Bibliographic dataset of literature for analysing global trends and progress of the machine learning paradigm in space weather research.

The field of space weather research has witnessed growing interest in the use of machine learning techniques. This could be attributed to the increasing accessibility of data, which has created a high demand for investigating scientific phenomena using data-driven methods. The dataset, which is based on bibliographic records from the Web of Science (WoS) and Scopus, was compiled over the last several decades and discusses multidisciplinary trends in this topic while revealing significant advances in current knowledge. It provides a comprehensive examination of trends in publication characteristics, with a focus on publications, document sources, authors, affiliations, and frequent word analysis as bibliometric indicators, all of which were analysed using the Biblioshiny application on the web. This dataset serves as the document profile metrics for emphasising the breadth and progress of current and previous studies, providing useful insights into hotspots for projection research subjects and influential entities that can be identified for future research.

Histopathology imagery dataset of Ph-negative myeloproliferative neoplasm.

Tumorous cancer has been a widely known and well-studied medical phenomenon; however, rare diseases like Myeloproliferative Neoplasm (MPN) have received less attention, leading to delayed diagnosis. Despite the availability of advanced technology in diagnostic tools that can boost the procedure, the morphological assessment of bone marrow trephine (BMT) images remains critical to confirm and differentiate MPN subtypes. This paper reports a histopathological imagery dataset that was created to focus on the most common MPN from the Philadelphia Chromosome (Ph)-negative type, namely Essential Thrombocythemia (ET), Polycythemia Vera (PV), and Primary Myelofibrosis (MF). The dataset consisted of 300 BMT images that can be used to enable computer vision applications, such as image segmentation, disease classification, and object recognition, in assisting the classification of the MPN disease. Ethical approval was obtained from the Ministry of Health, Malaysia and the bone marrow trephine images were captured using a digital microscope from the Olympus model (BX41 Dual head microscope) with x10, x20, and x40 lens types. The development of comprehensive tools deployed from this dataset can assist medical practitioners in diagnosing diseases, thus overcoming the current challenges.

Towards efficient Monte Carlo N-Particle simulation of a positron emission tomography (PET) via source volume definition.

Monte Carlo N-Particle (MCNP) simulation has been extensively proven in nuclear medicine imaging systems, most notably in designing and optimizing new medical imaging tools. It enables more complicated geometries and the simulation of particles passing through and interacting with materials. However, a relatively long simulation time is a drawback of Monte Carlo simulation, mainly when complex geometry exists. The current study presents an alternative variance reduction technique for a modeled positron emission tomography (PET) camera by reducing the height of the source volume definition while maintaining the geometry of the simulated model. The National Electrical Manufacturers Association (NEMA) of the International Electrotechnical Commission (IEC) PET's phantom was used with a 1 cm diameter and 7 cm height of line source placed in the middle. The first geometry was fully filled the line source with 0.50 mCi radioactivity. In contrast, the second geometry decreased the source definition to 2.4 cm in height, covering 1 cm above and below the sub-block detector level. The source volume definition approach led to a 71% reduction in the total photons to be simulated. Results showed that the proposed variance reduction strategy could produce spatial resolution as precise as fully filled geometry and sped up the simulation time by approximately 65%. Hence, this strategy can be utilized for further PET optimizing simulation studies.

Brain MRI dataset of multiple sclerosis with consensus manual lesion segmentation and patient meta information.

Magnetic resonance imaging (MRI) provides a significant key to diagnose and monitor the progression of multiple sclerosis (MS) disease. Manual MS-lesion segmentation, expanded disability status scale (EDSS) and patient's meta information can provide a gold standard for research in terms of automated MS-lesion quantification, automated EDSS prediction and identification of the correlation between MS-lesion and patient disability. In this dataset, we provide a novel multi-sequence MRI dataset of 60 MS patients with consensus manual lesion segmentation, EDSS, general patient information and clinical information. On this dataset, three radiologists and neurologist experts segmented and validated the manual MS-lesion segmentation for three MRI sequences T1-weighted, T2-weighted and fluid-attenuated inversion recovery (FLAIR). The dataset can be used to study the relationship between MS-lesion, EDSS and patient clinical information. Furthermore, it also can be used for the development of automated MS-lesion segmentation, patient disability prediction using MRI and correlation analysis between patient disability and MRI brain abnormalities include MS lesion location, size, number and type.

