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This paper presents a Matlab toolbox to perform basic image processing and visualization tasks, particularly designed for medical image processing. The functionalities available are similar to basic functions found in other non-Matlab…
We report our design, development, installation and troubleshooting of an open source Gnome X Scanning Microscopy (GXSM) software package for controlling and processing of modern Scanning Probe Microscopy (SPM) system as a development tool…
Computational methods are driving high impact microscopy techniques such as ptychography. However, the design and implementation of new algorithms is often a laborious process, as many parts of the code are written in close-to-the-hardware…
Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep…
We present an application, EasyScan_HEP, for connecting programs to scan the parameter space of High Energy Physics (HEP) models using various sampling algorithms. We develop EasyScan_HEP according to the principle of flexibility and…
Numerical stability is a crucial requirement of reliable scientific computing. However, despite the pervasiveness of Python in data science, analyzing large Python programs remains challenging due to the lack of scalable numerical analysis…
DeepInverse is an open-source PyTorch-based library for solving imaging inverse problems. The library covers all crucial steps in image reconstruction from the efficient implementation of forward operators (e.g., optics, MRI, tomography),…
In this work we detail a novel open source library, called MMLSpark, that combines the flexible deep learning library Cognitive Toolkit, with the distributed computing framework Apache Spark. To achieve this, we have contributed Java…
Biological image analysis has traditionally focused on measuring specific visual properties of interest for cells or other entities. A complementary paradigm gaining increasing traction is image-based profiling - quantifying many distinct…
Machine learning is an important tool for analyzing high-dimension hyperspectral data; however, existing software solutions are either closed-source or inextensible research products. In this paper, we present cuvis.ai, an open-source and…
We present PyMoosh, a Python-based simulation library designed to provide a comprehensive set of numerical tools allowing to compute essentially all optical characteristics of multilayered structures, ranging from reflectance and…
Open3D is an open-source library that supports rapid development of software that deals with 3D data. The Open3D frontend exposes a set of carefully selected data structures and algorithms in both C++ and Python. The backend is highly…
OpenML is an online platform for open science collaboration in machine learning, used to share datasets and results of machine learning experiments. In this paper we introduce OpenML-Python, a client API for Python, opening up the OpenML…
PyExperimenter is a tool to facilitate the setup, documentation, execution, and subsequent evaluation of results from an empirical study of algorithms and in particular is designed to reduce the involved manual effort significantly. It is…
The lack of freely available (real-life or synthetic) high or ultra-high dimensional, multi-class datasets may hamper the rapidly growing research on feature screening, especially in the field of biometrics, where the usage of such datasets…
PHYSBO (optimization tools for PHYSics based on Bayesian Optimization) is a Python library for fast and scalable Bayesian optimization. It has been developed mainly for application in the basic sciences such as physics and materials…
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…
Understanding porous media flow is inherently a multi-scale challenge, where at the core lies the aggregation of pore-level processes to a continuum, or Darcy-scale, description. This challenge is directly mirrored in image processing,…
The digitization of biological specimens has revolutionized the field of morphology, creating large collections of 3D data, and microCT in particular. This revolution was initially supported by the development of open-source software tools,…
Building the optical setup for investigating biological questions comes with challenges. A major such challenge is setting up and synchronizing the control of multiple hardware components such as stages, cameras and lasers. With UC2-ESP we…