Related papers: pyFRET: A Python Library for Single Molecule Fluor…
Time series data provided by single-molecule Forster resonance energy transfer (sm-FRET) experiments offer the opportunity to infer not only model parameters describing molecular complexes, e.g. rate constants, but also information about…
I present a fast Python tool, SpectRes, for carrying out the resampling of spectral flux densities and their associated uncertainties onto different wavelength grids. The function works with any grid of wavelength values, including…
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…
As camera pixel arrays have grown larger and faster, and optical microscopy techniques ever more refined, there has been an explosion in the quantity of data acquired during routine light microcopy. At the single-molecule level, analysis…
Multiplexed, real-time fluorescence detection at the single-molecule level is highly desirable to reveal the stoichiometry, dynamics, and interactions of individual molecular species within complex systems. However, traditionally…
In this article we report the release of a new program for batch processing and visualization of powder diffraction data. The program, which is free-of-charge for non-commercial use and can be obtained with its detailed documentation from…
In this paper, we introduce Pysimfrac, a open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. Pysimfrac allows the user to specify one of three fracture…
Computed tomography perfusion (CTP) and magnetic resonance perfusion (MRP) are widely used in acute ischemic stroke assessment and other cerebrovascular conditions to generate quantitative maps of cerebral hemodynamics. While commercial…
We introduce software for reading, writing and processing fluorescence single-molecule and image spectroscopy data and developing analysis pipelines that unifies various spectroscopic analysis tools. Our software can be used for processing…
Despite their widespread use in cell biology, fluorescence lifetime imaging microscopy (FLIM) data-sets are challenging to analyse, because each spatial position can contain a superposition of multiple fluorescent components. Here, we…
We report on a Python-toolbox for unbiased statistical analysis of fluorescence intermittency properties of single emitters. Intermittency, i.e., step-wise temporal variations in the instantaneous emission intensity and fluorescence decay…
Single-molecule F\"orster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key…
The applications of Fluorescence resonance energy transfer (FRET) have expanded tremendously in the last 25 years, and the technique has become a staple technique in many biological and biophysical fields. FRET can be used as spectroscopic…
We present BIFROST, a first-principles model of polarization mode dispersion (PMD) in optical fibers. Unlike conventional models, BIFROST employs physically motivated representations of the PMD properties of fibers, allowing users to…
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still…
Recent advances in Fluorescence Resonance Energy Transfer (FRET) provides a way to measure and understand different biological systems and molecular interactions in nanometer order. In this report the introduction and principle of the FRET…
The library scikit-fda is a Python package for Functional Data Analysis (FDA). It provides a comprehensive set of tools for representation, preprocessing, and exploratory analysis of functional data. The library is built upon and integrated…
We introduce the \texttt{pyunicorn} (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and…
Radio astronomy observatories with high throughput back end instruments require real-time data processing. While computing hardware continues to advance rapidly, development of real-time processing pipelines remains difficult and…
Single-particle imaging experiments of biomolecules at x-ray free-electron lasers (XFELs) require processing of hundreds of thousands (or more) of images that contain very few x-rays. Each low-flux image of the diffraction pattern is…