Mechanical and Imaging Properties of a Clinical-Grade Kidney Phantom Based on Polydimethylsiloxane and Elastomer.

Medical imaging phantoms are considered critical in mimicking the properties of human tissue for calibration, training, surgical planning, and simulation purposes. Hence, the stability and accuracy of the imaging phantom play a significant role in diagnostic imaging. This study aimed to evaluate the influence of hydrogen silicone (HS) and water (H2O) on the compression strength, radiation attenuation properties, and computed tomography (CT) number of the blended Polydimethylsiloxane (PDMS) samples, and to verify the best material to simulate kidney tissue. Four samples with different compositions were studied, including samples S1, S2, S3, and S4, which consisted of PDMS 100%, HS/PDMS 20:80, H2O/PDMS 20:80, and HS/H2O/PDMS 20:40:40, respectively. The stability of the samples was assessed using compression testing, and the attenuation properties of sample S2 were evaluated. The effective atomic number of S2 showed a similar pattern to the human kidney tissue at 1.50 × 10-1 to 1 MeV. With the use of a 120 kVp X-ray beam, the CT number quantified for S2, as well measured 40 HU, and had the highest contrast-to-noise ratio (CNR) value. Therefore, the S2 sample formulation exhibited the potential to mimic the human kidney, as it has a similar dynamic and is higher in terms of stability as a medical phantom.

Correlation between 18F-FDG dosage and SNR on various BMI patient groups tested in NEMA IEC PET phantom.

The present study was conducted to determine quantitatively the correlation between injected radiotracer and signal-to-noise ratio (SNR) based on differences in physiques and stages of cancer. Eight different activities were evaluated with modelled National Electrical Manufacturers Association (NEMA) of the International Electrotechnical Commission (IEC) PET's phantom with nine different tumour-to-background ratio (TBR). The findings suggest that the optimal value of dosage is required for all categories of patients in the early stages of cancer diagnosis.

Supervised retinal vessel segmentation from color fundus images based on matched filtering and AdaBoost classifier.

The structure and appearance of the blood vessel network in retinal fundus images is an essential part of diagnosing various problems associated with the eyes, such as diabetes and hypertension. In this paper, an automatic retinal vessel segmentation method utilizing matched filter techniques coupled with an AdaBoost classifier is proposed. The fundus image is enhanced using morphological operations, the contrast is increased using contrast limited adaptive histogram equalization (CLAHE) method and the inhomogeneity is corrected using Retinex approach. Then, the blood vessels are enhanced using a combination of B-COSFIRE and Frangi matched filters. From this preprocessed image, different statistical features are computed on a pixel-wise basis and used in an AdaBoost classifier to extract the blood vessel network inside the image. Finally, the segmented images are postprocessed to remove the misclassified pixels and regions. The proposed method was validated using publicly accessible Digital Retinal Images for Vessel Extraction (DRIVE), Structured Analysis of the Retina (STARE) and Child Heart and Health Study in England (CHASE_DB1) datasets commonly used for determining the accuracy of retinal vessel segmentation methods. The accuracy of the proposed segmentation method was comparable to other state of the art methods while being very close to the manual segmentation provided by the second human observer with an average accuracy of 0.972, 0.951 and 0.948 in DRIVE, STARE and CHASE_DB1 datasets, respectively.

Computer-Assisted Diagnosis System for Breast Cancer in Computed Tomography Laser Mammography (CTLM).

