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Johnsen KA, Cruzado NA, Menard ZC, Willats AA, Charles AS, Markowitz JE, Rozell CJ. Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.27.525963. [PMID: 39026717 PMCID: PMC11257437 DOI: 10.1101/2023.01.27.525963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Systems neuroscience has experienced an explosion of new tools for reading and writing neural activity, enabling exciting new experiments such as all-optical or closed-loop control that effect powerful causal interventions. At the same time, improved computational models are capable of reproducing behavior and neural activity with increasing fidelity. Unfortunately, these advances have drastically increased the complexity of integrating different lines of research, resulting in the missed opportunities and untapped potential of suboptimal experiments. Experiment simulation can help bridge this gap, allowing model and experiment to better inform each other by providing a low-cost testbed for experiment design, model validation, and methods engineering. Specifically, this can be achieved by incorporating the simulation of the experimental interface into our models, but no existing tool integrates optogenetics, two-photon calcium imaging, electrode recording, and flexible closed-loop processing with neural population simulations. To address this need, we have developed Cleo: the Closed-Loop, Electrophysiology, and Optophysiology experiment simulation testbed. Cleo is a Python package enabling injection of recording and stimulation devices as well as closed-loop control with realistic latency into a Brian spiking neural network model. It is the only publicly available tool currently supporting two-photon and multi-opsin/wavelength optogenetics. To facilitate adoption and extension by the community, Cleo is open-source, modular, tested, and documented, and can export results to various data formats. Here we describe the design and features of Cleo, validate output of individual components and integrated experiments, and demonstrate its utility for advancing optogenetic techniques in prospective experiments using previously published systems neuroscience models.
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Affiliation(s)
- Kyle A. Johnsen
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | | | - Zachary C. Menard
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Adam A. Willats
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Adam S. Charles
- Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey E. Markowitz
- Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
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2
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Köhler CA, Ulianych D, Grün S, Decker S, Denker M. Facilitating the Sharing of Electrophysiology Data Analysis Results Through In-Depth Provenance Capture. eNeuro 2024; 11:ENEURO.0476-23.2024. [PMID: 38777610 PMCID: PMC11181106 DOI: 10.1523/eneuro.0476-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/28/2024] [Accepted: 04/13/2024] [Indexed: 05/25/2024] Open
Abstract
Scientific research demands reproducibility and transparency, particularly in data-intensive fields like electrophysiology. Electrophysiology data are typically analyzed using scripts that generate output files, including figures. Handling these results poses several challenges due to the complexity and iterative nature of the analysis process. These stem from the difficulty to discern the analysis steps, parameters, and data flow from the results, making knowledge transfer and findability challenging in collaborative settings. Provenance information tracks data lineage and processes applied to it, and provenance capture during the execution of an analysis script can address those challenges. We present Alpaca (Automated Lightweight Provenance Capture), a tool that captures fine-grained provenance information with minimal user intervention when running data analysis pipelines implemented in Python scripts. Alpaca records inputs, outputs, and function parameters and structures information according to the W3C PROV standard. We demonstrate the tool using a realistic use case involving multichannel local field potential recordings of a neurophysiological experiment, highlighting how the tool makes result details known in a standardized manner in order to address the challenges of the analysis process. Ultimately, using Alpaca will help to represent results according to the FAIR principles, which will improve research reproducibility and facilitate sharing the results of data analyses.
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Affiliation(s)
- Cristiano A Köhler
- Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany
- Theoretical Systems Neurobiology, RWTH Aachen University, 52062 Aachen, Germany
| | - Danylo Ulianych
- Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany
| | - Sonja Grün
- Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany
- Theoretical Systems Neurobiology, RWTH Aachen University, 52062 Aachen, Germany
| | - Stefan Decker
- Chair of Databases and Information Systems, RWTH Aachen University, 52074 Aachen, Germany
- Fraunhofer Institute for Applied Information Technology (FIT), 53757 Sankt Augustin, Germany
| | - Michael Denker
- Institute for Advanced Simulation (IAS-6) and JARA Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany
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3
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Weydmann G, Palmieri I, Simões RAG, Centurion Cabral JC, Eckhardt J, Tavares P, Moro C, Alves P, Buchmann S, Schmidt E, Friedman R, Bizarro L. Switching to online: Testing the validity of supervised remote testing for online reinforcement learning experiments. Behav Res Methods 2023; 55:3645-3657. [PMID: 36220950 PMCID: PMC9552715 DOI: 10.3758/s13428-022-01982-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2022] [Indexed: 11/08/2022]
Abstract
Online experiments are an alternative for researchers interested in conducting behavioral research outside the laboratory. However, an online assessment might become a challenge when long and complex experiments need to be conducted in a specific order or with supervision from a researcher. The aim of this study was to test the computational validity and the feasibility of a remote and synchronous reinforcement learning (RL) experiment conducted during the social-distancing measures imposed by the pandemic. An additional feature of this study was to describe how a behavioral experiment originally created to be conducted in-person was transformed into an online supervised remote experiment. Open-source software was used to collect data, conduct statistical analysis, and do computational modeling. Python codes were created to replicate computational models that simulate the effect of working memory (WM) load over RL performance. Our behavioral results indicated that we were able to replicate remotely and with a modified behavioral task the effects of working memory (WM) load over RL performance observed in previous studies with in-person assessments. Our computational analyses using Python code also captured the effects of WM load over RL as expected, which suggests that the algorithms and optimization methods were reliable in their ability to reproduce behavior. The behavioral and computational validation shown in this study and the detailed description of the supervised remote testing may be useful for researchers interested in conducting long and complex experiments online.
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Affiliation(s)
- Gibson Weydmann
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
| | - Igor Palmieri
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Reinaldo A G Simões
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - João C Centurion Cabral
- Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande (FURG), Rio Grande, Brazil
| | - Joseane Eckhardt
- Programa de Pós-Graduação em Ciências Médicas: Endocrinologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Patrice Tavares
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Candice Moro
- Programa de Pós-Graduação em Ciências Médicas: Endocrinologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Paulina Alves
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Samara Buchmann
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Eduardo Schmidt
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Rogério Friedman
- Programa de Pós-Graduação em Ciências Médicas: Endocrinologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lisiane Bizarro
- Programa de Pós-Graduação em Psicologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
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4
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B C Girard C, Song D. Adaptive octree meshes for simulation of extracellular electrophysiology. J Neural Eng 2023; 20:056028. [PMID: 37722378 DOI: 10.1088/1741-2552/acfabf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/18/2023] [Indexed: 09/20/2023]
Abstract
Objective.The interaction between neural tissues and artificial electrodes is crucial for understanding and advancing neuroscientific research and therapeutic applications. However, accurately modeling this space around the neurons rapidly increases the computational complexity of neural simulations.Approach.This study demonstrates a dynamically adaptive simulation method that greatly accelerates computation by adjusting spatial resolution of the simulation as needed. Use of an octree structure for the mesh, in combination with the admittance method for discretizing conductivity, provides both accurate approximation and ease of modification on-the-fly.Main results.In tests of both local field potential estimation and multi-electrode stimulation, dynamically adapted meshes achieve accuracy comparable to high-resolution static meshes in an order of magnitude less time.Significance.The proposed simulation pipeline improves model scalability, allowing greater detail with fewer computational resources. The implementation is available as an open-source Python module, providing flexibility and ease of reuse for the broader research community.
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Affiliation(s)
- Christopher B C Girard
- Fowler School of Engineering, Chapman University, Orange, CA, United States of America
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States of America
| | - Dong Song
- Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States of America
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, United States of America
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Mischler G, Raghavan V, Keshishian M, Mesgarani N. naplib-python: Neural Acoustic Data Processing and Analysis Tools in Python. ARXIV 2023:arXiv:2304.01799v1. [PMID: 37064534 PMCID: PMC10104195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Recently, the computational neuroscience community has pushed for more transparent and reproducible methods across the field. In the interest of unifying the domain of auditory neuroscience, naplib-python provides an intuitive and general data structure for handling all neural recordings and stimuli, as well as extensive preprocessing, feature extraction, and analysis tools which operate on that data structure. The package removes many of the complications associated with this domain, such as varying trial durations and multi-modal stimuli, and provides a general-purpose analysis framework that interfaces easily with existing toolboxes used in the field.
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Affiliation(s)
- Gavin Mischler
- Mortimer B. Zuckerman Mind Brain Behavior, Columbia University, New York, United States
- Department of Electrical Engineering, Columbia University, New York, United States
| | - Vinay Raghavan
- Mortimer B. Zuckerman Mind Brain Behavior, Columbia University, New York, United States
- Department of Electrical Engineering, Columbia University, New York, United States
| | - Menoua Keshishian
- Mortimer B. Zuckerman Mind Brain Behavior, Columbia University, New York, United States
- Department of Electrical Engineering, Columbia University, New York, United States
| | - Nima Mesgarani
- Mortimer B. Zuckerman Mind Brain Behavior, Columbia University, New York, United States
- Department of Electrical Engineering, Columbia University, New York, United States
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6
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Aimone JB, Awile O, Diesmann M, Knight JC, Nowotny T, Schürmann F. Editorial: Neuroscience, computing, performance, and benchmarks: Why it matters to neuroscience how fast we can compute. Front Neuroinform 2023; 17:1157418. [PMID: 37064716 PMCID: PMC10098318 DOI: 10.3389/fninf.2023.1157418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Affiliation(s)
- James B. Aimone
- Neural Exploration and Research Laboratory, Center for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States
| | - Omar Awile
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
| | - Markus Diesmann
- Institute of Neuroscience and Medicine and Institute for Advanced Simulation and JARA-Institute Brain Structure-Function Relationships, Jülich Research Centre, Jülich, Germany
- Department of Physics, Faculty 1, RWTH Aachen University, Aachen, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, School of Medicine, RWTH Aachen University, Aachen, Germany
| | - James C. Knight
- School of Engineering and Informatics, University of Sussex, Brighton, United Kingdom
| | - Thomas Nowotny
- School of Engineering and Informatics, University of Sussex, Brighton, United Kingdom
| | - Felix Schürmann
- Blue Brain Project, École Polytechnique Fédérale de Lausanne, Geneva, Switzerland
- *Correspondence: Felix Schürmann
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7
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Connectivity concepts in neuronal network modeling. PLoS Comput Biol 2022; 18:e1010086. [PMID: 36074778 PMCID: PMC9455883 DOI: 10.1371/journal.pcbi.1010086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 04/07/2022] [Indexed: 11/19/2022] Open
Abstract
Sustainable research on computational models of neuronal networks requires published models to be understandable, reproducible, and extendable. Missing details or ambiguities about mathematical concepts and assumptions, algorithmic implementations, or parameterizations hinder progress. Such flaws are unfortunately frequent and one reason is a lack of readily applicable standards and tools for model description. Our work aims to advance complete and concise descriptions of network connectivity but also to guide the implementation of connection routines in simulation software and neuromorphic hardware systems. We first review models made available by the computational neuroscience community in the repositories ModelDB and Open Source Brain, and investigate the corresponding connectivity structures and their descriptions in both manuscript and code. The review comprises the connectivity of networks with diverse levels of neuroanatomical detail and exposes how connectivity is abstracted in existing description languages and simulator interfaces. We find that a substantial proportion of the published descriptions of connectivity is ambiguous. Based on this review, we derive a set of connectivity concepts for deterministically and probabilistically connected networks and also address networks embedded in metric space. Beside these mathematical and textual guidelines, we propose a unified graphical notation for network diagrams to facilitate an intuitive understanding of network properties. Examples of representative network models demonstrate the practical use of the ideas. We hope that the proposed standardizations will contribute to unambiguous descriptions and reproducible implementations of neuronal network connectivity in computational neuroscience.
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8
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Awile O, Kumbhar P, Cornu N, Dura-Bernal S, King JG, Lupton O, Magkanaris I, McDougal RA, Newton AJH, Pereira F, Săvulescu A, Carnevale NT, Lytton WW, Hines ML, Schürmann F. Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. Front Neuroinform 2022; 16:884046. [PMID: 35832575 PMCID: PMC9272742 DOI: 10.3389/fninf.2022.884046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/26/2022] [Indexed: 12/25/2022] Open
Abstract
The need for reproducible, credible, multiscale biological modeling has led to the development of standardized simulation platforms, such as the widely-used NEURON environment for computational neuroscience. Developing and maintaining NEURON over several decades has required attention to the competing needs of backwards compatibility, evolving computer architectures, the addition of new scales and physical processes, accessibility to new users, and efficiency and flexibility for specialists. In order to meet these challenges, we have now substantially modernized NEURON, providing continuous integration, an improved build system and release workflow, and better documentation. With the help of a new source-to-source compiler of the NMODL domain-specific language we have enhanced NEURON's ability to run efficiently, via the CoreNEURON simulation engine, on a variety of hardware platforms, including GPUs. Through the implementation of an optimized in-memory transfer mechanism this performance optimized backend is made easily accessible to users, providing training and model-development paths from laptop to workstation to supercomputer and cloud platform. Similarly, we have been able to accelerate NEURON's reaction-diffusion simulation performance through the use of just-in-time compilation. We show that these efforts have led to a growing developer base, a simpler and more robust software distribution, a wider range of supported computer architectures, a better integration of NEURON with other scientific workflows, and substantially improved performance for the simulation of biophysical and biochemical models.
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Affiliation(s)
- Omar Awile
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Pramod Kumbhar
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Nicolas Cornu
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Salvador Dura-Bernal
- Department Physiology and Pharmacology, SUNY Downstate, Brooklyn, NY, United States
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, United States
| | - James Gonzalo King
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Olli Lupton
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Ioannis Magkanaris
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Robert A. McDougal
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, United States
- Yale Center for Medical Informatics, Yale University, New Haven, CT, United States
| | - Adam J. H. Newton
- Department Physiology and Pharmacology, SUNY Downstate, Brooklyn, NY, United States
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Fernando Pereira
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | - Alexandru Săvulescu
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
| | | | - William W. Lytton
- Center for Biomedical Imaging and Neuromodulation, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, United States
| | - Michael L. Hines
- Department of Neuroscience, Yale University, New Haven, CT, United States
| | - Felix Schürmann
- Blue Brain Project, École Polytechnique Fédérale de Lausanne (EPFL), Geneva, Switzerland
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9
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Juavinett AL. The next generation of neuroscientists needs to learn how to code, and we need new ways to teach them. Neuron 2021; 110:576-578. [PMID: 35016038 DOI: 10.1016/j.neuron.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Abstract
Neuroscience education is at an impasse-we need to teach students coding, but many institutions do not have the resources to do so. Here, I outline three major barriers, as well as solutions, to bringing programming education into our undergraduate and graduate programs.
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Affiliation(s)
- Ashley L Juavinett
- Division of Biological Sciences, Neurobiology Section, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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10
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Arvin S, Rasmussen RN, Yonehara K. EyeLoop: An Open-Source System for High-Speed, Closed-Loop Eye-Tracking. Front Cell Neurosci 2021; 15:779628. [PMID: 34955752 PMCID: PMC8696164 DOI: 10.3389/fncel.2021.779628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
Eye-trackers are widely used to study nervous system dynamics and neuropathology. Despite this broad utility, eye-tracking remains expensive, hardware-intensive, and proprietary, limiting its use to high-resource facilities. It also does not easily allow for real-time analysis and closed-loop design to link eye movements to neural activity. To address these issues, we developed an open-source eye-tracker – EyeLoop – that uses a highly efficient vectorized pupil detection method to provide uninterrupted tracking and fast online analysis with high accuracy on par with popular eye tracking modules, such as DeepLabCut. This Python-based software easily integrates custom functions using code modules, tracks a multitude of eyes, including in rodents, humans, and non-human primates, and operates at more than 1,000 frames per second on consumer-grade hardware. In this paper, we demonstrate EyeLoop’s utility in an open-loop experiment and in biomedical disease identification, two common applications of eye-tracking. With a remarkably low cost and minimum setup steps, EyeLoop makes high-speed eye-tracking widely accessible.
