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Flow cytometry (FCM) is an analytic technique that is capable of detecting and recording the emission of fluorescence and light scattering of cells or particles (that are collectively called "events") in a population. A typical FCM…
CHEMSMART (Chemistry Simulation and Modeling Automation Toolkit) is an open-source, Python-based framework designed to streamline quantum chemistry workflows for homogeneous catalysis and molecular modeling. By integrating job preparation,…
Single molecule F\"orster resonance energy transfer (smFRET) is a powerful experimental technique for studying the properties of individual biological molecules in solution. However, as adoption of smFRET techniques becomes more widespread,…
In radiation therapy (RT), the reliance on pre-treatment computed tomography (CT) images encounter challenges due to anatomical changes, necessitating adaptive planning. Daily cone-beam CT (CBCT) imaging, pivotal for therapy adjustment,…
Proton computed tomography (pCT) is a novel medical imaging modality for mapping the distribution of proton relative stopping power (RSP) in medical objects of interest. Compared to conventional X-ray computed tomography, where range…
Myocardial perfusion cardiovascular magnetic resonance (pCMR) using first-pass contrast-enhanced imaging could play an important role in the detection of epicardial and microvascular coronary artery disease. Recently, the emergence of…
Simultaneously modeling source code and natural language has many exciting applications in automated software development and understanding. Pursuant to achieving such technology, we introduce PyMT5, the Python method text-to-text transfer…
Nowadays, data-intensive applications are gaining popularity and, together with this trend, processing-in-memory (PIM)-based systems are being given more attention and have become more relevant. This paper describes an analytical modeling…
Coronary artery disease (CAD) remains the world's leading cause of mortality and the disease burden is continually expanding as the population ages. Recently, the MR-INFORM randomised trial has demonstrated that the management of patients…
Positron emission tomography (PET) enables quantification of dynamic physiological processes through time-resolved imaging. In Rb-82 myocardial perfusion PET, kinetic compartment modeling is used to estimate physiological parameters and…
PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…
This paper presents and validates CTseg, a freely available software for brain CT segmentation, spatial normalisation, and volumetrics. CTseg builds on the Multi-Brain generative modelling framework, providing a CT-specific pipeline that…
Processing cores and the accompanying main memory working in tandem enable the modern processors. Dissipating heat produced from computation, memory access remains a significant problem for processors. Therefore, processor thermal…
Blood transfusion is a frequently performed medical procedure in surgical and nonsurgical contexts. Although it is frequently necessary or even life-saving, it has been identified as one of the most overused procedures in hospitals.…
We present the Python Tree Tensor Network package (pyTTN) for the evaluation of dynamical properties of closed and open quantum systems that makes use of Tree Tensor Network (TTN), or equivalently the multi-layer multiconfiguration…
To our knowledge, all deep computer-aided detection and diagnosis (CAD) systems for prostate cancer (PCa) detection consider bi-parametric magnetic resonance imaging (bp-MRI) only, including T2w and ADC sequences while excluding the 4D…
As modern scientific simulations grow ever more in size and complexity, even their analysis and post-processing becomes increasingly demanding, calling for the use of HPC resources and methods. yt is a parallel, open source post-processing…
Radiotherapy treatment planning remains a time-intensive iterative process requiring expert intervention in commercial treatment planning system (TPS). While machine learning approaches have demonstrated promise, most remain depedent on…
Information theory, i.e. the mathematical analysis of information and of its processing, has become a tenet of modern science; yet, its use in real-world studies is usually hindered by its computational complexity, the lack of coherent…
In recent years, there has been increasing interest in network diffusion models and related problems. The most popular of these are the independent cascade and linear threshold models. Much of the recent experimental work done on these…