Computed tomography laser mammography (Eid et al. Egyp J Radiol Nucl Med, 37(1): p. 633-643, 1) is a non-invasive imaging modality for breast cancer diagnosis, which is time-consuming and challenging for the radiologist to interpret the images. Some issues have increased the missed diagnosis of radiologists in visual manner assessment in CTLM images, such as technical reasons which are related to imaging quality and human error due to the structural complexity in appearance. The purpose of this study is to develop a computer-aided diagnosis framework to enhance the performance of radiologist in the interpretation of CTLM images. The proposed CAD system contains three main stages including segmentation of volume of interest (VOI), feature extraction and classification. A 3D Fuzzy segmentation technique has been implemented to extract the VOI. The shape and texture of angiogenesis in CTLM images are significant characteristics to differentiate malignancy or benign lesions. The 3D compactness features and 3D Grey Level Co-occurrence matrix (GLCM) have been extracted from VOIs. Multilayer perceptron neural network (MLPNN) pattern recognition has developed for classification of the normal and abnormal lesion in CTLM images. The performance of the proposed CAD system has been measured with different metrics including accuracy, sensitivity, and specificity and area under receiver operative characteristics (AROC), which are 95.2, 92.4, 98.1, and 0.98%, respectively.

Foundation and methodologies in computer-aided diagnosis systems for breast cancer detection.

Breast cancer is the most prevalent cancer that affects women all over the world. Early detection and treatment of breast cancer could decline the mortality rate. Some issues such as technical reasons, which related to imaging quality and human error, increase misdiagnosis of breast cancer by radiologists. Computer-aided detection systems (CADs) are developed to overcome these restrictions and have been studied in many imaging modalities for breast cancer detection in recent years. The CAD systems improve radiologists' performance in finding and discriminating between the normal and abnormal tissues. These procedures are performed only as a double reader but the absolute decisions are still made by the radiologist. In this study, the recent CAD systems for breast cancer detection on different modalities such as mammography, ultrasound, MRI, and biopsy histopathological images are introduced. The foundation of CAD systems generally consist of four stages: Pre-processing, Segmentation, Feature extraction, and Classification. The approaches which applied to design different stages of CAD system are summarised. Advantages and disadvantages of different segmentation, feature extraction and classification techniques are listed. In addition, the impact of imbalanced datasets in classification outcomes and appropriate methods to solve these issues are discussed. As well as, performance evaluation metrics for various stages of breast cancer detection CAD systems are reviewed.

Automatic liver tumor segmentation on computed tomography for patient treatment planning and monitoring.

Segmentation of liver tumors from Computed Tomography (CT) and tumor burden analysis play an important role in the choice of therapeutic strategies for liver diseases and treatment monitoring. In this paper, a new segmentation method for liver tumors from contrast-enhanced CT imaging is proposed. As manual segmentation of tumors for liver treatment planning is both labor intensive and time-consuming, a highly accurate automatic tumor segmentation is desired. The proposed framework is fully automatic requiring no user interaction. The proposed segmentation evaluated on real-world clinical data from patients is based on a hybrid method integrating cuckoo optimization and fuzzy c-means algorithm with random walkers algorithm. The accuracy of the proposed method was validated using a clinical liver dataset containing one of the highest numbers of tumors utilized for liver tumor segmentation containing 127 tumors in total with further validation of the results by a consultant radiologist. The proposed method was able to achieve one of the highest accuracies reported in the literature for liver tumor segmentation compared to other segmentation methods with a mean overlap error of 22.78 % and dice similarity coefficient of 0.75 in 3Dircadb dataset and a mean overlap error of 15.61 % and dice similarity coefficient of 0.81 in MIDAS dataset. The proposed method was able to outperform most other tumor segmentation methods reported in the literature while representing an overlap error improvement of 6 % compared to one of the best performing automatic methods in the literature. The proposed framework was able to provide consistently accurate results considering the number of tumors and the variations in tumor contrast enhancements and tumor appearances while the tumor burden was estimated with a mean error of 0.84 % in 3Dircadb dataset.

Automatic liver segmentation on Computed Tomography using random walkers for treatment planning.