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Affiliation(s)
- Simon Arvin
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Rune Nguyen Rasmussen
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Keisuke Yonehara
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark.,Multiscale Sensory Structure Laboratory, National Institute of Genetics, Mishima, Japan.,Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
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11
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Ho YY, Roeser A, Law G, Johnson BR. Pandemic Teaching: Using the Allen Cell Types Database for Final Semester Projects in an Undergraduate Neurophysiology Lab Course. JOURNAL OF UNDERGRADUATE NEUROSCIENCE EDUCATION : JUNE : A PUBLICATION OF FUN, FACULTY FOR UNDERGRADUATE NEUROSCIENCE 2021; 20:A100-A110. [PMID: 35540944 PMCID: PMC9053425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/05/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
We designed a final semester research project that allowed students to apply the electrophysiological concepts they learned in a lab course to propose and answer experimental questions without access to laboratory equipment. We created the activity based on lesson plans from Ashley Juavinett and the Allen Institute for Brain Science (AIBS) Allen SDK online examples. An interactive graphic interface was added for students to explore and easily quantify subtle neuronal voltage changes. Before starting the final project, students had experience with conventional extracellular and intracellular recording techniques to record and analyze extracellular action potential firing patterns and intracellular resting, action, and synaptic potentials. They demonstrated their understanding of neural signal transmission in required lab reports using data they gathered before the pandemic shutdown. After students left campus, they continued to analyze data and write lab reports focused on neuronal excitability in snail and fly neurons with data supplied by the instructors. For their final project, students were challenged to answer questions addressing neuronal excitability at both the single neuron and neuronal population level by analyzing and interpreting the open-access, patch clamp recording data from the Allen Cell Types Database using code we provided (Python/Jupyter Notebook). This virtual final semester project allowed students to ask real-world medical and scientific questions from "start to end". Through this project, students developed skills to navigate an extensive online database and gained experience with coding-based data analysis. They chose neuronal populations from human and mouse brains to compare passive properties and neuronal excitability between and within brain areas and across different species and disease states. Additionally, students learned to do simple manipulations of Python code, work remotely in teams, and polish their written scientific presentation skills. This activity could complement other remote learning options such as neuronal simulations. Few online sources offer such a wealth of neuroscience data that students can use for class assignments, and even for research and keystone projects. The activity extends the traditional material often taught in upper-level neuroscience courses, with or without a laboratory section, providing a deeper understanding of the range of excitability properties that neurons express.
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Affiliation(s)
- Yi-Yun Ho
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853
| | - Andrea Roeser
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853
| | - Gwenda Law
- Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853
| | - Bruce R. Johnson
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853
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12
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Tejada J, Freitag RMK, Pinheiro BFM, Cardoso PB, Souza VRA, Silva LS. Building and validation of a set of facial expression images to detect emotions: a transcultural study. PSYCHOLOGICAL RESEARCH 2021; 86:1996-2006. [PMID: 34652530 DOI: 10.1007/s00426-021-01605-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 09/28/2021] [Indexed: 11/26/2022]
Abstract
The automatic emotion recognition from facial expressions has become an exceptional tool in research involving human subjects and has made it possible to obtain objective measurements of the emotional state of research subjects. Different software and commercial solutions are offered to perform this task. However, the adaptation to cultural context and the recognition of complex expressions and/or emotions are two of the main challenges faced by these solutions. Here, we describe the construction and validation of a set of facial expression images suitable for training a recognition system. Our datasets consist of images of people with no experience in acting who were recorded with a webcam as they performed a computer-assisted task in a room with a light background and overhead illumination. The six basic emotions and mockery were included and a combination of OpenCV, Dlib and Scikit-learn Python libraries were used to develop a support vector machine classifier. The code is available at GitHub and the images will be provided upon request. Since transcultural facial expressions to evaluate complex emotions and open-source solutions were used in this study, we strongly believe that our dataset will be useful in different research contexts.
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Affiliation(s)
- Julian Tejada
- Departamento de Psicologia, Universidade Federal de Sergipe, São Cristóvão, Brazil.
- Facultad de Psicología, Fundación Universitaria Konrad Lorenz, Bogotá, Colombia.
| | | | | | | | | | - Lucas Santos Silva
- Departamento de Letras, Universidade Federal de Sergipe, São Cristóvão, Brazil
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13
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Sharing an Open Stimulation System for Auditory EEG Experiments Using Python, Raspberry Pi, and HifiBerry. eNeuro 2021; 8:ENEURO.0524-20.2021. [PMID: 34301720 PMCID: PMC8387158 DOI: 10.1523/eneuro.0524-20.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 06/10/2021] [Accepted: 07/16/2021] [Indexed: 11/21/2022] Open
Abstract
In auditory behavioral and EEG experiments, the variability of stimulation solutions, for both software and hardware, adds unnecessary technical constraints. Currently, there is no easy to use, inexpensive, and shareable solution that could improve collaborations and data comparisons across different sites and contexts. This article outlines a system composed by a Raspberry Pi coupled with Python programming and associated with a HifiBerry sound card. We compare its sound performances with those of a wide variety of materials and configurations. This solution achieves the high timing accuracy and sound quality important in auditory cognition experiments, while being simple to use and open source. The present system shows high performances and results along with excellent feedback from users. It is inexpensive, easy to build, share, and improve on. Working with such low-cost, powerful, and collaborative hardware and software tools allows people to create their own specific, adapted, and shareable system that can be standardized across different collaborative sites, while being extremely simple and robust in use.
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14
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Accuracy and precision of visual and auditory stimulus presentation in virtual reality in Python 2 and 3 environments for human behavior research. Behav Res Methods 2021; 54:729-751. [PMID: 34346042 PMCID: PMC9046309 DOI: 10.3758/s13428-021-01663-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2021] [Indexed: 11/08/2022]
Abstract
Virtual reality (VR) is a new methodology for behavioral studies. In such studies, the millisecond accuracy and precision of stimulus presentation are critical for data replicability. Recently, Python, which is a widely used programming language for scientific research, has contributed to reliable accuracy and precision in experimental control. However, little is known about whether modern VR environments have millisecond accuracy and precision for stimulus presentation, since most standard methods in laboratory studies are not optimized for VR environments. The purpose of this study was to systematically evaluate the accuracy and precision of visual and auditory stimuli generated in modern VR head-mounted displays (HMDs) from HTC and Oculus using Python 2 and 3. We used the newest Python tools for VR and Black Box Toolkit to measure the actual time lag and jitter. The results showed that there was an 18-ms time lag for visual stimulus in both HMDs. For the auditory stimulus, the time lag varied between 40 and 60 ms, depending on the HMD. The jitters of those time lags were 1 ms for visual stimulus and 4 ms for auditory stimulus, which are sufficiently low for general experiments. These time lags were robustly equal, even when auditory and visual stimuli were presented simultaneously. Interestingly, all results were perfectly consistent in both Python 2 and 3 environments. Thus, the present study will help establish a more reliable stimulus control for psychological and neuroscientific research controlled by Python environments.
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15
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Stapmanns J, Hahne J, Helias M, Bolten M, Diesmann M, Dahmen D. Event-Based Update of Synapses in Voltage-Based Learning Rules. Front Neuroinform 2021; 15:609147. [PMID: 34177505 PMCID: PMC8222618 DOI: 10.3389/fninf.2021.609147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
Due to the point-like nature of neuronal spiking, efficient neural network simulators often employ event-based simulation schemes for synapses. Yet many types of synaptic plasticity rely on the membrane potential of the postsynaptic cell as a third factor in addition to pre- and postsynaptic spike times. In some learning rules membrane potentials not only influence synaptic weight changes at the time points of spike events but in a continuous manner. In these cases, synapses therefore require information on the full time course of membrane potentials to update their strength which a priori suggests a continuous update in a time-driven manner. The latter hinders scaling of simulations to realistic cortical network sizes and relevant time scales for learning. Here, we derive two efficient algorithms for archiving postsynaptic membrane potentials, both compatible with modern simulation engines based on event-based synapse updates. We theoretically contrast the two algorithms with a time-driven synapse update scheme to analyze advantages in terms of memory and computations. We further present a reference implementation in the spiking neural network simulator NEST for two prototypical voltage-based plasticity rules: the Clopath rule and the Urbanczik-Senn rule. For both rules, the two event-based algorithms significantly outperform the time-driven scheme. Depending on the amount of data to be stored for plasticity, which heavily differs between the rules, a strong performance increase can be achieved by compressing or sampling of information on membrane potentials. Our results on computational efficiency related to archiving of information provide guidelines for the design of learning rules in order to make them practically usable in large-scale networks.
