Related papers: pyssam -- a Python library for statistical modelli…
Particle-based shape modeling (PSM) is a popular approach to automatically quantify shape variability in populations of anatomies. The PSM family of methods employs optimization to automatically populate a dense set of corresponding…
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…
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…
We present a numerical code to simulate maps of Galactic emission in intensity and polarization at microwave frequencies, aiding in the design of Cosmic Microwave Background experiments. This Python code builds on existing efforts to…
PySINDy is a Python package for the discovery of governing dynamical systems models from data. In particular, PySINDy provides tools for applying the sparse identification of nonlinear dynamics (SINDy) (Brunton et al. 2016) approach to…
This paper introduces Colossus, a public, open-source python package for calculations related to cosmology, the large-scale structure (LSS) of matter in the universe, and the properties of dark matter halos. The code is designed to be fast…
In this paper, we introduce Pysimfrac, a open-source python library for generating 3-D synthetic fracture realizations, integrating with fluid simulators, and performing analysis. Pysimfrac allows the user to specify one of three fracture…
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,…
PyLlama is a handy Python toolkit to compute the electromagnetic reflection and transmission properties of arbitrary multilayered linear media, including the case of anisotropy. Relying on a $4 \times 4$-matrix formalism, PyLlama implements…
Statistical shape modeling (SSM) is a valuable and powerful tool to generate a detailed representation of complex anatomy that enables quantitative analysis and the comparison of shapes and their variations. SSM applies mathematics,…
Statistical Shape Modeling (SSM) effectively analyzes anatomical variations within populations but is limited by the need for manual localization and segmentation, which relies on scarce medical expertise. Recent advances in deep learning…
Short Read Alignment Mapping Metrics (SRAMM): is an efficient and versatile command line tool providing additional short read mapping metrics, filtering, and graphs. Short read aligners report MAPing Quality (MAPQ), but these methods…
This paper presents hep-aid, a modular Python library conceived for utilising, implementing, and developing parameter scan algorithms. Originally devised for sample-efficient, multi-objective active search approaches in computationally…
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,…
Statistical shape models (SSMs) are a popular tool to conduct morphological analysis of anatomical structures which is a crucial step in clinical practices. However, shape representations through SSMs are based on shape coefficients and…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
Data exploration is an important step of every data science and machine learning project, including those involving textual data. We provide a novel language tool, in the form of a publicly available Python library for extracting patterns…
The characteristics and determinants of health and disease are often organised in space, reflecting our spatially extended nature. Understanding the influence of such factors requires models capable of capturing spatial relations. Though a…
Medical image analysis plays a key role in precision medicine as it allows the clinicians to identify anatomical abnormalities and it is routinely used in clinical assessment. Data curation and pre-processing of medical images are critical…
Statistical shape modeling (SSM) is an essential tool for analyzing variations in anatomical morphology. In a typical SSM pipeline, 3D anatomical images, gone through segmentation and rigid registration, are represented using…