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The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
HyperNetX (HNX) is an open source Python library for the analysis and visualization of complex network data modeled as hypergraphs. Initially released in 2019, HNX facilitates exploratory data analysis of complex networks using algebraic…
\texttt{Mixture-Models} is an open-source Python library for fitting Gaussian Mixture Models (GMM) and their variants, such as Parsimonious GMMs, Mixture of Factor Analyzers, MClust models, Mixture of Student's t distributions, etc. It…
{\mu}Manager, an open-source microscopy acquisition software, has been an essential tool for many microscopy experiments over the past 15 years, but is not easy to use for experiments in which image acquisition and analysis are closely…
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…
LiteX is a GitHub-hosted SoC builder / IP library and utilities that can be used to create SoCs and full FPGA designs. Besides being open-source and BSD licensed, its originality lies in the fact that its IP components are entirely…
Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and…
Advanced ultrasound computed tomography techniques like full-waveform inversion are mathematically challenging and orders of magnitude more computationally expensive than conventional ultrasound imaging methods. This computational and…
The increasing demand for spatial audio in applications such as virtual reality, immersive media, and spatial audio research necessitates robust solutions to generate binaural audio data sets for use in testing and validation. Binamix is an…
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),…
Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their…
DisCoPy (Distributional Compositional Python) is an open source toolbox for computing with string diagrams and functors. In particular, the diagram data structure allows to encode various kinds of quantum processes, with functors for…
Microbiology culture reports contain critical information for important clinical and public health applications. However, microbiology reports often have complex, semi-structured, free-text data that present a barrier for secondary use.…
In this paper, we evaluate Apache Spark for a data-intensive machine learning problem. Our use case focuses on policy diffusion detection across the state legislatures in the United States over time. Previous work on policy diffusion has…
TREXIO is an open-source file format and library developed for the storage and manipulation of data produced by quantum chemistry calculations. It is designed with the goal of providing a reliable and efficient method of storing and…
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…
This paper introduces pyRecLab, a software library written in C++ with Python bindings which allows to quickly train, test and develop recommender systems. Although there are several software libraries for this purpose, only a few let…
High content imaging is needed to catalogue the variety of cellular phenotypes and multi-cellular ecosystems present in metazoan tissues. We recently developed Iterative Bleaching Extends multi-pleXity (IBEX), an iterative immunolabeling…
We introduce Repro, an open-source library which aims at improving the reproducibility and usability of research code. The library provides a lightweight Python API for running software released by researchers within Docker containers which…
Optical multilayer thin-films are fundamental components that enable the precise control of reflectance, transmittance, and phase shift in the design of photonic systems. Rapid and accessible simulation of these structures holds critical…