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Standardized performance evaluation of fluorescence imaging systems remains a critical unmet need in the field of fluorescence-guided surgery (FGS). While the American Association of Physicists in Medicine (AAPM) TG311 report and recent FDA…
Fourier transforms are an often necessary component in many computational tasks, and can be computed efficiently through the fast Fourier transform (FFT) algorithm. However, many applications involve an underlying continuous signal, and a…
{\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…
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…
Linear operators and optimisation are at the core of many algorithms used in signal and image processing, remote sensing, and inverse problems. For small to medium-scale problems, existing software packages (e.g., MATLAB, Python numpy and…
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…
This manuscript describes the design, usage, and data-reduction pipeline developed for the Magellan Inamori Kyocera Echelle (MIKE) spectrometer used with the Magellan telescope at the Las Campanas Observatory. We summarize the basic…
Variational inference is an increasingly popular method in statistics and machine learning for approximating probability distributions. We developed LINFA (Library for Inference with Normalizing Flow and Annealing), a Python library for…
We present PyXtal FF, a package based on Python programming language, for developing machine learning potentials (MLPs). The aim of PyXtal FF is to promote the application of atomistic simulations by providing several choices of structural…
This paper describes the general characteristics of raw data from fiber-fed spectrographs in general and fiber-fed IFUs in particular. The different steps of the data reduction are presented, and the techniques used to address the unusual…
The pyFAI package has been designed to reduce X-ray diffraction images into powder diffraction curves to be further processed by scientists. This contribution describes how to convert an image into a radial profile using the Numpy package,…
PySE is a Python software package for finding and measuring sources in radio telescope images. The software was designed to detect sources in the LOFAR telescope images, but can be used with images from other radio telescopes as well. We…
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…
We present the pulsar_spectra software repository, an open-source pulsar flux density catalogue and automated spectral fitting software that finds the best spectral model and produces publication-quality plots. The Python-based software…
PyCPL provides full access to ESO's Common Pipeline Library ( CPL) for astronomical data reduction within a Python environment. Not only does it offer a Python interface to the robust CPL library, but it also lets users and developers fully…
We present PyRPL, an open source software package that allows the implementation of automatic digital feedback controllers for quantum optics experiments on commercially available, affordable FPGA boards. Our software implements the digital…
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,…
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…
The direct detection and characterization of planetary and substellar companions at small angular separations is a rapidly advancing field. Dedicated high-contrast imaging instruments deliver unprecedented sensitivity, enabling detailed…
PyUnfold is a Python package for incorporating imperfections of the measurement process into a data analysis pipeline. In an ideal world, we would have access to the perfect detector: an apparatus that makes no error in measuring a desired…