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Affiliation(s)
- Jonas Stapmanns
- Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA Institute Brain Structure Function Relationship (INM-10), Jülich Research Centre, Jülich, Germany
- Department of Physics, Institute for Theoretical Solid State Physics, RWTH Aachen University, Aachen, Germany
| | - Jan Hahne
- School of Mathematics and Natural Sciences, Bergische Universität Wuppertal, Wuppertal, Germany
| | - Moritz Helias
- Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA Institute Brain Structure Function Relationship (INM-10), Jülich Research Centre, Jülich, Germany
- Department of Physics, Institute for Theoretical Solid State Physics, RWTH Aachen University, Aachen, Germany
| | - Matthias Bolten
- School of Mathematics and Natural Sciences, Bergische Universität Wuppertal, Wuppertal, Germany
| | - Markus Diesmann
- Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA Institute Brain Structure Function Relationship (INM-10), Jülich Research Centre, Jülich, Germany
- Department of Physics, Faculty 1, RWTH Aachen University, Aachen, Germany
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - David Dahmen
- Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA Institute Brain Structure Function Relationship (INM-10), Jülich Research Centre, Jülich, Germany
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16
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Claudi F, Tyson AL, Petrucco L, Margrie TW, Portugues R, Branco T. Visualizing anatomically registered data with brainrender. eLife 2021; 10:e65751. [PMID: 33739286 PMCID: PMC8079143 DOI: 10.7554/elife.65751] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/17/2021] [Indexed: 11/13/2022] Open
Abstract
Three-dimensional (3D) digital brain atlases and high-throughput brain-wide imaging techniques generate large multidimensional datasets that can be registered to a common reference frame. Generating insights from such datasets depends critically on visualization and interactive data exploration, but this a challenging task. Currently available software is dedicated to single atlases, model species or data types, and generating 3D renderings that merge anatomically registered data from diverse sources requires extensive development and programming skills. Here, we present brainrender: an open-source Python package for interactive visualization of multidimensional datasets registered to brain atlases. Brainrender facilitates the creation of complex renderings with different data types in the same visualization and enables seamless use of different atlas sources. High-quality visualizations can be used interactively and exported as high-resolution figures and animated videos. By facilitating the visualization of anatomically registered data, brainrender should accelerate the analysis, interpretation, and dissemination of brain-wide multidimensional data.
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Affiliation(s)
| | - Adam L Tyson
- UCL Sainsbury Wellcome CentreLondonUnited Kingdom
| | - Luigi Petrucco
- Institute of Neuroscience, Technical University of MunichMunichGermany
- Max Planck Institute of Neurobiology, Research Group of Sensorimotor ControlMartinsriedGermany
| | | | - Ruben Portugues
- Institute of Neuroscience, Technical University of MunichMunichGermany
- Max Planck Institute of Neurobiology, Research Group of Sensorimotor ControlMartinsriedGermany
- Munich Cluster for Systems Neurology (SyNergy)MunichGermany
| | - Tiago Branco
- UCL Sainsbury Wellcome CentreLondonUnited Kingdom
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17
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Buccino AP, Hurwitz CL, Garcia S, Magland J, Siegle JH, Hurwitz R, Hennig MH. SpikeInterface, a unified framework for spike sorting. eLife 2020; 9:e61834. [PMID: 33170122 PMCID: PMC7704107 DOI: 10.7554/elife.61834] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Much development has been directed toward improving the performance and automation of spike sorting. This continuous development, while essential, has contributed to an over-saturation of new, incompatible tools that hinders rigorous benchmarking and complicates reproducible analysis. To address these limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sorting technologies into a single codebase and to facilitate straightforward comparison and adoption of different approaches. With a few lines of code, researchers can reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs; and more. In this paper, we provide an overview of SpikeInterface and, with applications to real and simulated datasets, demonstrate how it can be utilized to reduce the burden of manual curation and to more comprehensively benchmark automated spike sorters.
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Affiliation(s)
- Alessio P Buccino
- Department of Biosystems Science and Engineering, ETH ZurichZürichSwitzerland
- Centre for Integrative Neuroplasticity (CINPLA), University of OsloOsloNorway
| | - Cole L Hurwitz
- School of Informatics, University of EdinburghEdinburghUnited Kingdom
| | - Samuel Garcia
- Centre de Recherche en Neuroscience de Lyon, CNRSLyonFrance
| | | | | | | | - Matthias H Hennig
- School of Informatics, University of EdinburghEdinburghUnited Kingdom
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18
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Ježek P, Teeters JL, Sommer FT. NWB Query Engines: Tools to Search Data Stored in Neurodata Without Borders Format. Front Neuroinform 2020; 14:27. [PMID: 33041776 PMCID: PMC7526650 DOI: 10.3389/fninf.2020.00027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/20/2020] [Indexed: 11/19/2022] Open
Abstract
The Neurodata Without Borders (abbreviation NWB) format is a current technology for storing neurophysiology data along with the associated metadata. Data stored in the format is organized into separate HDF5 files, each file usually storing the data associated with a single recording session. While the NWB format provides a structured method for storing data, so far there have not been tools which enable searching a collection of NWB files in order to find data of interest for a particular purpose. We describe here three tools to enable searching NWB files. The tools have different features making each of them most useful for a particular task. The first tool, called the NWB Query Engine, is written in Java. It allows searching the complete content of NWB files. It was designed for the first version of NWB (NWB 1) and supports most (but not all) features of the most recent version (NWB 2). For some searches, it is the fastest tool. The second tool, called “search_nwb” is written in Python and also allow searching the complete contents of NWB files. It works with both NWB 1 and NWB 2, as does the third tool. The third tool, called “nwbindexer” enables searching a collection of NWB files using a two-step process. In the first step, a utility is run which creates an SQLite database containing the metadata in a collection of NWB files. This database is then searched in the second step, using another utility. Once the index is built, this two-step processes allows faster searches than are done by the other tools, but does not enable as complete of searches. All three tools use a simple query language which was developed for this project. Software integrating the three tools into a web-interface is provided which enables searching NWB files by submitting a web form.
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Affiliation(s)
- Petr Ježek
- Faculty of Applied Sciences, New Technologies for the Information Society, University of West Bohemia, Plzeň, Czechia
| | - Jeffery L Teeters
- Redwood Center for Theoretical Neuroscience & Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Friedrich T Sommer
- Redwood Center for Theoretical Neuroscience & Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States
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19
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MacInnes JJ, Adcock RA, Stocco A, Prat CS, Rao RPN, Dickerson KC. Pyneal: Open Source Real-Time fMRI Software. Front Neurosci 2020; 14:900. [PMID: 33041750 PMCID: PMC7522368 DOI: 10.3389/fnins.2020.00900] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/03/2020] [Indexed: 11/13/2022] Open
Abstract
Increasingly, neuroimaging researchers are exploring the use of real-time functional magnetic resonance imaging (rt-fMRI) as a way to access a participant's ongoing brain function throughout a scan. This approach presents novel and exciting experimental applications ranging from monitoring data quality in real time, to delivering neurofeedback from a region of interest, to dynamically controlling experimental flow, or interfacing with remote devices. Yet, for those interested in adopting this method, the existing software options are few and limited in application. This presents a barrier for new users, as well as hinders existing users from refining techniques and methods. Here we introduce a free, open-source rt-fMRI package, the Pyneal toolkit, designed to address this limitation. The Pyneal toolkit is python-based software that offers a flexible and user friendly framework for rt-fMRI, is compatible with all three major scanner manufacturers (GE, Siemens, Phillips), and, critically, allows fully customized analysis pipelines. In this article, we provide a detailed overview of the architecture, describe how to set up and run the Pyneal toolkit during an experimental session, offer tutorials with scan data that demonstrate how data flows through the Pyneal toolkit with example analyses, and highlight the advantages that the Pyneal toolkit offers to the neuroimaging community.
