Related papers: A processing and analytics system for microscopy d…
Microscopy, in particular scanning probe and electron microscopy, has been pivotal in improving our understanding of structure-function relationships at the nanoscale and is by now ubiquitous in most research characterization labs and…
Materials science is undergoing profound changes due to advances in characterization instrumentation that have resulted in an explosion of data in terms of volume, velocity, variety and complexity. Harnessing these data for scientific…
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…
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…
{\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…
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…
The analysis of experimental results with Python often requires writing many code scripts which all need access to the same set of functions. In a common field of research, this set will be nearly the same for many users. The qspec Python…
The study of complex many-body systems via analysis of the trajectories of the units that dynamically move and interact within them is a non-trivial task. The workflow for extracting meaningful information from the raw trajectory data is…
The SunPy Project is a community of scientists and software developers creating an ecosystem of Python packages for solar physics. The project includes the sunpy core package as well as a set of affiliated packages. The sunpy core package…
Scientific communities naturally tend to organize around data ecosystems created by the combination of their observational devices, their data repositories, and the workflows essential to carry their research from observation to discovery.…
pyspeckit is a toolkit and library for spectroscopic analysis in Python. We describe the pyspeckit package and highlight some of its capabilities, such as interactively fitting a model to data, akin to the historically widely-used splot…
X-ray ptychography imaging at synchrotron facilities like the Advanced Photon Source (APS) involves controlling instrument hardwares to collect a set of diffraction patterns from overlapping coherent illumination spots on extended samples,…
PaPy, which stands for parallel pipelines in Python, is a highly flexible framework that enables the construction of robust, scalable workflows for either generating or processing voluminous datasets. A workflow is created from user-written…
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…
There are numerous approaches to building analysis applications across the high-energy physics community. Among them are Python-based, or at least Python-driven, analysis workflows. We aim to ease the adoption of a Python-based analysis…
In a continued quest to monitor subsecond surface dynamics on the atomic scale and to improve imaging resolution, a FAST module to accelerate existing scanning probe microscopy setups was previously presented. Hereby, the speedup is enabled…
Imaging and hyperspectral data analysis is central to progress across biology, medicine, chemistry, and physics. The core challenge lies in converting high-resolution or high-dimensional datasets into interpretable representations that…
Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly…
The increased computational and experimental interest in perovskite systems comprising novel phases and reduced dimensionality has greatly expanded the search space for this class of materials. In similar fields, unified frameworks exist…
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…