Graphical User Interface

Radiological imaging to examine intracranial blood vessels is critical for preoperative planning and postoperative follow-up. Automated segmentation of cerebrovascular anatomy from Time-Of-Flight Magnetic Resonance Angiography (TOF-MRA) can provide radiologists with a more detailed and precise view of these vessels. This paper introduces a domain generalized artificial intelligence (AI) solution for volumetric monitoring of cerebrovascular structures from multi-center MRAs. Our approach utilizes a multi-task deep convolutional neural network (CNN) with a topology-aware loss function to learn voxel-wise segmentation of the cerebrovascular tree...

Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets...

MOTIVATION: Trajectories, which are sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory analysis requires the quantification and classification of curves, either by using statistical descriptors or physics-based features. To date, no extensive and user-friendly package for trajectory analysis has been readily available, despite its importance and potential application across various domains...

BACKGROUND: Drug-resistant tuberculosis (TB) is a major threat to global public health. Whole-genome sequencing (WGS) is a useful tool for species identification and drug resistance prediction, and many clinical laboratories are transitioning to WGS as a routine diagnostic tool. However, user-friendly and high-confidence automated bioinformatics tools are needed to rapidly identify M. tuberculosis complex (MTBC) and non-tuberculous mycobacteria (NTM), detect drug resistance, and further guide treatment options...

Deep brain stimulation (DBS) is a method of electrical neuromodulation used to treat a variety of neuropsychiatric conditions including essential tremor, Parkinson's disease, epilepsy, and obsessive-compulsive disorder. The procedure requires precise placement of electrodes such that the electrical contacts lie within or in close proximity to specific target nuclei and tracts located deep within the brain. DBS electrode trajectory planning has become increasingly dependent on direct targeting with the need for precise visualization of targets...

This paper describes a methodology for the assessment of training simulator-based computer-assisted intervention skills on an AR/VR-guided procedure making use of CT axial slice views for a neurosurgical procedure: external ventricular drain (EVD) placement. The task requires that trainees scroll through a stack of axial slices and form a mental representation of the anatomical structures in order to subsequently target the ventricles to insert an EVD. The process of observing the 2D CT image slices in order to build a mental representation of the 3D anatomical structures is the skill being taught, along with the cognitive control of the subsequent targeting, by planned motor actions, of the EVD tip to the ventricular system to drain cerebrospinal fluid (CSF)...

Behavioral studies contribute largely to a broader understanding of human brain mechanisms and the process of learning and memory. An established method to quantify motor learning is the analysis of thumb activity. In combination with brain stimulation, the effect of various treatments on neural plasticity and motor learning can be assessed. So far, the setups for thumb abduction measurements employed consist of bulky amplifiers and digital-to-analog devices to record the data. We developed a compact hardware setup to measure acceleration data which can be integrated into a wearable, including a sensor board and a microcontroller board which can be connected to a PC via USB...

BACKGROUND: Pseudonymization has become a best practice to securely manage the identities of patients and study participants in medical research projects and data sharing initiatives. This method offers the advantage of not requiring the direct identification of data to support various research processes while still allowing for advanced processing activities, such as data linkage. Often, pseudonymization and related functionalities are bundled in specific technical and organization units known as trusted third parties (TTPs)...

Magnetic resonance-guided focused ultrasound (MRgFUS) is one of the newest surgical treatments for essential tremor (ET). During this procedure, a lesion is created within the thalamus to mitigate tremor. Targeting is done using a combination of stereotaxy, MR tractography, and sublesional heating, with tremor assessed during the procedure to gauge therapeutic effectiveness. Currently, tremor assessments are done qualitatively, but this approach requires the tremor change to be above a subjective threshold and provides no objective record of surgical tremor progression...

Recent advancements in pre-trained language-image models have ushered in a new era of visual comprehension. Leveraging the power of these models, this paper tackles two issues within the realm of visual analytics: (1) the efficient exploration of large-scale image datasets and identification of data biases within them; (2) the evaluation of image captions and steering of their generation process. On the one hand, by visually examining the captions generated from language-image models for an image dataset, we gain deeper insights into the visual contents, unearthing data biases that may be entrenched within the dataset...