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Affiliation(s)
- Jeff J MacInnes
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, United States
| | - R Alison Adcock
- Department of Psychiatry and Behavioral Sciences, Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Duke University, Durham, NC, United States
| | - Andrea Stocco
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, United States.,Department of Psychology, University of Washington, Seattle, WA, United States
| | - Chantel S Prat
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, United States.,Department of Psychology, University of Washington, Seattle, WA, United States
| | - Rajesh P N Rao
- Department of Computer Science and Engineering, Center for Neurotechnology, University of Washington, Seattle, WA, United States
| | - Kathryn C Dickerson
- Department of Psychiatry and Behavioral Sciences, Center for Cognitive Neuroscience, Duke Institute for Brain Sciences, Duke University, Durham, NC, United States
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20
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Carvalho VR, Moraes MF, Braga AP, Mendes EM. Evaluating five different adaptive decomposition methods for EEG signal seizure detection and classification. Biomed Signal Process Control 2020. [DOI: 10.1016/j.bspc.2020.102073] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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21
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Széll A, Martínez-Bellver S, Hegedüs P, Hangya B. OPETH: Open Source Solution for Real-Time Peri-Event Time Histogram Based on Open Ephys. Front Neuroinform 2020; 14:21. [PMID: 32508613 PMCID: PMC7251067 DOI: 10.3389/fninf.2020.00021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/17/2020] [Indexed: 12/22/2022] Open
Abstract
Single cell electrophysiology remains one of the most widely used approaches of systems neuroscience. Decisions made by the experimenter during electrophysiology recording largely determine recording quality, duration of the project and value of the collected data. Therefore, online feedback aiding these decisions can lower monetary and time investment, and substantially speed up projects as well as allow novel studies otherwise not possible due to prohibitively low throughput. Real-time feedback is especially important in studies that involve optogenetic cell type identification by enabling a systematic search for neurons of interest. However, such tools are scarce and limited to costly commercial systems with high degree of specialization, which hitherto prevented wide-ranging benefits for the community. To address this, we present an open-source tool that enables online feedback during electrophysiology experiments and provides a Python interface for the widely used Open Ephys open source data acquisition system. Specifically, our software allows flexible online visualization of spike alignment to external events, called the online peri-event time histogram (OPETH). These external events, conveyed by digital logic signals, may indicate photostimulation time stamps for in vivo optogenetic cell type identification or the times of behaviorally relevant events during in vivo behavioral neurophysiology experiments. Therefore, OPETH allows real-time identification of genetically defined neuron types or behaviorally responsive populations. By allowing "hunting" for neurons of interest, OPETH significantly reduces experiment time and thus increases the efficiency of experiments that combine in vivo electrophysiology with behavior or optogenetic tagging of neurons.
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Affiliation(s)
- András Széll
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
| | - Sergio Martínez-Bellver
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
- Laboratory of Neural Circuitry, Faculty of Medicine and Dentistry, University of Valencia, Valencia, Spain
| | - Panna Hegedüs
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
- János Szentágothai Doctoral School of Neurosciences, Semmelweis University, Budapest, Hungary
| | - Balázs Hangya
- Lendület Laboratory of Systems Neuroscience, Institute of Experimental Medicine, Budapest, Hungary
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22
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Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, Polat İ, Feng Y, Moore EW, VanderPlas J, Laxalde D, Perktold J, Cimrman R, Henriksen I, Quintero EA, Harris CR, Archibald AM, Ribeiro AH, Pedregosa F, van Mulbregt P. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods 2020; 17:261-272. [PMID: 32015543 PMCID: PMC7056644 DOI: 10.1038/s41592-019-0686-2] [Citation(s) in RCA: 6975] [Impact Index Per Article: 1743.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/09/2019] [Accepted: 11/14/2019] [Indexed: 11/28/2022]
Abstract
SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.
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Affiliation(s)
| | | | - Travis E Oliphant
- Quansight LLC, Austin, TX, USA
- Ultrasound Imaging, Mayo Clinic, Rochester, MN, USA
- Electrical Engineering, Brigham Young University, Provo, UT, USA
- Enthought, Inc., Austin, TX, USA
- Anaconda Inc., Austin, TX, USA
| | - Matt Haberland
- BioResource and Agricultural Engineering Department, California Polytechnic State University, San Luis Obispo, CA, USA.
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA, USA.
| | - Tyler Reddy
- Los Alamos National Laboratory, Los Alamos, NM, USA.
| | | | - Evgeni Burovski
- National Research University Higher School of Economics, Moscow, Russia
| | - Pearu Peterson
- Independent researcher, Saue, Estonia
- Department of Mechanics and Applied Mathematics, Institute of Cybernetics at Tallinn Technical University, Tallinn, Estonia
| | - Warren Weckesser
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Stéfan J van der Walt
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
| | - Matthew Brett
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - K Jarrod Millman
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
- Division of Biostatistics, University of California Berkeley, Berkeley, CA, USA
| | | | - Andrew R J Nelson
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | | | | | - Eric Larson
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA
| | - C J Carey
- College of Information and Computing Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - İlhan Polat
- Independent researcher, Amsterdam, the Netherlands
| | - Yu Feng
- Berkeley Center for Cosmological Physics, University of California Berkeley, Berkeley, CA, USA
| | | | | | | | | | - Robert Cimrman
- New Technologies Research Centre, University of West Bohemia, Plzeň, Czech Republic
| | - Ian Henriksen
- Anaconda Inc., Austin, TX, USA
- Department of Mathematics, Brigham Young University, Provo, UT, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - E A Quintero
- Independent researcher, Belmont, Massachusetts, USA
| | - Charles R Harris
- Space Dynamics Laboratory, North Logan, UT, USA
- Independent researcher, Logan, Utah, USA
| | | | - Antônio H Ribeiro
- Graduate Program in Electrical Engineering, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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23
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Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, Polat İ, Feng Y, Moore EW, VanderPlas J, Laxalde D, Perktold J, Cimrman R, Henriksen I, Quintero EA, Harris CR, Archibald AM, Ribeiro AH, Pedregosa F, van Mulbregt P. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods 2020. [PMID: 32015543 DOI: 10.1038/s41592-019–0686-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.
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Affiliation(s)
| | | | - Travis E Oliphant
- Quansight LLC, Austin, TX, USA
- Ultrasound Imaging, Mayo Clinic, Rochester, MN, USA
- Electrical Engineering, Brigham Young University, Provo, UT, USA
- Enthought, Inc., Austin, TX, USA
- Anaconda Inc., Austin, TX, USA
| | - Matt Haberland
- BioResource and Agricultural Engineering Department, California Polytechnic State University, San Luis Obispo, CA, USA.
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA, USA.
| | - Tyler Reddy
- Los Alamos National Laboratory, Los Alamos, NM, USA.
| | | | - Evgeni Burovski
- National Research University Higher School of Economics, Moscow, Russia
| | - Pearu Peterson
- Independent researcher, Saue, Estonia
- Department of Mechanics and Applied Mathematics, Institute of Cybernetics at Tallinn Technical University, Tallinn, Estonia
| | - Warren Weckesser
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Stéfan J van der Walt
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
| | - Matthew Brett
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - K Jarrod Millman
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
- Division of Biostatistics, University of California Berkeley, Berkeley, CA, USA
| | | | - Andrew R J Nelson
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | | | | | - Eric Larson
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA
| | - C J Carey
- College of Information and Computing Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - İlhan Polat
- Independent researcher, Amsterdam, the Netherlands
| | - Yu Feng
- Berkeley Center for Cosmological Physics, University of California Berkeley, Berkeley, CA, USA
| | | | | | | | | | - Robert Cimrman
- New Technologies Research Centre, University of West Bohemia, Plzeň, Czech Republic
| | - Ian Henriksen
- Anaconda Inc., Austin, TX, USA
- Department of Mathematics, Brigham Young University, Provo, UT, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - E A Quintero
- Independent researcher, Belmont, Massachusetts, USA
| | - Charles R Harris
- Space Dynamics Laboratory, North Logan, UT, USA
- Independent researcher, Logan, Utah, USA
| | | | - Antônio H Ribeiro
- Graduate Program in Electrical Engineering, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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24
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Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, van der Walt SJ, Brett M, Wilson J, Millman KJ, Mayorov N, Nelson ARJ, Jones E, Kern R, Larson E, Carey CJ, Polat İ, Feng Y, Moore EW, VanderPlas J, Laxalde D, Perktold J, Cimrman R, Henriksen I, Quintero EA, Harris CR, Archibald AM, Ribeiro AH, Pedregosa F, van Mulbregt P. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods 2020. [PMID: 32015543 DOI: 10.1017/9781108778039.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.
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Affiliation(s)
| | | | - Travis E Oliphant
- Quansight LLC, Austin, TX, USA
- Ultrasound Imaging, Mayo Clinic, Rochester, MN, USA
- Electrical Engineering, Brigham Young University, Provo, UT, USA
- Enthought, Inc., Austin, TX, USA
- Anaconda Inc., Austin, TX, USA
| | - Matt Haberland
- BioResource and Agricultural Engineering Department, California Polytechnic State University, San Luis Obispo, CA, USA.
