scholarly journals Fully Automated 3D Cardiac MRI Localisation and Segmentation Using Deep Neural Networks

2020 ◽  
Vol 6 (7) ◽  
pp. 65 ◽  
Author(s):  
Sulaiman Vesal ◽  
Andreas Maier ◽  
Nishant Ravikumar
Keyword(s):  
Cardiac Mri ◽  
State Of The Art ◽  
Automatic Segmentation ◽  
Learning Approaches ◽  
Target Structure ◽  
Low Contrast ◽  
Fully Convolutional Networks ◽  
Multi Stage ◽  
Density Map ◽  
End To End

Cardiac magnetic resonance (CMR) imaging is used widely for morphological assessment and diagnosis of various cardiovascular diseases. Deep learning approaches based on 3D fully convolutional networks (FCNs), have improved state-of-the-art segmentation performance in CMR images. However, previous methods have employed several pre-processing steps and have focused primarily on segmenting low-resolutions images. A crucial step in any automatic segmentation approach is to first localize the cardiac structure of interest within the MRI volume, to reduce false positives and computational complexity. In this paper, we propose two strategies for localizing and segmenting the heart ventricles and myocardium, termed multi-stage and end-to-end, using a 3D convolutional neural network. Our method consists of an encoder–decoder network that is first trained to predict a coarse localized density map of the target structure at a low resolution. Subsequently, a second similar network employs this coarse density map to crop the image at a higher resolution, and consequently, segment the target structure. For the latter, the same two-stage architecture is trained end-to-end. The 3D U-Net with some architectural changes (referred to as 3D DR-UNet) was used as the base architecture in this framework for both the multi-stage and end-to-end strategies. Moreover, we investigate whether the incorporation of coarse features improves the segmentation. We evaluate the two proposed segmentation strategies on two cardiac MRI datasets, namely, the Automatic Cardiac Segmentation Challenge (ACDC) STACOM 2017, and Left Atrium Segmentation Challenge (LASC) STACOM 2018. Extensive experiments and comparisons with other state-of-the-art methods indicate that the proposed multi-stage framework consistently outperforms the rest in terms of several segmentation metrics. The experimental results highlight the robustness of the proposed approach, and its ability to generate accurate high-resolution segmentations, despite the presence of varying degrees of pathology-induced changes to cardiac morphology and image appearance, low contrast, and noise in the CMR volumes.

scholarly journals Fully Convolutional Networks and Geographic Object-Based Image Analysis for the Classification of VHR Imagery

2019 ◽  
Vol 11 (5) ◽  
pp. 597 ◽  
Author(s):  
Nicholus Mboga ◽  
Stefanos Georganos ◽  
Tais Grippa ◽  
Moritz Lennert ◽  
Sabine Vanhuysse ◽  
...  
Keyword(s):  
Democratic Republic Of Congo ◽  
State Of The Art ◽  
Computational Cost ◽  
Convolutional Networks ◽  
Object Based Image Analysis ◽  
Fully Convolutional Networks ◽  
Object Based ◽  
Geographic Object ◽  
End To End ◽  
Future Work

Land cover Classified maps obtained from deep learning methods such as Convolutional neural networks (CNNs) and fully convolutional networks (FCNs) usually have high classification accuracy but with the detailed structures of objects lost or smoothed. In this work, we develop a methodology based on fully convolutional networks (FCN) that is trained in an end-to-end fashion using aerial RGB images only as input. Skip connections are introduced into the FCN architecture to recover high spatial details from the lower convolutional layers. The experiments are conducted on the city of Goma in the Democratic Republic of Congo. We compare the results to a state-of-the art approach based on a semi-automatic Geographic object image-based analysis (GEOBIA) processing chain. State-of-the art classification accuracies are obtained by both methods whereby FCN and the best baseline method have an overall accuracy of 91.3% and 89.5% respectively. The maps have good visual quality and the use of an FCN skip architecture minimizes the rounded edges that is characteristic of FCN maps. Additional experiments are done to refine FCN classified maps using segments obtained from GEOBIA generated at different scale and minimum segment size. High OA of up to 91.5% is achieved accompanied with an improved edge delineation in the FCN maps, and future work will involve explicitly incorporating boundary information from the GEOBIA segmentation into the FCN pipeline in an end-to-end fashion. Finally, we observe that FCN has a lower computational cost than the standard patch-based CNN approach especially at inference.