PURPOSE: This study aimed to evaluate the ability of Kidney Stone Calculator (KSC), a flexible ureteroscopy surgical planning software, to predict the lithotripsy duration with both holmium:YAG (Ho:YAG) and thulium fiber laser (TFL). METHODS: A multicenter prospective study was conducted from January 2020 to April 2023. Patients with kidney or ureteral stones confirmed at non-contrast computed tomography and treated by flexible ureteroscopy with laser lithotripsy were enrolled...

This paper illustrates a novel and cost-effective wireless monitoring system specifically developed for operational modal analysis of bridges. The system employs battery-powered wireless sensors based on MEMS accelerometers that dynamically balance power consumption with high processing features and a low-power, low-cost Wi-Fi module that ensures operation for at least five years. The paper focuses on the system's characteristics, stressing the challenges of wireless communication, such as data preprocessing, synchronization, system lifetime, and simple configurability, achieved through the integration of a user-friendly, web-based graphical user interface...

Generative models are used as an alternative data augmentation technique to alleviate the data scarcity problem faced in the medical imaging field. Diffusion models have gathered special attention due to their innovative generation approach, the high quality of the generated images, and their relatively less complex training process compared with Generative Adversarial Networks. Still, the implementation of such models in the medical domain remains at an early stage. In this work, we propose exploring the use of diffusion models for the generation of high-quality, full-field digital mammograms using state-of-the-art conditional diffusion pipelines...

Preplaced aggregate concrete (PAC) also known as two-stage concrete (TSC) is widely used in construction engineering for various applications. To produce PAC, a mixture of Portland cement, sand, and admixtures is injected into a mold subsequent to the deposition of coarse aggregate. This process complicates the prediction of compressive strength (CS), demanding thorough investigation. Consequently, the emphasis of this study is on enhancing the comprehension of PAC compressive strength using machine learning models...

Proteins are well known 'shapeshifters' which change conformation to function. In crystallography, multiple conformational states are often present within the crystal and the resulting electron-density map. Yet, explicitly incorporating alternative states into models to disentangle multi-conformer ensembles is challenging. We previously reported the tool FLEXR , which, within a few minutes, automatically separates conformational signal from noise and builds the corresponding, often missing, structural features into a multi-conformer model...

This work introduces X-Ray Calc ( XRC ), an open-source software package designed to simulate X-ray reflectivity (XRR) and address the inverse problem of reconstructing film structures on the basis of measured XRR curves. XRC features a user-friendly graphical interface that facilitates interactive simulation and reconstruction. The software employs a recursive approach based on the Fresnel equations to calculate XRR and incorporates specialized tools for modeling periodic multilayer structures. This article presents the latest version of the X-Ray Calc software ( XRC3 ), with notable improvements...

Data collection at X-ray free electron lasers has particular experimental challenges, such as continuous sample delivery or the use of novel ultrafast high-dynamic-range gain-switching X-ray detectors. This can result in a multitude of data artefacts, which can be detrimental to accurately determining structure-factor amplitudes for serial crystallography or single-particle imaging experiments. Here, a new data-classification tool is reported that offers a variety of machine-learning algorithms to sort data trained either on manual data sorting by the user or by profile fitting the intensity distribution on the detector based on the experiment...

In the pursuit of magnesium (Mg) alloys with targeted mechanical properties, a multi-objective Bayesian optimisation workflow is presented to enable optimal Mg-alloy design. A probabilistic Gaussian process regressor model was trained through an active learning loop, while balancing the exploration and exploitation trade-off via an acquisition function of the upper confidence bound. New candidate alloys suggested by the optimiser within each iteration were appended to the training data, and the performance of this sequential strategy was validated via a regret analysis...

Advanced manufacturing creates increasingly complex objects with material compositions that are often difficult to characterize by a single modality. Our collaborating domain scientists are going beyond traditional methods by employing both X-ray and neutron computed tomography to obtain complementary representations expected to better resolve material boundaries. However, the use of two modalities creates its own challenges for visualization, requiring either complex adjustments of bimodal transfer functions or the need for multiple views...

The U.S. Geological Survey (USGS) has published a guideline to improve the quality of digital photogrammetric reconstructions created with the widely used Agisoft Metashape Professional software. The suggested workflows aim at filtering out low-quality tie points from the tie point cloud to optimize the camera model. However, the optimization procedure relies on an iteratively performed trial-and-error approach. If manually performed, the time expenditure required from the operator can be significant and the optimization process can be affected by the degree of diligence that is applied...