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA, USA.
| | - Tyler Reddy
- Los Alamos National Laboratory, Los Alamos, NM, USA.
| | | | - Evgeni Burovski
- National Research University Higher School of Economics, Moscow, Russia
| | - Pearu Peterson
- Independent researcher, Saue, Estonia
- Department of Mechanics and Applied Mathematics, Institute of Cybernetics at Tallinn Technical University, Tallinn, Estonia
| | - Warren Weckesser
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Stéfan J van der Walt
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
| | - Matthew Brett
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
| | | | - K Jarrod Millman
- Berkeley Institute for Data Science, University of California Berkeley, Berkeley, CA, USA
- Division of Biostatistics, University of California Berkeley, Berkeley, CA, USA
| | | | - Andrew R J Nelson
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW, Australia
| | | | | | - Eric Larson
- Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA
| | - C J Carey
- College of Information and Computing Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - İlhan Polat
- Independent researcher, Amsterdam, the Netherlands
| | - Yu Feng
- Berkeley Center for Cosmological Physics, University of California Berkeley, Berkeley, CA, USA
| | | | | | | | | | - Robert Cimrman
- New Technologies Research Centre, University of West Bohemia, Plzeň, Czech Republic
| | - Ian Henriksen
- Anaconda Inc., Austin, TX, USA
- Department of Mathematics, Brigham Young University, Provo, UT, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX, USA
| | - E A Quintero
- Independent researcher, Belmont, Massachusetts, USA
| | - Charles R Harris
- Space Dynamics Laboratory, North Logan, UT, USA
- Independent researcher, Logan, Utah, USA
| | | | - Antônio H Ribeiro
- Graduate Program in Electrical Engineering, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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25
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Stimberg M, Brette R, Goodman DFM. Brian 2, an intuitive and efficient neural simulator. eLife 2019; 8:e47314. [PMID: 31429824 PMCID: PMC6786860 DOI: 10.7554/elife.47314] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/19/2019] [Indexed: 01/20/2023] Open
Abstract
Brian 2 allows scientists to simply and efficiently simulate spiking neural network models. These models can feature novel dynamical equations, their interactions with the environment, and experimental protocols. To preserve high performance when defining new models, most simulators offer two options: low-level programming or description languages. The first option requires expertise, is prone to errors, and is problematic for reproducibility. The second option cannot describe all aspects of a computational experiment, such as the potentially complex logic of a stimulation protocol. Brian addresses these issues using runtime code generation. Scientists write code with simple and concise high-level descriptions, and Brian transforms them into efficient low-level code that can run interleaved with their code. We illustrate this with several challenging examples: a plastic model of the pyloric network, a closed-loop sensorimotor model, a programmatic exploration of a neuron model, and an auditory model with real-time input.
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Affiliation(s)
- Marcel Stimberg
- Sorbonne Université, INSERM, CNRS, Institut de la VisionParisFrance
| | - Romain Brette
- Sorbonne Université, INSERM, CNRS, Institut de la VisionParisFrance
| | - Dan FM Goodman
- Department of Electrical and Electronic EngineeringImperial College LondonLondonUnited Kingdom
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26
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Huntenburg JM, Steele CJ, Bazin PL. Nighres: processing tools for high-resolution neuroimaging. Gigascience 2018; 7:5049008. [PMID: 29982501 PMCID: PMC6065481 DOI: 10.1093/gigascience/giy082] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 01/22/2023] Open
Abstract
With recent improvements in human magnetic resonance imaging (MRI) at ultra-high fields, the amount of data collected per subject in a given MRI experiment has increased considerably. Standard image processing packages are often challenged by the size of these data. Dedicated methods are needed to leverage their extraordinary spatial resolution. Here, we introduce a flexible Python toolbox that implements a set of advanced techniques for high-resolution neuroimaging. With these tools, segmentation and laminar analysis of cortical MRI data can be performed at resolutions up to 500 μm in reasonable times. Comprehensive online documentation makes the toolbox easy to use and install. An extensive developer’s guide encourages contributions from other researchers that will help to accelerate progress in the promising field of high-resolution neuroimaging.
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Affiliation(s)
- Julia M Huntenburg
- Max Planck Research Group for Neuroanatomy & Connectivity, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, Leipzig, 04103, Germany.,Neurocomputation and Neuroimaging Unit, Department of Education and Psychology, Free University of Berlin, Habelschwerdter Allee 45, Berlin, 14195, Germany
| | - Christopher J Steele
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, Leipzig, 04103, Germany.,Cerebral Imaging Center, Douglas Mental Health University Institute, 6875 LaSalle Boulevard, Montreal, Quebec, H4H 1R3, Canada.,Department of Psychology, Concordia University, 7141 Sherbrooke West, Montreal, Quebec, H4B IR6, Canada
| | - Pierre-Louis Bazin
- Department of Neurology, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, Leipzig, 04103, Germany.,Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstrasse 1a, Leipzig, 04103, Germany.,Psychology Department, University of Amsterdam, Nieuwe Achtergracht 129B, Amsterdam, 1018 WT, Netherlands
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27
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Gleeson P, Lung D, Grosu R, Hasani R, Larson SD. c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0379. [PMID: 30201842 PMCID: PMC6158223 DOI: 10.1098/rstb.2017.0379] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2018] [Indexed: 01/03/2023] Open
Abstract
The OpenWorm project has the ambitious goal of producing a highly detailed in silico model of the nematode Caenorhabditis elegans. A crucial part of this work will be a model of the nervous system encompassing all known cell types and connections. The appropriate level of biophysical detail required in the neuronal model to reproduce observed high-level behaviours in the worm has yet to be determined. For this reason, we have developed a framework, c302, that allows different instances of neuronal networks to be generated incorporating varying levels of anatomical and physiological detail, which can be investigated and refined independently or linked to other tools developed in the OpenWorm modelling toolchain. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
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Affiliation(s)
- Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - David Lung
- Cyber-Physical Systems, Technische Universität Wien, Vienna, Austria
| | - Radu Grosu
- Cyber-Physical Systems, Technische Universität Wien, Vienna, Austria
| | - Ramin Hasani
- Cyber-Physical Systems, Technische Universität Wien, Vienna, Austria
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28
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Cantarelli M, Marin B, Quintana A, Earnshaw M, Court R, Gleeson P, Dura-Bernal S, Silver RA, Idili G. Geppetto: a reusable modular open platform for exploring neuroscience data and models. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2017.0380. [PMID: 30201843 PMCID: PMC6158222 DOI: 10.1098/rstb.2017.0380] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 11/25/2022] Open
Abstract
Geppetto is an open-source platform that provides generic middleware infrastructure for building both online and desktop tools for visualizing neuroscience models and data and managing simulations. Geppetto underpins a number of neuroscience applications, including Open Source Brain (OSB), Virtual Fly Brain (VFB), NEURON-UI and NetPyNE-UI. OSB is used by researchers to create and visualize computational neuroscience models described in NeuroML and simulate them through the browser. VFB is the reference hub for Drosophila melanogaster neural anatomy and imaging data including neuropil, segmented neurons, microscopy stacks and gene expression pattern data. Geppetto is also being used to build a new user interface for NEURON, a widely used neuronal simulation environment, and for NetPyNE, a Python package for network modelling using NEURON. Geppetto defines domain agnostic abstractions used by all these applications to represent their models and data and offers a set of modules and components to integrate, visualize and control simulations in a highly accessible way. The platform comprises a backend which can connect to external data sources, model repositories and simulators together with a highly customizable frontend. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.
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Affiliation(s)
- Matteo Cantarelli
- OpenWorm Foundation, USA .,MetaCell Limited, UK.,Department of Neuroscience, Physiology and Pharmacology, University College London, UK
| | - Boris Marin
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK.,Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Brazil
| | - Adrian Quintana
- MetaCell Limited, UK.,Department of Neuroscience, Physiology and Pharmacology, University College London, UK.,EyeSeeTea Limited, UK
| | - Matt Earnshaw
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK
| | - Robert Court
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK
| | | | - R Angus Silver
- Department of Neuroscience, Physiology and Pharmacology, University College London, UK
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29
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Tennøe S, Halnes G, Einevoll GT. Uncertainpy: A Python Toolbox for Uncertainty Quantification and Sensitivity Analysis in Computational Neuroscience. Front Neuroinform 2018; 12:49. [PMID: 30154710 PMCID: PMC6102374 DOI: 10.3389/fninf.2018.00049] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/20/2018] [Indexed: 11/13/2022] Open
Abstract
Computational models in neuroscience typically contain many parameters that are poorly constrained by experimental data. Uncertainty quantification and sensitivity analysis provide rigorous procedures to quantify how the model output depends on this parameter uncertainty. Unfortunately, the application of such methods is not yet standard within the field of neuroscience. Here we present Uncertainpy, an open-source Python toolbox, tailored to perform uncertainty quantification and sensitivity analysis of neuroscience models. Uncertainpy aims to make it quick and easy to get started with uncertainty analysis, without any need for detailed prior knowledge. The toolbox allows uncertainty quantification and sensitivity analysis to be performed on already existing models without needing to modify the model equations or model implementation. Uncertainpy bases its analysis on polynomial chaos expansions, which are more efficient than the more standard Monte-Carlo based approaches. Uncertainpy is tailored for neuroscience applications by its built-in capability for calculating characteristic features in the model output. The toolbox does not merely perform a point-to-point comparison of the "raw" model output (e.g., membrane voltage traces), but can also calculate the uncertainty and sensitivity of salient model response features such as spike timing, action potential width, average interspike interval, and other features relevant for various neural and neural network models. Uncertainpy comes with several common models and features built in, and including custom models and new features is easy. The aim of the current paper is to present Uncertainpy to the neuroscience community in a user-oriented manner. To demonstrate its broad applicability, we perform an uncertainty quantification and sensitivity analysis of three case studies relevant for neuroscience: the original Hodgkin-Huxley point-neuron model for action potential generation, a multi-compartmental model of a thalamic interneuron implemented in the NEURON simulator, and a sparsely connected recurrent network model implemented in the NEST simulator.
