud) is also discussed, considering the accuracy of the obtainable results.</p></li></ul>

scholarly journals Neovascularization Detection and Localization in Fundus Images Using Deep Learning

Sensors ◽  
2021 ◽  
Vol 21 (16) ◽  
pp. 5327
Author(s):  
Michael Chi Seng Tang ◽  
Soo Siang Teoh ◽  
Haidi Ibrahim ◽  
Zunaina Embong
Keyword(s):  
Neural Network ◽  
Image Processing ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Architecture ◽  
Semantic Segmentation ◽  
Optic Disk ◽  
Diabetic Patients ◽  
Fundus Images ◽  
Testing Set

Proliferative Diabetic Retinopathy (PDR) is a severe retinal disease that threatens diabetic patients. It is characterized by neovascularization in the retina and the optic disk. PDR clinical features contain highly intense retinal neovascularization and fibrous spreads, leading to visual distortion if not controlled. Different image processing techniques have been proposed to detect and diagnose neovascularization from fundus images. Recently, deep learning methods are getting popular in neovascularization detection due to artificial intelligence advancement in biomedical image processing. This paper presents a semantic segmentation convolutional neural network architecture for neovascularization detection. First, image pre-processing steps were applied to enhance the fundus images. Then, the images were divided into small patches, forming a training set, a validation set, and a testing set. A semantic segmentation convolutional neural network was designed and trained to detect the neovascularization regions on the images. Finally, the network was tested using the testing set for performance evaluation. The proposed model is entirely automated in detecting and localizing neovascularization lesions, which is not possible with previously published methods. Evaluation results showed that the model could achieve accuracy, sensitivity, specificity, precision, Jaccard similarity, and Dice similarity of 0.9948, 0.8772, 0.9976, 0.8696, 0.7643, and 0.8466, respectively. We demonstrated that this model could outperform other convolutional neural network models in neovascularization detection.

scholarly journals Orchard Mapping with Deep Learning Semantic Segmentation

Sensors ◽  
2021 ◽  
Vol 21 (11) ◽  
pp. 3813
Author(s):  
Athanasios Anagnostis ◽  
Aristotelis C. Tagarakis ◽  
Dimitrios Kateris ◽  
Vasileios Moysiadis ◽  
Claus Grøn Sørensen ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Semantic Segmentation ◽  
Automated Detection ◽  
Aerial Images ◽  
Training Dataset ◽  
Field Boundary ◽  
Different Seasons ◽  
Detection And Localization ◽  
Different Levels

This study aimed to propose an approach for orchard trees segmentation using aerial images based on a deep learning convolutional neural network variant, namely the U-net network. The purpose was the automated detection and localization of the canopy of orchard trees under various conditions (i.e., different seasons, different tree ages, different levels of weed coverage). The implemented dataset was composed of images from three different walnut orchards. The achieved variability of the dataset resulted in obtaining images that fell under seven different use cases. The best-trained model achieved 91%, 90%, and 87% accuracy for training, validation, and testing, respectively. The trained model was also tested on never-before-seen orthomosaic images or orchards based on two methods (oversampling and undersampling) in order to tackle issues with out-of-the-field boundary transparent pixels from the image. Even though the training dataset did not contain orthomosaic images, it achieved performance levels that reached up to 99%, demonstrating the robustness of the proposed approach.

scholarly journals Analysis of the Nosema Cells Identification for Microscopic Images

Sensors ◽  
2021 ◽  
Vol 21 (9) ◽  
pp. 3068
Author(s):  
Soumaya Dghim ◽  
Carlos M. Travieso-González ◽  
Radim Burget
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Image Processing ◽  
Deep Learning ◽  
The Other ◽  
Support Vector ◽  
Learning Approaches ◽  
Microscopic Images ◽  
Trained Neural Network ◽  
Nosema Disease

The use of image processing tools, machine learning, and deep learning approaches has become very useful and robust in recent years. This paper introduces the detection of the Nosema disease, which is considered to be one of the most economically significant diseases today. This work shows a solution for recognizing and identifying Nosema cells between the other existing objects in the microscopic image. Two main strategies are examined. The first strategy uses image processing tools to extract the most valuable information and features from the dataset of microscopic images. Then, machine learning methods are applied, such as a neural network (ANN) and support vector machine (SVM) for detecting and classifying the Nosema disease cells. The second strategy explores deep learning and transfers learning. Several approaches were examined, including a convolutional neural network (CNN) classifier and several methods of transfer learning (AlexNet, VGG-16 and VGG-19), which were fine-tuned and applied to the object sub-images in order to identify the Nosema images from the other object images. The best accuracy was reached by the VGG-16 pre-trained neural network with 96.25%.

scholarly journals Real-time deep learning semantic segmentation during intra-operative surgery for 3D augmented reality assistance

