Related papers: A processing and analytics system for microscopy d…
The increasing importance of Computational Science and Engineering has highlighted the need for high-quality scientific software. However, research software development is often hindered by limited funding, time, staffing, and technical…
SpectraPy is an Astropy affiliated package for spectroscopic data reduction. It collects algorithms and methods for data reduction of astronomical spectra obtained by through-slits spectrographs. It has been created to fill the gap in…
Automated searches for strong gravitational lensing in optical imaging survey datasets often employ machine learning and deep learning approaches. These techniques require more example systems to train the algorithms than have presently…
One of the most noticeable trends in healthcare over the last years is the continuous growth of data volume produced and its heterogeneity. In the medical imaging field, the evolution of digital systems is supported by the PACS concept and…
The increasing volumes of data produced by high-throughput instruments coupled with advanced computational infrastructures for scientific computing have enabled what is often called a {\em Fourth Paradigm} for scientific research based on…
Hierarchical clustering is one of the standard methods taught for identifying and exploring the underlying structures that may be present within a data set. Students are shown examples in which the dendrogram, a visual representation of the…
In this paper we describe the main features of the software package named FITSH, intended to provide a standalone environment for analysis of data acquired by imaging astronomical detectors. The package provides utilities both for the full…
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…
We present kikuchipy, an open-source toolbox for analysis of electron backscatter diffraction patterns, written in Python. The software is capable of both Hough and dictionary indexing and orientation and/or projection center refinement of…
The use of third-party packages is becoming increasingly popular and has led to the emergence of large software package ecosystems with a maze of inter-dependencies. Since the reliance on these ecosystems enables developers to reduce…
The study of trajectories is often a core task in several research fields. In environmental modelling, trajectories are crucial to study fluid pollution, animal migrations, oil slick patterns or land movements. In this contribution, we…
The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological…
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…
In recent years, x-ray speckle tracking techniques have emerged as viable tools for wavefront metrology and sample imaging applications. These methods are based on the measurement of near-field images. Thanks to the simple experimental…
Ptychography has become an indispensable tool for high-resolution, non-destructive imaging using coherent light sources. The processing of ptychographic data critically depends on robust, efficient, and flexible computational reconstruction…
Curating, processing, and combining large-scale medical imaging datasets from national studies is a non-trivial task due to the intense computation and data throughput required, variability of acquired data, and associated financial…
PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range…
Scientists are drawn to synchrotrons and accelerator based light sources because of their brightness, coherence and flux. The rate of improvement in brightness and detector technology has outpaced Moore's law growth seen for computers,…
At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parametrising such models to conform to the multitude of available experimental constraints is a global nonlinear optimisation…
In this paper we argue that the data management community should devote far more effort to building data integration (DI) systems, in order to truly advance the field. Toward this goal, we make three contributions. First, we draw on our…