Automatic Segmentation of Color Tongue Image Using Deep Asymmetric Convolution Skip Net

2021 ◽  
Vol 11 (8) ◽  
pp. 2100-2108
Author(s):  
He Huang ◽  
Xi Guan ◽  
Wenbo Zhang ◽  
Juhua Zhou ◽  
Bofeng Wu ◽  
...  
Keyword(s):  
Image Segmentation ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
State Of The Art ◽  
Automatic Segmentation ◽  
Color Images ◽  
End To End ◽  
Collection Methods

Segmentation of the tongue body from color images is vital for tongue diagnoses in traditional Chinese medicine. In tongue images, the tongue body is easily confused with the skin and lips, and the shadow also causes incorrect segmentation. To address these issues, we proposed a novel ACS-Net for tongue image segmentation and implemented the end-to-end form. In our ACS-Net architecture, the following innovations proposed: (1) ordinary convolution was replaced with ACB Module, (2) decoder block restores the features extracted by the encoder block, (3) skip connections are implemented between and within blocks. We use our own datasets named S1 and S2 that collected from the partner hospital. The collection methods of these two datasets are different: S1 was collected by professionals while S2 was taken by nurses. The method achieved state-of-the-art results on both two datasets, we use two metrics to reflect the segmentation performance, which are accuracy (acc) and mean intersection over Union (mIoU), in which the acc reaches 0.984 on S1 and 0.981 on S2; the mIoU reaches 0.925 on S1 and 0.958 on S2.

scholarly journals FCN Based Approach for the Automatic Segmentation of Bone Surfaces in Ultrasound Images

10.29007/bncb ◽  
2018 ◽  
Author(s):  
Mateo Villa ◽  
Guillaume Dardenne ◽  
Maged Nasan ◽  
Hoel Letissier ◽  
Chafiaa Hamitouche ◽  
...  
Keyword(s):  
State Of The Art ◽  
Imaging Modality ◽  
Automatic Segmentation ◽  
Ultrasound Images ◽  
Manual Segmentation ◽  
Bone Segmentation ◽  
Bone Morphology ◽  
Convolutional Networks ◽  
Fully Convolutional Networks ◽  
Phase Symmetry

In CAOS, ultrasound imaging has been proposed as a solution for obtaining the specific bone morphology of the patient, avoiding limitations of existing technologies. However, this imaging modality presents different drawbacks that make difficult the automatic bone segmentation. A new algorithm, based on Fully Convolutional Networks (FCN), is proposed. The aim of this paper is to compare and validate this method with (1) a manual segmentation that was performed by three independent experts, and (2) a state of the art method called Confidence in Phase Symmetry (CPS). The FCN based approach outperforms the CPS algorithm and the RMSE is close to the manual segmentation variability.

Building Attention and Edge Convolution Neural Networks for Bioactivity and Physical-Chemical Property Prediction

2019 ◽  
Author(s):  
Michael Withnall ◽  
Edvard Lindelöf ◽  
Ola Engkvist ◽  
Hongming Chen
Keyword(s):  
Message Passing ◽  
State Of The Art ◽  
A Priori ◽  
Model Performance ◽  
Learning Approaches ◽  
Physical Chemical ◽  
Chemical Descriptor ◽  
Derived Properties ◽  
Memory Schemes ◽  
Hyperparameter Selection

We introduce Attention and Edge Memory schemes to the existing Message Passing Neural Network framework for graph convolution, and benchmark our approaches against eight different physical-chemical and bioactivity datasets from the literature. We remove the need to introduce <i>a priori</i> knowledge of the task and chemical descriptor calculation by using only fundamental graph-derived properties. Our results consistently perform on-par with other state-of-the-art machine learning approaches, and set a new standard on sparse multi-task virtual screening targets. We also investigate model performance as a function of dataset preprocessing, and make some suggestions regarding hyperparameter selection.

scholarly journals Distinguishing Adenocarcinomas from Granulomas in the CT scan of the chest: performance degradation evaluation in the automatic segmentation framework

