16 papers · ranked by Valyu relevance
Immo Schuetz, Harun Karimpur, Katja Fiehler
Virtual reality (VR) is a powerful tool for researchers due to its potential to study dynamic human behavior in highly naturalistic environments while retaining full control over the presented stimuli. Due to advancements in consumer hardware, VR devices are now very affordable and have also started to include…
Venus N. Sherathiya, Michael D. Schaid, Jillian L. Seiler, Gabriela C. Lopez + 1 more
Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages. However, analysis of FP data can be challenging for…
Jin Hyun Cheong, Eshin Jolly, Tiankang Xie, Sophie Byrne + 2 more
'Matthew Kenney' 'Luke J. Chang'] Studying facial expressions is a notoriously difficult endeavor. Recent advances in the field of affective computing have yielded impressive progress in automatically detecting facial expressions from pictures and videos. However, much of this work has yet to be widely disseminated in…
Mats W. J. van Es, Chetan Gohil, Andrew J. Quinn, Mark W. Woolrich
We describe OHBA Software Library for the analysis of electrophysiology data (osl-ephys). This toolbox builds on top of the widely used MNE-Python package and provides unique analysis tools for magneto−/electro-encephalography (M/EEG) sensor and source space analysis, which can be used modularly. In particular, it…
Lucas S P Rudden, Samuel C Musson, Justin L P Benesch, Matteo T Degiacomi + 1 more
Models rationalizing sparse and low-resolution information on biomolecular structure, dynamics and interactions can provide key insight into biological function at the atomic level. Such models are generally produced by exploiting or combining collections of available molecular structures so as to recapitulate…
Laura E. Suárez, Agoston Mihalik, Filip Milisav, Kenji Marshall + 4 more
The connection patterns of neural circuits form a complex network. How signaling in these circuits manifests as complex cognition and adaptive behaviour remains the central question in neuroscience. Concomitant advances in connectomics and artificial intelligence open fundamentally new opportunities to understand how…
Márton Á Goda, Peter H Charlton, Joachim A Behar
Objective. Photoplethysmography is a non-invasive optical technique that measures changes in blood volume within tissues. It is commonly and being increasingly used for a variety of research and clinical applications to assess vascular dynamics and physiological parameters. Yet, contrary to heart rate variability…
Natalia Favila, David Madrigal-Trejo, Daniel Legorreta, Jazmín Sánchez-Pérez + 4 more
'Jazmín Sánchez-Pérez' 'Laura Espinosa-Asuar' 'Luis E. Eguiarte' 'Valeria Souza' 'Kazuhiro Takemoto'] Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper…
Jonathan B. Martin, Heng Sun, Madison Albert, Kevin M. Johnson + 1 more
We present PulPy (Pulses in Python), an extensive set of open-source, Python-based tools for magnetic resonance imaging (MRI) radiofrequency (RF) and gradient pulse design. PulPy is a Python package containing implementations of a wide range of commonly used RF and gradient pulse design tools. Our implemented functions…
Jens Lucht, Paul Meyer, Leon Merten Lohse, Tim Salditt + 1 more
We present HoToPy, a toolbox for X-ray holo-tomography in Python. It offers state-of-the-art phase retrieval methods for synchrotron and laboratory sources as well as tomographic reconstruction and alignment methods.
Haocheng Zhu, Ulrik Beierholm, Ladan Shams, Michael Moutoussis
Psychological and neuroscientific research over the past two decades has shown that the Bayesian causal inference (BCI) is a potential unifying theory that can account for a wide range of perceptual and sensorimotor processes in humans. Therefore, we introduce the BCI Toolbox, a statistical and analytical tool in…
William R. P. Nourse, Clayton Jackson, Nicholas S. Szczecinski, Roger D. Quinn + 2 more
'Roger D. Quinn' 'Mingguo Zhao' 'Biao Hu'] One developing approach for robotic control is the use of networks of dynamic neurons connected with conductance-based synapses, also known as Synthetic Nervous Systems (SNS). These networks are often developed using cyclic topologies and heterogeneous mixtures of spiking and…
Christoph Redies, Ralf Bartho, Lisa Koßmann, Branka Spehar + 3 more
'Ronald Hübner' 'Johan Wagemans' 'Gregor U. Hayn-Leichsenring'] Over the past two decades, researchers in the field of visual aesthetics have studied numerous quantitative (objective) image properties and how they relate to visual aesthetic appreciation. However, results are difficult to compare between research…
Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo + 7 more
'Marius van den Beek' 'Bérénice Batut' 'Helena Rasche' 'Martin Čech' 'Peter J.A. Cock' 'Björn Grüning' 'Anton Nekrutenko'] There are thousands of well-maintained high-quality open-source software utilities for all aspects of scientific data analysis. For more than a decade, the Galaxy Project has been providing…
Benjamin M. Gyori, Charles Tapley Hoyt
Understanding the complex molecular processes governing how cells respond to external stimuli crucially relies on prior knowledge about signaling, regulatory, and metabolic pathways. Standardized representations are necessary to exchange such pathway knowledge and allow interoperability between tools. BioPAX () is a…
Jan Janssen, Janine George, Julian Geiger, Marnik Bercx + 7 more
Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow…