Related papers: pyFRET: A Python Library for Single Molecule Fluor…
We present SPIKE (Spectrometry Processing Innovative KErnel), an open-source Python package dedicated to Fourier spectroscopies. It provides basic functionalities such as apodisation, a complete set of Fourier transforms, phasing for NMR),…
Major advancements in fields as diverse as biology and quantum computing have relied on a multitude of microscopic techniques. All optical, electron and scanning probe microscopy advanced with new detector technologies and integration of…
PySPH is an open-source, Python-based, framework for particle methods in general and Smoothed Particle Hydrodynamics (SPH) in particular. PySPH allows a user to define a complete SPH simulation using pure Python. High-performance code is…
In the rapidly evolving field of bioimaging, the integration and orchestration of Findable, Accessible, Interoperable, and Reusable (FAIR) image analysis workflows remains a challenge. We introduce BIOMERO, a bridge connecting OMERO, a…
The diffraction of light imposes a fundamental limit on the resolution of light microscopes. This limit can be circumvented by creating and exploiting independent behaviors of the sample at length scales below the diffraction limit. In…
High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta…
We present a fast and user friendly exoplanet transit light curve modelling package PyTransit, implementing optimised versions of the Gimen\'ez and the Mandel & Agol transit models. The package offers an object-oriented Python interface to…
\textsc{Pykat} is a Python package which extends the popular optical interferometer modelling software \textsc{Finesse}. It provides a more modern and efficient user interface for conducting complex numerical simulations, as well as…
The success of deep learning in supervised fine-grained recognition for domain-specific tasks relies heavily on expert annotations. The Open-Set for fine-grained Self-Supervised Learning (SSL) problem aims to enhance performance on…
As data are generated more and more from multiple disparate sources, multiview data sets, where each sample has features in distinct views, have ballooned in recent years. However, no comprehensive package exists that enables…
Deep Frequency Modulation Interferometry (DFMI) is an emerging laser interferometry technique for high-precision metrology, offering picometer-level displacement measurements and the potential for absolute length determination with…
Concomitant amplified spontaneous emission (ASE) and F\"orster resonance energy transfer (FRET) are investigated in electrospun light-emitting fibers. Upon dye-doping with a proper FRET couple system, free-standing fibrous mats exhibit…
We present the open-source image processing software package PySAP (Python Sparse data Analysis Package) developed for the COmpressed Sensing for Magnetic resonance Imaging and Cosmology (COSMIC) project. This package provides a set of…
Integrated information theory provides a mathematical framework to fully characterize the cause-effect structure of a physical system. Here, we introduce PyPhi, a Python software package that implements this framework for causal analysis…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
We introduce pymovements: a Python package for analyzing eye-tracking data that follows best practices in software development, including rigorous testing and adherence to coding standards. The package provides functionality for key…
Stellar abundance analysis relies on flexible, high-performance spectral synthesis. To meet these needs, we present PySME v1.0, an updated Python implementation of Spectroscopy Made Easy (SME) designed for precise and survey-scale modelling…
Running complex sets of machine learning experiments is challenging and time-consuming due to the lack of a unified framework. This leaves researchers forced to spend time implementing necessary features such as parallelization, caching,…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
Using the Monte Carlo ray tracing package McStas, we illustrate the possibilities of creating virtual experiments of the neutron spectrometer BIFROST at the European Spallation Source, ESS. With this model, we are able to benchmark BIFROST…