Neuro-TransUNet: Segmentation of stroke lesion in MRI using transformers

Accurate segmentation of the stroke lesions using magnetic resonance imaging (MRI) is associated with difficulties due to the complicated anatomy of the brain and the different properties of the lesions. This study introduces the Neuro-TransUNet framework, which synergizes the U-Net's spatial feature extraction with SwinUNETR's global contextual processing ability, further enhanced by advanced feature fusion and segmentation synthesis techniques. The comprehensive data pre-processing pipeline improves the framework's efficiency, which involves resampling, bias correction, and data standardization, enhancing data quality and consistency. Ablation studies confirm the significant impact of the advanced integration of U-Net with SwinUNETR and data pre-processing pipelines on performance and demonstrate the model's effectiveness. The proposed Neuro-TransUNet model, trained with the ATLAS v2.0 \emph{training} dataset, outperforms existing deep learning algorithms and establishes a new benchmark in stroke lesion segmentation.

Transformers-based architectures for stroke segmentation: A review

Stroke remains a significant global health concern, necessitating precise and efficient diagnostic tools for timely intervention and improved patient outcomes. The emergence of deep learning methodologies has transformed the landscape of medical image analysis. Recently, Transformers, initially designed for natural language processing, have exhibited remarkable capabilities in various computer vision applications, including medical image analysis. This comprehensive review aims to provide an in-depth exploration of the cutting-edge Transformer-based architectures applied in the context of stroke segmentation. It commences with an exploration of stroke pathology, imaging modalities, and the challenges associated with accurate diagnosis and segmentation. Subsequently, the review delves into the fundamental ideas of Transformers, offering detailed insights into their architectural intricacies and the underlying mechanisms that empower them to effectively capture complex spatial information within medical images. The existing literature is systematically categorized and analyzed, discussing various approaches that leverage Transformers for stroke segmentation. A critical assessment is provided, highlighting the strengths and limitations of these methods, including considerations of performance and computational efficiency. Additionally, this review explores potential avenues for future research and development

Brain Stroke Segmentation Using Deep Learning Models: A Comparative Study

Stroke segmentation plays a crucial role in the diagnosis and treatment of stroke patients by providing spatial information about affected brain regions and the extent of damage. Segmenting stroke lesions accurately is a challenging task, given that conventional manual techniques are time consuming and prone to errors. Recently, advanced deep models have been introduced for general medical image segmentation, demonstrating promising results that surpass many state of the art networks when evaluated on specific datasets. With the advent of the vision Transformers, several models have been introduced based on them, while others have aimed to design better modules based on traditional convolutional layers to extract long-range dependencies like Transformers. The question of whether such high-level designs are necessary for all segmentation cases to achieve the best results remains unanswered. In this study, we selected four types of deep models that were recently proposed and evaluated their performance for stroke segmentation: a pure Transformer-based architecture (DAE-Former), two advanced CNN-based models (LKA and DLKA) with attention mechanisms in their design, an advanced hybrid model that incorporates CNNs with Transformers (FCT), and the well-known self-adaptive nnUNet framework with its configuration based on given data. We examined their performance on two publicly available datasets, and found that the nnUNet achieved the best results with the simplest design among all. Revealing the robustness issue of Transformers to such variabilities serves as a potential reason for their weaker performance. Furthermore, nnUNet's success underscores the significant impact of preprocessing and postprocessing techniques in enhancing segmentation results, surpassing the focus solely on architectural designs

SHARM: Segmented Head Anatomical Reference Models

Reliable segmentation of anatomical tissues of human head is a major step in several clinical applications such as brain mapping, surgery planning and associated computational simulation studies. Segmentation is based on identifying different anatomical structures through labeling different tissues through medical imaging modalities. The segmentation of brain structures is commonly feasible with several remarkable contributions mainly for medical perspective; however, non-brain tissues are of less interest due to anatomical complexity and difficulties to be observed using standard medical imaging protocols. The lack of whole head segmentation methods and unavailability of large human head segmented datasets limiting the variability studies, especially in the computational evaluation of electrical brain stimulation (neuromodulation), human protection from electromagnetic field, and electroencephalography where non-brain tissues are of great importance. To fill this gap, this study provides an open-access Segmented Head Anatomical Reference Models (SHARM) that consists of 196 subjects. These models are segmented into 15 different tissues; skin, fat, muscle, skull cancellous bone, skull cortical bone, brain white matter, brain gray matter, cerebellum white matter, cerebellum gray matter, cerebrospinal fluid, dura, vitreous humor, lens, mucous tissue and blood vessels. The segmented head models are generated using open-access IXI MRI dataset through convolutional neural network structure named ForkNet+. Results indicate a high consistency in statistical characteristics of different tissue distribution in age scale with real measurements. SHARM is expected to be a useful benchmark not only for electromagnetic dosimetry studies but also for different human head segmentation applications.

COVID-19 Status Forecasting Using New Viral variants and Vaccination Effectiveness Models

Background: Recently, a high number of daily positive COVID-19 cases have been reported in regions with relatively high vaccination rates; hence, booster vaccination has become necessary. In addition, infections caused by the different variants and correlated factors have not been discussed in depth. With large variabilities and different co-factors, it is difficult to use conventional mathematical models to forecast the incidence of COVID-19. Methods: Machine learning based on long short-term memory was applied to forecasting the time series of new daily positive cases (DPC), serious cases, hospitalized cases, and deaths. Data acquired from regions with high rates of vaccination, such as Israel, were blended with the current data of other regions in Japan to factor in the potential effects of vaccination. The protection provided by symptomatic infection was also considered in terms of the population effectiveness of vaccination as well as the waning protection and ratio and infectivity of viral variants. To represent changes in public behavior, public mobility and interactions through social media were also included in the analysis. Findings: Comparing the observed and estimated new DPC in Tel Aviv, Israel, the parameters characterizing vaccination effectiveness and the waning protection from infection were well estimated; the vaccination effectiveness of the second dose after 5 months and the third dose after two weeks from infection by the delta variant were 0.24 and 0.95, respectively. Using the extracted parameters regarding vaccination effectiveness, new cases in three prefectures of Japan were replicated.