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Affiliation(s)
- Simen Tennøe
- Centre for Integrative Neuroplasticity, University of Oslo, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Geir Halnes
- Centre for Integrative Neuroplasticity, University of Oslo, Oslo, Norway.,Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway
| | - Gaute T Einevoll
- Centre for Integrative Neuroplasticity, University of Oslo, Oslo, Norway.,Faculty of Science and Technology, Norwegian University of Life Sciences, Ås, Norway.,Department of Physics, University of Oslo, Oslo, Norway
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30
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Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow. Neuroinformatics 2018; 15:333-342. [PMID: 28770487 DOI: 10.1007/s12021-017-9337-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features. Finally, to maximize automation, we extended our NeuroManager workflow automation suite to include these tools plus a separate investigation database. The extended suite allows the user to integrate ABI experimental and modeling data into an automated workflow deployed on heterogeneous computer infrastructures, from local servers, to high performance computing environments, to the cloud. Since our approach is focused on workflow procedures our tools can be modified to interact with the increasing number of neuroscience databases being developed to cover all scales and properties of the nervous system.
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31
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Kim H, Kim M. PyMUS: Python-Based Simulation Software for Virtual Experiments on Motor Unit System. Front Neuroinform 2018; 12:15. [PMID: 29695959 PMCID: PMC5904262 DOI: 10.3389/fninf.2018.00015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/23/2018] [Indexed: 02/04/2023] Open
Abstract
We constructed a physiologically plausible computationally efficient model of a motor unit and developed simulation software that allows for integrative investigations of the input-output processing in the motor unit system. The model motor unit was first built by coupling the motoneuron model and muscle unit model to a simplified axon model. To build the motoneuron model, we used a recently reported two-compartment modeling approach that accurately captures the key cell-type-related electrical properties under both passive conditions (somatic input resistance, membrane time constant, and signal attenuation properties between the soma and the dendrites) and active conditions (rheobase current and afterhyperpolarization duration at the soma and plateau behavior at the dendrites). To construct the muscle unit, we used a recently developed muscle modeling approach that reflects the experimentally identified dependencies of muscle activation dynamics on isometric, isokinetic and dynamic variation in muscle length over a full range of stimulation frequencies. Then, we designed the simulation software based on the object-oriented programing paradigm and developed the software using open-source Python language to be fully operational using graphical user interfaces. Using the developed software, separate simulations could be performed for a single motoneuron, muscle unit and motor unit under a wide range of experimental input protocols, and a hierarchical analysis could be performed from a single channel to the entire system behavior. Our model motor unit and simulation software may represent efficient tools not only for researchers studying the neural control of force production from a cellular perspective but also for instructors and students in motor physiology classroom settings.
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Affiliation(s)
- Hojeong Kim
- Convergence Research Institute, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
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32
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Szécsi L, Kacsó Á, Zeck G, Hantz P. Interactive Light Stimulus Generation with High Performance Real-Time Image Processing and Simple Scripting. Front Neuroinform 2018; 11:70. [PMID: 29326579 PMCID: PMC5733361 DOI: 10.3389/fninf.2017.00070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 11/23/2017] [Indexed: 11/13/2022] Open
Abstract
Light stimulation with precise and complex spatial and temporal modulation is demanded by a series of research fields like visual neuroscience, optogenetics, ophthalmology, and visual psychophysics. We developed a user-friendly and flexible stimulus generating framework (GEARS GPU-based Eye And Retina Stimulation Software), which offers access to GPU computing power, and allows interactive modification of stimulus parameters during experiments. Furthermore, it has built-in support for driving external equipment, as well as for synchronization tasks, via USB ports. The use of GEARS does not require elaborate programming skills. The necessary scripting is visually aided by an intuitive interface, while the details of the underlying software and hardware components remain hidden. Internally, the software is a C++/Python hybrid using OpenGL graphics. Computations are performed on the GPU, and are defined in the GLSL shading language. However, all GPU settings, including the GPU shader programs, are automatically generated by GEARS. This is configured through a method encountered in game programming, which allows high flexibility: stimuli are straightforwardly composed using a broad library of basic components. Stimulus rendering is implemented solely in C++, therefore intermediary libraries for interfacing could be omitted. This enables the program to perform computationally demanding tasks like en-masse random number generation or real-time image processing by local and global operations.
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Affiliation(s)
- László Szécsi
- Computer Graphics Research Group, Budapest University of Technology and Economics, Budapest, Hungary
| | - Ágota Kacsó
- Computer Graphics Research Group, Budapest University of Technology and Economics, Budapest, Hungary
| | - Günther Zeck
- Neurochip Research Group, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Péter Hantz
- Department of Laboratory Medicine, University of Pécs, Pécs, Hungary
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33
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Zhang B, Dai J, Zhang T. NeoAnalysis: a Python-based toolbox for quick electrophysiological data processing and analysis. Biomed Eng Online 2017; 16:129. [PMID: 29132360 PMCID: PMC5683334 DOI: 10.1186/s12938-017-0419-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/03/2017] [Indexed: 02/07/2023] Open
Abstract
Background In a typical electrophysiological experiment, especially one that includes studying animal behavior, the data collected normally contain spikes, local field potentials, behavioral responses and other associated data. In order to obtain informative results, the data must be analyzed simultaneously with the experimental settings. However, most open-source toolboxes currently available for data analysis were developed to handle only a portion of the data and did not take into account the sorting of experimental conditions. Additionally, these toolboxes require that the input data be in a specific format, which can be inconvenient to users. Therefore, the development of a highly integrated toolbox that can process multiple types of data regardless of input data format and perform basic analysis for general electrophysiological experiments is incredibly useful. Results Here, we report the development of a Python based open-source toolbox, referred to as NeoAnalysis, to be used for quick electrophysiological data processing and analysis. The toolbox can import data from different data acquisition systems regardless of their formats and automatically combine different types of data into a single file with a standardized format. In cases where additional spike sorting is needed, NeoAnalysis provides a module to perform efficient offline sorting with a user-friendly interface. Then, NeoAnalysis can perform regular analog signal processing, spike train, and local field potentials analysis, behavioral response (e.g. saccade) detection and extraction, with several options available for data plotting and statistics. Particularly, it can automatically generate sorted results without requiring users to manually sort data beforehand. In addition, NeoAnalysis can organize all of the relevant data into an informative table on a trial-by-trial basis for data visualization. Finally, NeoAnalysis supports analysis at the population level. Conclusions With the multitude of general-purpose functions provided by NeoAnalysis, users can easily obtain publication-quality figures without writing complex codes. NeoAnalysis is a powerful and valuable toolbox for users doing electrophysiological experiments. Electronic supplementary material The online version of this article (10.1186/s12938-017-0419-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bo Zhang
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji Dai
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China. .,Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Shenzhen Key Lab of Neuropsychiatric Modulation and Collaborative Innovation Center for Brain Science, CAS Center for Excellence in Brain Science and Intelligence Technology, the Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen, 518055, China.
