Related papers: Simulated single molecule microscopy with SMeagol
Slime mould P. polycephalum is a single cells visible by unaided eye. The cells shows a wide spectrum of intelligent behaviour. By interpreting the behaviour in terms of computation one can make a slime mould based computing device. The…
Tracking single molecules is instrumental for quantifying the transport of molecules and nanoparticles in biological samples, e.g., in brain drug delivery studies. Existing intensity-based localisation methods are not developed for imaging…
Microscopy and particle-based simulations are both powerful techniques to study aggregated particulate matter such as colloidal gels. The data provided by these techniques often contains information on a wide array of length scales, but…
In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical…
A simple Monte Carlo (MC) algorithm for the simulation of the passage of low-energy gamma rays and electrons through any material medium is presented. The algorithm includes several approximations that accelerate the simulation while…
We present a fully modular and scalable software pipeline for processing electron microscope (EM) images of brain slices into 3D visualization of individual neurons and demonstrate an end-to-end segmentation of a large EM volume using a…
We propose a simple additive approach to simulate X-ray photoelectron spectra (XPS) of macromolecules based on the $GW$ method. Single-shot $GW$ ($G_0W_0$) is a promising technique to compute accurate core-electron binding energies (BEs).…
We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing…
The increasing size of cosmological simulations has led to the need for new visualization techniques. We focus on Smoothed Particle Hydrodynamical (SPH) simulations run with the GADGET code and describe methods for visually accessing the…
Quantum computing, an innovative computing system carrying prominent processing rate, is meant to be the solutions to problems in many fields. Among these realms, the most intuitive application is to help chemical researchers correctly…
This paper presents a software platform, named BiNS2, able to simulate diffusion-based molecular communications with drift inside blood vessels. The contribution of the paper is twofold. First a detailed description of the simulator is…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
This paper summarizes and presents PulsatioMech: an open-source MATLAB toolbox for seismocardiography (SCG) signal processing. The toolbox may be found here: https://github.com/nzavanelli/SCG_master_toolbox PulsatioMech is currently under…
Automated and computerised control of scientific instrumentation is almost ubiquitous in the modern laboratory. Most instrumentation is controlled over decades old communication busses or is accessed via proprietary system libraries. This…
The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
The Speckle Imager via MUlti Layer Atmospheric Turbulence Object Reconstructor (SIMULATOR) is a lab-based testbed instrument developed to test for speckle correlation-based techniques in the optical regime. However, this instrument can be…
This study presents a new computational approach for simulating the microbial decomposition of organic matter, from 3D micro-computed tomography (micro-CT) images of soil. The method employs a valuated graph of connected voxels to simulate…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Many of the intriguing properties of blood originate from its cellular nature. Bulk effects, such as viscosity, depend on the local shear rates and on the size of the vessels. While empirical descriptions of bulk rheology are available for…
The MIGALE project (http://www.sai.msu.su/migale) provides databases and data analysis tools to study the evolution of galaxies from z=1 to z=0. It develops and maintain a general database, HyperLeda, to give a homogenized parameterization…