Knowledge discovery from emergency ambulance dispatch during COVID-19: A case study of Nagoya City, Japan

Accurate forecasting of medical service requirements is an important big data problem that is crucial for resource management in critical times such as natural disasters and pandemics. With the global spread of coronavirus disease 2019 (COVID-19), several concerns have been raised regarding the ability of medical systems to handle sudden changes in the daily routines of healthcare providers. One significant problem is the management of ambulance dispatch and control during a pandemic. To help address this problem, we first analyze ambulance dispatch data records from April 2014 to August 2020 for Nagoya City, Japan. Significant changes were observed in the data during the pandemic, including the state of emergency (SoE) declared across Japan. In this study, we propose a deep learning framework based on recurrent neural networks to estimate the number of emergency ambulance dispatches (EADs) during a SoE. The fusion of data includes environmental factors, the localization data of mobile phone users, and the past history of EADs, thereby providing a general framework for knowledge discovery and better resource management. The results indicate that the proposed blend of training data can be used efficiently in a real-world estimation of EAD requirements during periods of high uncertainties such as pandemics.

Influence of segmentation accuracy in structural MR head scans on electric field computation for TMS and tES

In several diagnosis and therapy procedures based on electrostimulation effect, the internal physical quantity related to the stimulation is the induced electric field. To estimate the induced electric field in an individual human model, the segmentation of anatomical imaging, such as (magnetic resonance image (MRI) scans, of the corresponding body parts into tissues is required. Then, electrical properties associated with different annotated tissues are assigned to the digital model to generate a volume conductor. An open question is how segmentation accuracy of different tissues would influence the distribution of the induced electric field. In this study, we applied parametric segmentation of different tissues to exploit the segmentation of available MRI to generate different quality of head models using deep learning neural network architecture, named ForkNet. Then, the induced electric field are compared to assess the effect of model segmentation variations. Computational results indicate that the influence of segmentation error is tissue-dependent. In brain, sensitivity to segmentation accuracy is relatively high in cerebrospinal fluid (CSF), moderate in gray matter (GM) and low in white matter for transcranial magnetic stimulation (TMS) and transcranial electrical stimulation (tES). A CSF segmentation accuracy reduction of 10% in terms of Dice coefficient (DC) lead to decrease up to 4% in normalized induced electric field in both applications. However, a GM segmentation accuracy reduction of 5.6% DC leads to increase of normalized induced electric field up to 6%. Opposite trend of electric field variation was found between CSF and GM for both TMS and tES. The finding obtained here would be useful to quantify potential uncertainty of computational results.

Model-based approach for analyzing prevalence of nuclear cataracts in elderly residents

Recent epidemiological studies have hypothesized that the prevalence of cortical cataracts is closely related to ultraviolet radiation. However, the prevalence of nuclear cataracts is higher in elderly people in tropical areas than in temperate areas. The dominant factors inducing nuclear cataracts have been widely debated. In this study, the temperature increase in the lens due to exposure to ambient conditions was computationally quantified in subjects of 50-60 years of age in tropical and temperate areas, accounting for differences in thermoregulation. A thermoregulatory response model was extended to consider elderly people in tropical areas. The time course of lens temperature for different weather conditions in five cities in Asia was computed. The temperature was higher around the mid and posterior part of the lens, which coincides with the position of the nuclear cataract. The duration of higher temperatures in the lens varied, although the daily maximum temperatures were comparable. A strong correlation (adjusted R2 > 0.85) was observed between the prevalence of nuclear cataract and the computed cumulative thermal dose in the lens. We propose the use of a cumulative thermal dose to assess the prevalence of nuclear cataracts. Cumulative wet-bulb globe temperature, a new metric computed from weather data, would be useful for practical assessment in different cities.

Deep learning approach for breast cancer diagnosis

Breast cancer is one of the leading fatal disease worldwide with high risk control if early discovered. Conventional method for breast screening is x-ray mammography, which is known to be challenging for early detection of cancer lesions. The dense breast structure produced due to the compression process during imaging lead to difficulties to recognize small size abnormalities. Also, inter- and intra-variations of breast tissues lead to significant difficulties to achieve high diagnosis accuracy using hand-crafted features. Deep learning is an emerging machine learning technology that requires a relatively high computation power. Yet, it proved to be very effective in several difficult tasks that requires decision making at the level of human intelligence. In this paper, we develop a new network architecture inspired by the U-net structure that can be used for effective and early detection of breast cancer. Results indicate a high rate of sensitivity and specificity that indicate potential usefulness of the proposed approach in clinical use.

Neural networks approach for mammography diagnosis using wavelets features

A supervised diagnosis system for digital mammogram is developed. The diagnosis processes are done by transforming the data of the images into a feature vector using wavelets multilevel decomposition. This vector is used as the feature tailored toward separating different mammogram classes. The suggested model consists of artificial neural networks designed for classifying mammograms according to tumor type and risk level. Results are enhanced from our previous study by extracting feature vectors using multilevel decompositions instead of one level of decomposition. Radiologist-labeled images were used to evaluate the diagnosis system. Results are very promising and show possible guide for future work.