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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…
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,…
The freud Python package is a powerful library for analyzing simulation data. Written with modern simulation and data analysis workflows in mind, freud provides a Python interface to fast, parallelized C++ routines that run efficiently on…
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…
Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a…
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…
Recent advances in Foundation Models for Materials Science are poised to revolutionize the discovery, manufacture, and design of novel materials with tailored properties and responses. Although great strides have been made, successes have…
Advanced ultrasound computed tomography techniques like full-waveform inversion are mathematically challenging and orders of magnitude more computationally expensive than conventional ultrasound imaging methods. This computational and…
This paper identifies OpenSDI, a challenge for spotting diffusion-generated images in open-world settings. In response to this challenge, we define a new benchmark, the OpenSDI dataset (OpenSDID), which stands out from existing datasets due…
We develop a Python-based open-source package to analyze the results stemming from ab initio molecular-dynamics simulations of fluids. The package is best suited for applications on natural systems, like silicate and oxide melts,…
Hyperspectral pansharpening consists of fusing a high-resolution panchromatic band and a low-resolution hyperspectral image to obtain a new image with high resolution in both the spatial and spectral domains. These remote sensing products…
In this thesis we investigate high throughput computational methods for processing large quantities of data collected from synchrotrons and their application to spectral analysis of powder diffraction data. We also present the main product…
We present the first public release (v0.1) of the open-source GADGET Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing…
Recently, Big Data applications have rapidly expanded into different industries. Healthcare is also one the industries willing to use big data platforms so that some big data analytics tools have been adopted in this field to some extent.…
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…
Backgr: Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology.…
Electron ptychography has recently achieved unprecedented resolution, offering valuable insights across diverse material systems, including in three dimensions. However, high-quality ptychographic reconstruction is computationally expensive…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
{\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…
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…