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Mahsa Bank Tavakoli ◽  
Mahdi Orooji ◽  
Mehdi Teimouri ◽  
Ramita Shahabifar
Keyword(s):  
State Of The Art ◽  
Automatic Segmentation ◽  
Texture Features ◽  
Standards Of Care ◽  
Shape Features ◽  
Selection Methods ◽  
Segmentation Framework ◽  
Vessel Tortuosity ◽  
Benign Nodules ◽  
Degradation Evaluation

Abstract Objective The most common histopathologic malignant and benign nodules are Adenocarcinoma and Granuloma, respectively, which have different standards of care. In this paper, we propose an automatic framework for the diagnosis of the Adenocarcinomas and the Granulomas in the CT scans of the chest from a private dataset. We use the radiomic features of the nodules and the attached vessel tortuosity for the diagnosis. The private dataset includes 22 CTs for each nodule type, i.e., adenocarcinoma and granuloma. The dataset contains the CTs of the non-smoker patients who are between 30 and 60 years old. To automatically segment the delineated nodule area and the attached vessels area, we apply a morphological-based approach. For distinguishing the malignancy of the segmented nodule, two texture features of the nodule, the curvature Mean and the number of the attached vessels are extracted. Results We compare our framework with the state-of-the-art feature selection methods for differentiating Adenocarcinomas from Granulomas. These methods employ only the shape features of the nodule, the texture features of the nodule, or the torsion features of the attached vessels along with the radiomic features of the nodule. The accuracy of our framework is improved by considering the four selected features.

scholarly journals Efficient End-to-End Sentence-Level Lipreading with Temporal Convolutional Networks

2021 ◽  
Vol 11 (15) ◽  
pp. 6975
Author(s):  
Tao Zhang ◽  
Lun He ◽  
Xudong Li ◽  
Guoqing Feng
Keyword(s):  
Performance Improvement ◽  
State Of The Art ◽  
Error Rates ◽  
Convolutional Network ◽  
Convolutional Networks ◽  
Sentence Level ◽  
End To End ◽  
High Level ◽  
Improved Accuracy ◽  
Talking Face

Lipreading aims to recognize sentences being spoken by a talking face. In recent years, the lipreading method has achieved a high level of accuracy on large datasets and made breakthrough progress. However, lipreading is still far from being solved, and existing methods tend to have high error rates on the wild data and have the defects of disappearing training gradient and slow convergence. To overcome these problems, we proposed an efficient end-to-end sentence-level lipreading model, using an encoder based on a 3D convolutional network, ResNet50, Temporal Convolutional Network (TCN), and a CTC objective function as the decoder. More importantly, the proposed architecture incorporates TCN as a feature learner to decode feature. It can partly eliminate the defects of RNN (LSTM, GRU) gradient disappearance and insufficient performance, and this yields notable performance improvement as well as faster convergence. Experiments show that the training and convergence speed are 50% faster than the state-of-the-art method, and improved accuracy by 2.4% on the GRID dataset.

scholarly journals Using spatial-temporal ensembles of convolutional neural networks for lumen segmentation in ureteroscopy

2021 ◽  
Author(s):  
Jorge F. Lazo ◽  
Aldo Marzullo ◽  
Sara Moccia ◽  
Michele Catellani ◽  
Benoit Rosa ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
State Of The Art ◽  
Automatic Segmentation ◽  
Temporal Information ◽  
Invasive Technique ◽  
Dice Similarity Coefficient ◽  
Specular Reflections ◽  
Lumen Segmentation ◽  
Previous State

Abstract Purpose Ureteroscopy is an efficient endoscopic minimally invasive technique for the diagnosis and treatment of upper tract urothelial carcinoma. During ureteroscopy, the automatic segmentation of the hollow lumen is of primary importance, since it indicates the path that the endoscope should follow. In order to obtain an accurate segmentation of the hollow lumen, this paper presents an automatic method based on convolutional neural networks (CNNs). Methods The proposed method is based on an ensemble of 4 parallel CNNs to simultaneously process single and multi-frame information. Of these, two architectures are taken as core-models, namely U-Net based in residual blocks ($$m_1$$ m 1 ) and Mask-RCNN ($$m_2$$ m 2 ), which are fed with single still-frames I(t). The other two models ($$M_1$$ M 1 , $$M_2$$ M 2 ) are modifications of the former ones consisting on the addition of a stage which makes use of 3D convolutions to process temporal information. $$M_1$$ M 1 , $$M_2$$ M 2 are fed with triplets of frames ($$I(t-1)$$ I ( t - 1 ) , I(t), $$I(t+1)$$ I ( t + 1 ) ) to produce the segmentation for I(t). Results The proposed method was evaluated using a custom dataset of 11 videos (2673 frames) which were collected and manually annotated from 6 patients. We obtain a Dice similarity coefficient of 0.80, outperforming previous state-of-the-art methods. Conclusion The obtained results show that spatial-temporal information can be effectively exploited by the ensemble model to improve hollow lumen segmentation in ureteroscopic images. The method is effective also in the presence of poor visibility, occasional bleeding, or specular reflections.

