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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…
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…
{\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…
Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements…
PypeIt is a Python package for semi-automated reduction of astronomical, spectroscopic data. Its algorithms build on decades-long development of previous data reduction pipelines by the developers (Bernstein, Burles, & Prochaska, 2015;…
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…
In medical imaging, there is a growing interest to provide real-time images with good quality for large anatomical structures. To cope with this issue, we developed a library that allows to replace, for some specific clinical applications,…
We describe SynthPix, a synthetic image generator for Particle Image Velocimetry (PIV) with a focus on performance and parallelism on accelerators, implemented in JAX. SynthPix produces PIV image pairs from prescribed flow fields while…
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…
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…
PyArmadillo is a linear algebra library for the Python language, with the aim of closely mirroring the programming interface of the widely used Armadillo C++ library, which in turn is deliberately similar to Matlab. PyArmadillo hence…
Pyxel is a novel python tool for end-to-end detection chain simulation i.e. from detector optical effects to readout electronics effects. It is an easy-to-use framework to host and pipeline any detector effect model. It is suited for…
We present pyroomacoustics, a software package aimed at the rapid development and testing of audio array processing algorithms. The content of the package can be divided into three main components: an intuitive Python object-oriented…
A large amount of data is produced every second from modern information systems such as mobile devices, the world wide web, Internet of Things, social media, etc. Analysis and mining of this massive data requires a lot of advanced tools and…
The lack of flexible annotation tools has hindered the deployment of AI models in some scientific areas. Most existing image annotation software requires users to upload a precollected dataset, which limits support for on-demand pipelines…
$\textit{Pymc-learn}$ is a Python package providing a variety of state-of-the-art probabilistic models for supervised and unsupervised machine learning. It is inspired by $\textit{scikit-learn}$ and focuses on bringing probabilistic machine…
pyspeckit is a toolkit and library for spectroscopic analysis in Python. We describe the pyspeckit package and highlight some of its capabilities, such as interactively fitting a model to data, akin to the historically widely-used splot…
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),…
HYPERTILING is a high-performance Python library for the generation and visualization of regular hyperbolic lattices embedded in the Poincar\'e disk model. Using highly optimized, efficient algorithms, hyperbolic tilings with millions of…
Distributed, large-scale quantum computing will need architectures that combine matter-based qubits with photonic links, but today's software stacks target either gate-based chips or linear-optical devices in isolation. We introduce Optyx,…