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Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and Nextflow enable users to automate the…
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…
Tomographic imaging has benefited from advances in X-ray sources, detectors and optics to enable novel observations in science, engineering and medicine. These advances have come with a dramatic increase of input data in the form of faster…
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…
Image processing at scale is a powerful tool for creating new data sets and integrating them with existing data sets and performing analysis and quality assurance investigations. Workflow managers offer advantages in this type of…
Data cubes are used for analyzing large data sets usually contained in data warehouses. The most popular data cube tools use graphical user interfaces (GUI) to do the data analysis. Traditionally this was fine since data analysts were not…
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…
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 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…
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface that is agnostic to the backend docking engine with which to…
There are high technological and software demands associated with conducting brain-computer interface (BCI) research. In order to accelerate the development and accessibility of BCI, it is worthwhile to focus on open-source and desired…
Medical image analysis plays a key role in precision medicine as it allows the clinicians to identify anatomical abnormalities and it is routinely used in clinical assessment. Data curation and pre-processing of medical images are critical…
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…
The Montage image mosaic engine has found wide applicability in astronomy research, integration into processing environments, and is an examplar application for the development of advanced cyber-infrastructure. It is written in C to provide…
The use of Python is noticeably growing among the scientific community, and Astronomy is not an exception. The power of Python consists of being an extremely versatile high-level language, easy to program that combines both traditional…
Materials science is undergoing profound changes due to advances in characterization instrumentation that have resulted in an explosion of data in terms of volume, velocity, variety and complexity. Harnessing these data for scientific…
Advances in semiconductor manufacturing processes and large scale integration keep pushing demanding applications further away from centralized processing, and closer to the edges of the network (i.e. Edge Computing). It has become possible…
The increasing availability of high-quality optical and near-infrared spectroscopic data, as well as advances in modelling techniques, have greatly expanded the scientific potential of spectroscopic studies. However, the software tools…
We introduce \texttt{pycobra}, a Python library devoted to ensemble learning (regression and classification) and visualisation. Its main assets are the implementation of several ensemble learning algorithms, a flexible and generic interface…