Related papers: pyFRET: A Python Library for Single Molecule Fluor…
The recomputability and reproducibility of results from scientific software requires access to both the source code and all associated input and output data. However, the full collection of these resources often does not accompany the key…
Motivated by recent experiments on photon statistics from individual dye pairs planted on biomolecules and coupled by fluorescence resonance energy transfer (FRET), we show here that the FRET dynamics can be modelled by Gaussian random…
The Linac Coherent Light Source (LCLS) is an X- ray free electron laser (XFEL) facility enabling the study of the structure and dynamics of single macromolecules. A major upgrade will bring the repetition rate of the X-ray source from 120…
There is a need for open-source libraries in emission tomography that (i) use modern and popular backend code to encourage community contributions and (ii) offer support for the multitude of reconstruction techniques available in recent…
We introduce \texttt{pycobra}, a Python library devoted to ensemble learning (regression and classification) and visualisation. Its main assets are the implementation of several ensemble learning algorithms, a flexible and generic interface…
We present an analytical model for Forster resonance energy transfer (FRET) between a donor and an acceptor placed in inhomogeneous and absorptive environment characterized by complex dielectric function, e.g., near a metal-dielectric…
Diffusion coefficient measurements are important for many biological and material investigations, such as particle dynamics, kinetics, and size determinations. Amongst current measurement methods, single particle tracking (SPT) offers the…
Photon-HDF5 is an open-source and open file format for storing photon-counting data from single molecule microscopy experiments, introduced to simplify data exchange and increase the reproducibility of data analysis. Part of the Photon-HDF5…
Background and Objective: Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues…
Multiplexed immunofluorescence microscopy captures detailed measurements of spatially resolved, multiple biomarkers simultaneously, revealing tissue composition and cellular interactions in situ among single cells. The growing scale and…
The development of X-ray Free Electron Lasers (XFELs) has opened numerous opportunities to probe atomic structure and ultrafast dynamics of various materials. Single Particle Imaging (SPI) with XFELs enables the investigation of biological…
The development and generation of synthetic data are becoming increasingly vital in the field of statistical disclosure control. The PSInference package provides tools to perform exact inferential analysis on singly imputed synthetic data…
A reformulated implementation of single-sideband ptychography enables analysis and display of live detector data streams in 4D scanning transmission electron microscopy (STEM) using the LiberTEM open-source platform. This is combined with…
This paper reports the development of a Python Non-Uniform Fast Fourier Transform (PyNUFFT) package, which accelerates non-Cartesian image reconstruction on heterogeneous platforms. Scientific computing with Python encompasses a mature and…
This is a companion Focus Demonstration article to the PyMUSE python package, demonstrating its usage and utilities for VLT/MUSE data analysis, that include a wide range of options for spectra extractions, the creation of different types of…
Recent technological advances in cutting-edge ultrasensitive fluorescence microscopy have allowed single-molecule imaging experiments in living cells across all three domains of life to become commonplace. Single-molecule live-cell data is…
Single-molecule fluorescence spectroscopy is a powerful method that avoids ensemble averaging, but its temporal resolution is limited by the fluorescence lifetime to nanoseconds at most. At the ensemble level, two-dimensional spectroscopy…
F\"{o}rster Resonance Energy Transfer Calculator (FRET$-$Calc) is a program and web server that analyzes molar extinction coefficient of the acceptor, emission spectrum of the donor, and the refractive index spectrum of the donor/acceptor…
Inversions of airborne EM data are often an iterative process, not only requiring that the researcher be able to explore the impact of changing components such as the choice of regularization functional or model parameterization, but also…
In this thesis we investigate high throughput computational methods for processing large quantities of data collected from synchrotrons and their application to spectral analysis of powder diffraction data. We also present the main product…