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We present PyAtoms, an interactive open-source software that rapidly simulates atomic-scale scanning tunneling microscopy (STM) and other scanning probe microscopy (SPM) images of two-dimensional (2D) layered materials, moir\'{e} systems,…
The multi-billion dollar, worldwide medical ultrasound (US) market continues to grow annually. Its non-ionizing nature, real-time capabilities and relatively low cost, compared to other imaging modalities, have led to significant…
Scientific results in high-energy physics and in many other fields often rely on complex software stacks. In order to support reproducibility and scrutiny of the results, it is good practice to use open source software and to cite software…
Leveraging medical record information in the era of big data and machine learning comes with the caveat that data must be cleaned and de-identified. Facilitating data sharing and harmonization for multi-center collaborations are…
Hyperspectral imaging (HSI) allows researchers to study plant traits non-destructively. By capturing hundreds of narrow spectral bands per pixel, it reveals details about plant biochemistry and stress that standard cameras miss. However,…
The reduction of integral-field spectrograph (IFS) data is demanding work. Many repetitive operations are required in order to convert raw data into, typically a large number of, spectra. This effort can be markedly simplified through the…
Background: Digital Image Correlation (DIC) is a widely used full-field measurement technique, but both open-source and commercial packages often have limitations such as operating-system restrictions, lack of support for deployment on…
Reliable parameter extraction from experimental data is central to quantitative analysis in spectroscopy, diffraction, photoluminescence, chromatography, microscopy, and time-resolved measurements. We present FitED, a Python-based desktop…
Curvilinear structure segmentation (CSS) is essential in various domains, including medical imaging, landscape analysis, industrial surface inspection, and plant analysis. While existing methods achieve high performance within specific…
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…
Raman spectroscopy is a non-destructive and label-free chemical analysis technique, which plays a key role in the analysis and discovery cycle of various branches of science. Nonetheless, progress in Raman spectroscopic analysis is still…
We present OpenICS, an image compressive sensing toolbox that includes multiple image compressive sensing and reconstruction algorithms proposed in the past decade. Due to the lack of standardization in the implementation and evaluation of…
Biosciences have been revolutionized by next generation sequencing (NGS) technologies in last years, leading to new perspectives in medical, industrial and environmental applications. And although our motivation comes from biosciences, the…
Scientific data has been growing in both size and complexity across the modern physical, engineering, life and social sciences. Spatial structure, for example, is a hallmark of many of the most important real-world complex systems, but its…
Computer-aided design (CAD) has become a critical element in the creation of nanopatterned structures and devices. In particular, with the increased adoption of easy-to-learn programming languages like Python there has been a significant…
The storage and manipulation of digital images and the analysis of the information held in those images are essential requirements for next-generation medical information systems. The medical community has been exploring collaborative…
PySPH is an open-source, Python-based, framework for particle methods in general and Smoothed Particle Hydrodynamics (SPH) in particular. PySPH allows a user to define a complete SPH simulation using pure Python. High-performance code is…
We introduce STRAUSS (Sonification Tools and Resources for Analysis Using Sound Synthesis) a modular, self-contained and flexible Python sonification package, operating in a free and open source (FOSS) capacity. STRAUSS is intended to be a…
We present UMI-3D, a multimodal extension of the Universal Manipulation Interface (UMI) for robust and scalable data collection in embodied manipulation. While UMI enables portable, wrist-mounted data acquisition, its reliance on monocular…
Spectral pixels are often a mixture of the pure spectra of the materials, called endmembers, due to the low spatial resolution of hyperspectral sensors, double scattering, and intimate mixtures of materials in the scenes. Unmixing estimates…