Related papers: LibCPIXE: a PIXE simulation open-source library fo…
LibBi is a software package for state-space modelling and Bayesian inference on modern computer hardware, including multi-core central processing units (CPUs), many-core graphics processing units (GPUs) and distributed-memory clusters of…
scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal "Modified BSD" open source license, provides a well-documented…
This paper introduces Ciw, an open source library for conducting discrete event simulations that has been developed in Python. The strengths of the library are illustrated in terms of best practice and reproducibility for computational…
This paper provides the description of a novel, multi-purpose spline library. In accordance with the increasingly diverse modes of usage of splines, it is multi-purpose in the sense that it supports geometry representation, finite element…
PepSIRF is a command-line, module-based open-source software package that facilitates the analysis of data from highly-multiplexed serology assays (e.g., PepSeq or PhIP-Seq). It has nine separate modules in its current release (v1.5.0):…
We present the first public release of ShapePipe, an open-source and modular weak-lensing measurement, analysis, and validation pipeline written in Python. We describe the design of the software and justify the choices made. We provide a…
Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, protocols and more, to…
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables to simulate operational light-sheet microscopes by combining data…
The Herschel Interactive Processing Environment (HIPE) was developed by the European Space Agency (ESA) in collaboration with NASA and the Herschel Instrument Control Centres to provide the astronomical community a complete environment to…
MOCVXPY is an open-source Python library for convex vector optimization. It is built on top of CVXPY, a domain-specific language for single-objective convex optimization. MOCVXPY enables practitioners to describe their convex vector…
We introduce SpreadPy as a Python library for simulating spreading activation in cognitive single-layer and multiplex networks. Our tool is designed to perform numerical simulations testing structure-function relationships in cognitive…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Understanding how the brain functions is one of the biggest challenges of our time. The analysis of experimentally recorded neural firing patterns (spike trains) plays a crucial role in addressing this problem. Here, the PySpike library is…
Biophysics is a subject that is spread over many disciplines and transcends the skills and knowledge of the individual student. This makes it challenging both to teach and to learn. Educational materials are described to aid in teaching…
We present an open source Python 3 library aimed at practitioners of molecular simulation, especially Monte Carlo simulation. The aims of the library are to facilitate the generation of simulation data for a wide range of problems; and to…
Recent advancements in language-guided diffusion models for image editing are often bottle-necked by cumbersome prompt engineering to precisely articulate desired changes. An intuitive alternative calls on guidance from in-the-wild image…
BlackJAX is a library implementing sampling and variational inference algorithms commonly used in Bayesian computation. It is designed for ease of use, speed, and modularity by taking a functional approach to the algorithms' implementation.…
We present libsharp, a code library for spherical harmonic transforms (SHTs), which evolved from the libpsht library, addressing several of its shortcomings, such as adding MPI support for distributed memory systems and SHTs of fields with…
Turning the current experimental plasma accelerator state-of-the-art from a promising technology into mainstream scientific tools depends critically on high-performance, high-fidelity modeling of complex processes that develop over a wide…
We present PyOECP, a Python-based flexible open-source software for estimating and modeling the complex permittivity obtained from the open-ended coaxial probe (OECP) technique. The transformation of the measured reflection coefficient to…