Related papers: Pycro-manager: open-source software for integrated…
Microscopy, in particular scanning probe and electron microscopy, has been pivotal in improving our understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most research characterization labs and…
Live time-lapse microscopy is essential for a wide range of biological applications. Software-based automation is the gold standard for the operation of hardware accessories necessary for image acquisition. Given that current software…
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…
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…
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 open-source PyNX toolkit [Favre-Nicolin et al (2011) arXiv:1010.2641, Mandula et al (2016)] has been extended to provide tools for coherent X-ray imaging data analysis and simulation. All calculations can be executed on graphical…
With the increased availability of rich tactile sensors, there is an equally proportional need for open-source and integrated software capable of efficiently and effectively processing raw touch measurements into high-level signals that can…
PymePix is a new Python 3 library that provides control and acquisition for the Timepix3-SPIDR hardware. The rich set of data-structures and intuitive routines reduces time and coding effort to quickly configure, acquire, and visualize data…
A holographic microscope captures interference patterns, or holograms, that encode three-dimensional (3D) information about the object being viewed. Computation is essential to extracting that 3D information. By wrapping low-level…
Real time computer control is an essential feature of scanning probe microscopes, which have become essential tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe…
Automated and computerised control of scientific instrumentation is almost ubiquitous in the modern laboratory. Most instrumentation is controlled over decades old communication busses or is accessed via proprietary system libraries. This…
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…
High-Content Digital Microscopy enhances user comfort, data storage and analysis throughput, paving the way to new researches and medical diagnostics. A digital microscopy platform aims at capturing an image of a cover slip, at storing…
Exploratory visual data analysis tools empower data analysts to efficiently and intuitively explore data insights throughout the entire analysis cycle. However, the gap between common programmatic analysis (e.g., within computational…
Deep metric learning algorithms have a wide variety of applications, but implementing these algorithms can be tedious and time consuming. PyTorch Metric Learning is an open source library that aims to remove this barrier for both…
This article introduces MCNP-GO (https://github.com/afriou/mcnpgo), a Python package designed to manipulate and assemble MCNP input files, allowing users to assemble a set of independent objects, each described by a valid MCNP file, into a…
The rapid development of computation power and machine learning algorithms has paved the way for automating scientific discovery with a scanning probe microscope (SPM). The key elements towards operationalization of automated SPM are the…
Laboratory measurements often use several instruments to fully explore the relevant parameter space; such as, an external lock-in amplifier, an electromagnet, an RF generator, etc.. Ordinarily, these instruments have to be individually…
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…
First-principles computational spectroscopy is a critical tool for interpreting experiment, performing structure refinement, and developing new physical understanding. Systematically setting up input files for different simulation codes and…