Curvilinear structure enhancement by multiscale top-hat tensor in 2D/3D images

A wide range of biomedical applications require enhancement, detection, quantification and modelling of curvilinear structures in 2D and 3D images. Curvilinear structure enhancement is a crucial step for further analysis, but many of the enhancement approaches still suffer from contrast variations and noise. This can be addressed using a multiscale approach that produces a better quality enhancement for low contrast and noisy images compared with a single-scale approach in a wide range of biomedical images. Here, we propose the Multiscale Top-Hat Tensor (MTHT) approach, which combines multiscale morphological filtering with a local tensor representation of curvilinear structures in 2D and 3D images. The proposed approach is validated on synthetic and real data, and is also compared to the state-of-the-art approaches. Our results show that the proposed approach achieves high-quality curvilinear structure enhancement in synthetic examples and in a wide range of 2D and 3D images

A Deep Learning-Based Mobile Application for Monkeypox Detection

The recent outbreak of monkeypox has raised significant concerns in the field of public health, primarily because it has quickly spread to over 40 countries outside of Africa. Detecting monkeypox in its early stages can be quite challenging because its symptoms can resemble those of chickenpox and measles. However, there is hope that potential use of computer-assisted tools may be used to identify monkeypox cases rapidly and efficiently. A promising approach involves the use of technology, specifically deep learning methods, which have proven effective in automatically detecting skin lesions when sufficient training examples are available. To improve monkeypox diagnosis through mobile applications, we have employed a particular neural network called MobileNetV2, which falls under the category of Fully Connected Convolutional Neural Networks (FCCNN). It enables us to identify suspected monkeypox cases accurately compared to classical machine learning approaches. The proposed approach was evaluated using the recall, precision, F score, and accuracy. The experimental results show that our architecture achieves an accuracy of 0.99%, a Recall of 1.0%, an F-score of 0.98%, and a Precision of 0.95%. We believe that such experimental evaluation will contribute to the medical domain and many use cases

Detection of Cavities from Dental Panoramic X-ray Images Using Nested U-Net Models

Dental caries is one of the most prevalent and chronic diseases worldwide. Dental X-ray radiography is considered a standard tool and a valuable resource for radiologists to identify dental diseases and problems that are hard to recognize by visual inspection alone. However, the available dental panoramic image datasets are extremely limited and only include a small number of images. U-Net is one of the deep learning networks that are showing promising performance in medical image segmentation. In this work, different U-Net models are applied to dental panoramic X-ray images to detect caries lesions. The Detection, Numbering, and Segmentation Panoramic Images (DNS) dataset, which includes 1500 panoramic X-ray images obtained from Ivisionlab, is used in this experiment. The major objective of this work is to extend the DNS Panoramic Images dataset by detecting the cavities in the panoramic image and generating the binary ground truth of this image to use as the ground truth for the evaluation of models. These ground truths are revised by experts to ensure their robustness and correctness. Firstly, we expand the Panoramic Images (DNS) dataset by detecting the cavities in the panoramic images and generating the images’ binary ground truth. Secondly, we apply U-Net, U-Net++ and U-Net3+ to the expanded DNS dataset to learn the hierarchical features and to enhance the cavity boundary. The results show that U-Net3+ outperforms the other versions of U-Net with 95% in testing accuracy

The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images

Quantification and modelling of curvilinear structures in 2D and 3D images is a common challenge in a wide range of biomedical applications. Image enhancement is a crucial pre-processing step for curvilinear structure quantification. Many of the existing state-of-the-art enhancement approaches still suffer from contrast variations and noise. In this paper, we propose to address such problems via the use of a multiscale image processing approach, called Multiscale Top-Hat Tensor (MTHT). MTHT produces a better quality enhancement of curvilinear structures in low contrast and noisy images compared with other approaches in a range of 2D and 3D biomedical images. The proposed approach combines multiscale morphological filtering with a local tensor representation of curvilinear structure. The MTHT approach is validated on 2D and 3D synthetic and real images, and is also compared to the state-of-the-art curvilinear structure enhancement approaches. The obtained results demonstrate that the proposed approach provides high-quality curvilinear structure enhancement, allowing high accuracy segmentation and quantification in a wide range of 2D and 3D image datasets

The relationship between curvilinear structure enhancement and ridge detection approaches

Curvilinear structure detection and quantification is a large research area with many imaging applications in fields such as biology, medicine, and engineering. Curvilinear enhancement is often used as a pre-processing stage for ridge detection, but there has been little investigation into the relationship between enhancement and ridge detection. In this paper, we thoroughly evaluate the pair-wise combinations of different curvilinear enhancement and ridge detection methods across two highly varied datasets, as well as samples of three other datasets. In particular, we present the approaches complementing one another and the gained insights, which will aid researchers in designing generic ridge detectors

The multiscale top-hat tensor enables specific enhancement of curvilinear structures in 2D and 3D images