Segmentation of the liver from Computed Tomography (CT) volumes plays an important role during the choice of treatment strategies for liver diseases. Despite lots of attention, liver segmentation remains a challenging task due to the lack of visible edges on most boundaries of the liver coupled with high variability of both intensity patterns and anatomical appearances with all these difficulties becoming more prominent in pathological livers. To achieve a more accurate segmentation, a random walker based framework is proposed that can segment contrast-enhanced livers CT images with great accuracy and speed. Based on the location of the right lung lobe, the liver dome is automatically detected thus eliminating the need for manual initialization. The computational requirements are further minimized utilizing rib-caged area segmentation, the liver is then extracted by utilizing random walker method. The proposed method was able to achieve one of the highest accuracies reported in the literature against a mixed healthy and pathological liver dataset compared to other segmentation methods with an overlap error of 4.47 % and dice similarity coefficient of 0.94 while it showed exceptional accuracy on segmenting the pathological livers with an overlap error of 5.95 % and dice similarity coefficient of 0.91.

Computer-aided detection/diagnosis of breast cancer in mammography and ultrasound: a review.

Breast cancer is the most common form of cancer among women worldwide. Early detection of breast cancer can increase treatment options and patients' survivability. Mammography is the gold standard for breast imaging and cancer detection. However, due to some limitations of this modality such as low sensitivity especially in dense breasts, other modalities like ultrasound and magnetic resonance imaging are often suggested to achieve additional information. Recently, computer-aided detection or diagnosis (CAD) systems have been developed to help radiologists in order to increase diagnosis accuracy. Generally, a CAD system consists of four stages: (a) preprocessing, (b) segmentation of regions of interest, (c) feature extraction and selection, and finally (d) classification. This paper presents the approaches which are applied to develop CAD systems on mammography and ultrasound images. The performance evaluation metrics of CAD systems are also reviewed.

Discriminant analysis of intermediate brain atrophy rates in longitudinal diagnosis of Alzheimer's disease.

Diagnosing Alzheimer's disease through MRI neuroimaging biomarkers has been used as a complementary marker for traditional clinical markers to improve diagnostic accuracy and also help in developing new pharmacotherapeutic trials. It has been revealed that longitudinal analysis of the whole brain atrophy has the power of discriminating Alzheimer's disease and elderly normal controls. In this work, effect of involving intermediate atrophy rates and impact of using uncorrelated principal components of these features instead of original ones on discriminating normal controls and Alzheimer's disease subjects, is inspected. In fact, linear discriminative analysis of atrophy rates is used to classify subjects into Alzheimer's disease and controls. Leave-one-out cross-validation has been adopted to evaluate the generalization rate of the classifier along with its memorization. Results show that incorporating uncorrelated version of intermediate features leads to the same memorization performance as the original ones but higher generalization rate. As a conclusion, it is revealed that in a longitudinal study, using intermediate MRI scans and transferring them to an uncorrelated feature space can improve diagnostic accuracy.

Brain magnetic resonance image segmentation using novel improvement for expectation maximizing.

OBJECTIVE: To improve the quality of expectation maximizing (EM) for brain image segmentation, and to evaluate the accuracy of segmentation results. METHODS: This brain segmentation study was conducted in Universiti Putra Malaysia in Serdong, Malaysia between February and November 2010 on simulated and real images using novel improvement for EM. The EM-1 (proposed algorithm) was compared with neighborhood based extensions for fuzzy C-mean (FCM). The EM-1 was also applied to all 20 normal real MRI volumes and compared with reported results from the Internet Brain Segmentation Repository. RESULTS: In simulated images, the EM-1 outperforms neighborhood based extensions for FCM. The average similarity index value of the proposed algorithm for all 20 normal images is 0.802. The EM-1 produces the average Jaccard indices ρ higher than other algorithms and near to manual results. The average similarity indices ρ for EM-1 and FCM extensions (FCM with spatial information [FCM-S], Fast Generalized FCM [FGFCM]) for all 20 normal images are: EM-1=0.802, FCM-S=0.7517, enhanced FCM=0.7581, and FGFCM=0.7597. CONCLUSION: Experimental results show that the proposed algorithm performs better than other studied algorithms on various noise levels in terms of similarity index, ρ.