scholarly journals Efficient Rank-Based Diffusion Process with Assured Convergence

2021 ◽  
Vol 7 (3) ◽  
pp. 49
Author(s):  
Daniel Carlos Guimarães Pedronette ◽  
Lucas Pascotti Valem ◽  
Longin Jan Latecki
Keyword(s):  
Diffusion Process ◽  
Learning Strategies ◽  
State Of The Art ◽  
Representation Learning ◽  
Theoretical Background ◽  
High Dimensional ◽  
Visual Features ◽  
Learning Approaches ◽  
Previous Decade ◽  
Asymptotic Complexity

Visual features and representation learning strategies experienced huge advances in the previous decade, mainly supported by deep learning approaches. However, retrieval tasks are still performed mainly based on traditional pairwise dissimilarity measures, while the learned representations lie on high dimensional manifolds. With the aim of going beyond pairwise analysis, post-processing methods have been proposed to replace pairwise measures by globally defined measures, capable of analyzing collections in terms of the underlying data manifold. The most representative approaches are diffusion and ranked-based methods. While the diffusion approaches can be computationally expensive, the rank-based methods lack theoretical background. In this paper, we propose an efficient Rank-based Diffusion Process which combines both approaches and avoids the drawbacks of each one. The obtained method is capable of efficiently approximating a diffusion process by exploiting rank-based information, while assuring its convergence. The algorithm exhibits very low asymptotic complexity and can be computed regionally, being suitable to outside of dataset queries. An experimental evaluation conducted for image retrieval and person re-ID tasks on diverse datasets demonstrates the effectiveness of the proposed approach with results comparable to the state-of-the-art.

scholarly journals Building Multi-Feature Fusion Refined Network for Building Extraction from High-Resolution Remote Sensing Images

2021 ◽  
Vol 13 (14) ◽  
pp. 2794
Author(s):  
Shuhao Ran ◽  
Xianjun Gao ◽  
Yuanwei Yang ◽  
Shaohua Li ◽  
Guangbin Zhang ◽  
...  
Keyword(s):  
Feature Fusion ◽  
Small Scale ◽  
Automatic Extraction ◽  
Learning Approaches ◽  
Building Extraction ◽  
Visual Interpretation ◽  
Learning Capacity ◽  
Convolutional Networks ◽  
Fully Convolutional Networks ◽  
Great Progress

Deep learning approaches have been widely used in building automatic extraction tasks and have made great progress in recent years. However, the missing detection and wrong detection causing by spectrum confusion is still a great challenge. The existing fully convolutional networks (FCNs) cannot effectively distinguish whether the feature differences are from one building or the building and its adjacent non-building objects. In order to overcome the limitations, a building multi-feature fusion refined network (BMFR-Net) was presented in this paper to extract buildings accurately and completely. BMFR-Net is based on an encoding and decoding structure, mainly consisting of two parts: the continuous atrous convolution pyramid (CACP) module and the multiscale output fusion constraint (MOFC) structure. The CACP module is positioned at the end of the contracting path and it effectively minimizes the loss of effective information in multiscale feature extraction and fusion by using parallel continuous small-scale atrous convolution. To improve the ability to aggregate semantic information from the context, the MOFC structure performs predictive output at each stage of the expanding path and integrates the results into the network. Furthermore, the multilevel joint weighted loss function effectively updates parameters well away from the output layer, enhancing the learning capacity of the network for low-level abstract features. The experimental results demonstrate that the proposed BMFR-Net outperforms the other five state-of-the-art approaches in both visual interpretation and quantitative evaluation.

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