Quantification and modelling of curvilinear structures in 2D and 3D images is a common challenge in a wide range of biomedical applications. Image enhancement is a crucial pre-processing step for curvilinear structure quantification. Many of the existing state-of-the-art enhancement approaches still suffer from contrast variations and noise. In this paper, we propose to address such problems via the use of a multiscale image processing approach, called Multiscale Top-Hat Tensor (MTHT). MTHT produces a better quality enhancement of curvilinear structures in low contrast and noisy images compared with other approaches in a range of 2D and 3D biomedical images. The proposed approach combines multiscale morphological filtering with a local tensor representation of curvilinear structure. The MTHT approach is validated on 2D and 3D synthetic and real images, and is also compared to the state-of-the-art curvilinear structure enhancement approaches. The obtained results demonstrate that the proposed approach provides high-quality curvilinear structure enhancement, allowing high accuracy segmentation and quantification in a wide range of 2D and 3D image datasets

Sequential graph-based extraction of curvilinear structures

In this paper, a new approach is proposed to extract an ordered sequence of curvilinear structures in images, capturing the largest and most influential paths first and then progressively extracting smaller paths until a prespecified size is reached. The results are demonstrated both quantitatively and qualitatively using synthetic and real-world images. The method is shown to outperform comparator methods for certain cases of noise, object class, and scale, while remaining fundamentally easier to use due to its low parameter requirement

Improvement of protein tertiary and quaternary structure predictions using the ReFOLD refinement method and the AlphaFold2 recycling process

Motivation The accuracy gap between predicted and experimental structures has been significantly reduced following the development of AlphaFold2 (AF2). However, for many targets, AF2 models still have room for improvement. In previous CASP experiments, highly computationally intensive MD simulation-based methods have been widely used to improve the accuracy of single 3D models. Here, our ReFOLD pipeline was adapted to refine AF2 predictions while maintaining high model accuracy at a modest computational cost. Furthermore, the AF2 recycling process was utilised to improve 3D models by using them as custom template inputs for tertiary and quaternary structure predictions. Results According to the Molprobity score, 94% of the generated 3D models by ReFOLD were improved. AF2 recycling showed an improvement rate of 87.5% (using MSAs) and 81.25% (using single sequences) for monomeric AF2 models and 100% (MSA) and 97.8% (single sequence) for monomeric non-AF2 models, as measured by the average change in lDDT. By the same measure, the recycling of multimeric models showed an improvement rate of as much as 80% for AF2-Multimer (AF2M) models and 94% for non-AF2M model

Estimation of model accuracy in CASP15 using the ModFOLDdock server

In CASP15 there was a greater emphasis on multimeric modelling than in previous experiments, with assembly structures nearly doubling in number (41 up from 22) since the previous round. CASP15 also included a new estimation of model accuracy (EMA) category in recognition of the importance of objective quality assessment for quaternary structure models. ModFOLDdock is a multimeric model quality assessment server developed by the McGuffin group at the University of Reading, which brings together a range of single-model, clustering and deep learning methods to form a consensus of approaches. For CASP15 three variants of ModFOLDdock were developed to optimise for the different facets of the quality estimation problem. The standard ModFOLDdock variant produced predicted scores optimised for positive linear correlations with the observed scores. The ModFOLDdockR variant produced predicted scores optimised for ranking, i.e., the top-ranked models have highest accuracy. In addition, the ModFOLDdockS variant used a quasi-single model approach to score each model on an individual basis. The scores from all three variants achieved strongly positive Pearson correlation coefficients with the CASP observed scores (oligo-lDDT) in excess of 0.70, which were maintained across both homomeric and heteromeric model populations. In addition, at least one of the ModFOLDdock variants was consistently ranked in the top two methods across all three EMA categories. Specifically, for overall global fold prediction accuracy, ModFOLDdock placed second and ModFOLDdockR placed third; for overall interface quality prediction accuracy ModFOLDdockR, ModFOLDdock and ModFOLDdockS were placed above all other predictor methods, and ModFOLDdockR and ModFOLDdockS were placed second and third respectively for individual residue confidence scores. The ModFOLDdock server is available at: https://www.reading.ac.uk/bioinf/ModFOLDdock/. ModFOLDdock is also available as part of the MultiFOLD docker package: https://hub.docker.com/r/mcguffin/multifol

Arabic Speech Recognition: Advancement and Challenges

Speech recognition is a captivating process that revolutionizes human-computer interactions, allowing us to interact and control machines through spoken commands. The foundation of speech recognition lies in understanding a given language’s linguistic and textual characteristics. Although automatic speech recognition (ASR) systems flawlessly convert speech into text for various international languages, their implementation for Arabic remains inadequate. In this research, we diligently explore the current state of Arabic ASR systems and unveil the challenges encountered during their development. We categorize these challenges into two groups: those specific to the Arabic language and those more general. We propose strategies to overcome these obstacles and emphasize the need for ASR architectures tailored to the Arabic language’s unique grammatical and phonetic structure. In addition, we provide a comprehensive and explicit description of various feature extraction methods, language models, and acoustic models utilized in the Arabic ASR system