2021 ◽  
Author(s):  
Leonardo Tanzi ◽  
Pietro Piazzolla ◽  
Francesco Porpiglia ◽  
Enrico Vezzetti
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Augmented Reality ◽  
Ad Hoc ◽  
Geodesic Distance ◽  
Semantic Segmentation ◽  
Endoscopic Image ◽  
Operative Surgery ◽  
Endoscopic Videos

Abstract Purpose The current study aimed to propose a Deep Learning (DL) and Augmented Reality (AR) based solution for a in-vivo robot-assisted radical prostatectomy (RARP), to improve the precision of a published work from our group. We implemented a two-steps automatic system to align a 3D virtual ad-hoc model of a patient’s organ with its 2D endoscopic image, to assist surgeons during the procedure. Methods This approach was carried out using a Convolutional Neural Network (CNN) based structure for semantic segmentation and a subsequent elaboration of the obtained output, which produced the needed parameters for attaching the 3D model. We used a dataset obtained from 5 endoscopic videos (A, B, C, D, E), selected and tagged by our team’s specialists. We then evaluated the most performing couple of segmentation architecture and neural network and tested the overlay performances. Results U-Net stood out as the most effecting architectures for segmentation. ResNet and MobileNet obtained similar Intersection over Unit (IoU) results but MobileNet was able to elaborate almost twice operations per seconds. This segmentation technique outperformed the results from the former work, obtaining an average IoU for the catheter of 0.894 (σ = 0.076) compared to 0.339 (σ = 0.195). This modifications lead to an improvement also in the 3D overlay performances, in particular in the Euclidean Distance between the predicted and actual model’s anchor point, from 12.569 (σ= 4.456) to 4.160 (σ = 1.448) and in the Geodesic Distance between the predicted and actual model’s rotations, from 0.266 (σ = 0.131) to 0.169 (σ = 0.073). Conclusion This work is a further step through the adoption of DL and AR in the surgery domain. In future works, we will overcome the limits of this approach and finally improve every step of the surgical procedure.

Automated Pancreas Segmentation And Volumetry Using Deep Neural Network On Computed Tomography

2021 ◽  
Author(s):  
Sang-Heon Lim ◽  
Young Jae Kim ◽  
Yeon-Ho Park ◽  
Doojin Kim ◽  
Kwang Gi Kim ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Deep Learning ◽  
Automatic Segmentation ◽  
External Validation ◽  
Three Dimensional ◽  
Semantic Segmentation ◽  
Quantitative Information ◽  
Similarity Coefficients ◽  
Internal Validation ◽  
Pancreas Segmentation

Abstract Pancreas segmentation is necessary for observing lesions, analyzing anatomical structures, and predicting patient prognosis. Therefore, various studies have designed segmentation models based on convolutional neural networks for pancreas segmentation. However, the deep learning approach is limited by a lack of data, and studies conducted on a large computed tomography dataset are scarce. Therefore, this study aims to perform deep-learning-based semantic segmentation on 1,006 participants and evaluate the automatic segmentation performance of the pancreas via four individual three-dimensional segmentation networks. In this study, we performed internal validation with 1,006 patients and external validation using the Cancer Imaging Archive (TCIA) pancreas dataset. We obtained mean precision, recall, and dice similarity coefficients of 0.869, 0.842, and 0.842, respectively, for internal validation via a relevant approach among the four deep learning networks. Using the external dataset, the deep learning network achieved mean precision, recall, and dice similarity coefficients of 0.779, 0.749, and 0.735, respectively. We expect that generalized deep-learning-based systems can assist clinical decisions by providing accurate pancreatic segmentation and quantitative information of the pancreas for abdominal computed tomography.

scholarly journals Compression of Phase-Only Holograms with JPEG Standard and Deep Learning

2018 ◽  
Vol 8 (8) ◽  
pp. 1258 ◽  
Author(s):  
Shuming Jiao ◽  
Zhi Jin ◽  
Chenliang Chang ◽  
Changyuan Zhou ◽  
Wenbin Zou ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
High Frequency ◽  
Critical Issue ◽  
Compression Process ◽  
Compression Scheme ◽  
Quality Degradation ◽  
Digital Format ◽  
Enormous Amount ◽  
Frequency Features

It is a critical issue to reduce the enormous amount of data in the processing, storage and transmission of a hologram in digital format. In photograph compression, the JPEG standard is commonly supported by almost every system and device. It will be favorable if JPEG standard is applicable to hologram compression, with advantages of universal compatibility. However, the reconstructed image from a JPEG compressed hologram suffers from severe quality degradation since some high frequency features in the hologram will be lost during the compression process. In this work, we employ a deep convolutional neural network to reduce the artifacts in a JPEG compressed hologram. Simulation and experimental results reveal that our proposed “JPEG + deep learning” hologram compression scheme can achieve satisfactory reconstruction results for a computer-generated phase-only hologram after compression.

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