| | - Tao Zhang
- State Key Laboratory of Brain and Cognitive Sciences, Institute of Psychology, Chinese Academy of Sciences, Beijing, 100101, China.,Department of Psychology, University of Chinese Academy of Sciences, Beijing, 100049, China
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34
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Tikidji-Hamburyan RA, Narayana V, Bozkus Z, El-Ghazawi TA. Software for Brain Network Simulations: A Comparative Study. Front Neuroinform 2017; 11:46. [PMID: 28775687 PMCID: PMC5517781 DOI: 10.3389/fninf.2017.00046] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/26/2017] [Indexed: 11/13/2022] Open
Abstract
Numerical simulations of brain networks are a critical part of our efforts in understanding brain functions under pathological and normal conditions. For several decades, the community has developed many software packages and simulators to accelerate research in computational neuroscience. In this article, we select the three most popular simulators, as determined by the number of models in the ModelDB database, such as NEURON, GENESIS, and BRIAN, and perform an independent evaluation of these simulators. In addition, we study NEST, one of the lead simulators of the Human Brain Project. First, we study them based on one of the most important characteristics, the range of supported models. Our investigation reveals that brain network simulators may be biased toward supporting a specific set of models. However, all simulators tend to expand the supported range of models by providing a universal environment for the computational study of individual neurons and brain networks. Next, our investigations on the characteristics of computational architecture and efficiency indicate that all simulators compile the most computationally intensive procedures into binary code, with the aim of maximizing their computational performance. However, not all simulators provide the simplest method for module development and/or guarantee efficient binary code. Third, a study of their amenability for high-performance computing reveals that NEST can almost transparently map an existing model on a cluster or multicore computer, while NEURON requires code modification if the model developed for a single computer has to be mapped on a computational cluster. Interestingly, parallelization is the weakest characteristic of BRIAN, which provides no support for cluster computations and limited support for multicore computers. Fourth, we identify the level of user support and frequency of usage for all simulators. Finally, we carry out an evaluation using two case studies: a large network with simplified neural and synaptic models and a small network with detailed models. These two case studies allow us to avoid any bias toward a particular software package. The results indicate that BRIAN provides the most concise language for both cases considered. Furthermore, as expected, NEST mostly favors large network models, while NEURON is better suited for detailed models. Overall, the case studies reinforce our general observation that simulators have a bias in the computational performance toward specific types of the brain network models.
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Affiliation(s)
- Ruben A Tikidji-Hamburyan
- School of Engineering and Applied Science, George Washington University, Washington, DC, United States
| | - Vikram Narayana
- School of Engineering and Applied Science, George Washington University, Washington, DC, United States
| | - Zeki Bozkus
- Computer Engineering Department, Kadir Has University, Istanbul, Turkey
| | - Tarek A El-Ghazawi
- School of Engineering and Applied Science, George Washington University, Washington, DC, United States
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35
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Ippen T, Eppler JM, Plesser HE, Diesmann M. Constructing Neuronal Network Models in Massively Parallel Environments. Front Neuroinform 2017; 11:30. [PMID: 28559808 PMCID: PMC5432669 DOI: 10.3389/fninf.2017.00030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 04/04/2017] [Indexed: 11/13/2022] Open
Abstract
Recent advances in the development of data structures to represent spiking neuron network models enable us to exploit the complete memory of petascale computers for a single brain-scale network simulation. In this work, we investigate how well we can exploit the computing power of such supercomputers for the creation of neuronal networks. Using an established benchmark, we divide the runtime of simulation code into the phase of network construction and the phase during which the dynamical state is advanced in time. We find that on multi-core compute nodes network creation scales well with process-parallel code but exhibits a prohibitively large memory consumption. Thread-parallel network creation, in contrast, exhibits speedup only up to a small number of threads but has little overhead in terms of memory. We further observe that the algorithms creating instances of model neurons and their connections scale well for networks of ten thousand neurons, but do not show the same speedup for networks of millions of neurons. Our work uncovers that the lack of scaling of thread-parallel network creation is due to inadequate memory allocation strategies and demonstrates that thread-optimized memory allocators recover excellent scaling. An analysis of the loop order used for network construction reveals that more complex tests on the locality of operations significantly improve scaling and reduce runtime by allowing construction algorithms to step through large networks more efficiently than in existing code. The combination of these techniques increases performance by an order of magnitude and harnesses the increasingly parallel compute power of the compute nodes in high-performance clusters and supercomputers.
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Affiliation(s)
- Tammo Ippen
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research CentreJülich, Germany.,Faculty of Science and Technology, Norwegian University of Life SciencesÅs, Norway
| | - Jochen M Eppler
- Simulation Laboratory Neuroscience-Bernstein Facility Simulation and Database Technology, Institute for Advanced Simulation, Jülich Research Centre and JARAJülich, Germany
| | - Hans E Plesser
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research CentreJülich, Germany.,Faculty of Science and Technology, Norwegian University of Life SciencesÅs, Norway.,Department of Biosciences, Centre for Integrative Neuroplasticity, University of OsloOslo, Norway
| | - Markus Diesmann
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research CentreJülich, Germany.,Department of Psychiatry, Psychotherapy and Psychosomatics, Medical Faculty, RWTH Aachen UniversityAachen, Germany.,Department of Physics, Faculty 1, RWTH Aachen UniversityAachen, Germany
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36
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Meyer R, Obermayer K. pypet: A Python Toolkit for Data Management of Parameter Explorations. Front Neuroinform 2016; 10:38. [PMID: 27610080 PMCID: PMC4996826 DOI: 10.3389/fninf.2016.00038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/09/2016] [Indexed: 11/16/2022] Open
Abstract
pypet (Python parameter exploration toolkit) is a new multi-platform Python toolkit for managing numerical simulations. Sampling the space of model parameters is a key aspect of simulations and numerical experiments. pypet is designed to allow easy and arbitrary sampling of trajectories through a parameter space beyond simple grid searches. pypet collects and stores both simulation parameters and results in a single HDF5 file. This collective storage allows fast and convenient loading of data for further analyses. pypet provides various additional features such as multiprocessing and parallelization of simulations, dynamic loading of data, integration of git version control, and supervision of experiments via the electronic lab notebook Sumatra. pypet supports a rich set of data formats, including native Python types, Numpy and Scipy data, Pandas DataFrames, and BRIAN(2) quantities. Besides these formats, users can easily extend the toolkit to allow customized data types. pypet is a flexible tool suited for both short Python scripts and large scale projects. pypet's various features, especially the tight link between parameters and results, promote reproducible research in computational neuroscience and simulation-based disciplines.
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Affiliation(s)
- Robert Meyer
- Neuroinformatics Group, Department of Software Engineering and Theoretical Computer Science, Technical University BerlinBerlin, Germany; Bernstein Center for Computational NeuroscienceBerlin, Germany
| | - Klaus Obermayer
- Neuroinformatics Group, Department of Software Engineering and Theoretical Computer Science, Technical University Berlin Berlin, Germany
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37
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Van Geit W, Gevaert M, Chindemi G, Rössert C, Courcol JD, Muller EB, Schürmann F, Segev I, Markram H. BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience. Front Neuroinform 2016; 10:17. [PMID: 27375471 PMCID: PMC4896051 DOI: 10.3389/fninf.2016.00017] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/06/2016] [Indexed: 11/13/2022] Open
Abstract
At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases.
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Affiliation(s)
- Werner Van Geit
- Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland
| | - Michael Gevaert
- Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland
| | - Giuseppe Chindemi
- Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland
| | - Christian Rössert
- Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland
| | - Jean-Denis Courcol
- Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland
| | - Eilif B Muller
- Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland
| | - Felix Schürmann
- Blue Brain Project, École Polytechnique Fédérale de Lausanne Geneva, Switzerland
| | - Idan Segev
- Department of Neurobiology, Alexander Silberman Institute of Life Sciences, The Hebrew University of JerusalemJerusalem, Israel; The Edmond and Lily Safra Centre for Brain Sciences, The Hebrew University of JerusalemJerusalem, Israel
| | - Henry Markram
- Blue Brain Project, École Polytechnique Fédérale de LausanneGeneva, Switzerland; Laboratory of Neural Microcircuitry, Brain Mind Institute, École Polytechnique Fédérale de LausanneLausanne, Switzerland
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Doucet G, Gulli RA, Martinez-Trujillo JC. Cross-species 3D virtual reality toolbox for visual and cognitive experiments. J Neurosci Methods 2016; 266:84-93. [PMID: 27015795 DOI: 10.1016/j.jneumeth.2016.03.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/10/2016] [Accepted: 03/11/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Although simplified visual stimuli, such as dots or gratings presented on homogeneous backgrounds, provide strict control over the stimulus parameters during visual experiments, they fail to approximate visual stimulation in natural conditions. Adoption of virtual reality (VR) in neuroscience research has been proposed to circumvent this problem, by combining strict control of experimental variables and behavioral monitoring within complex and realistic environments. NEW METHOD We have created a VR toolbox that maximizes experimental flexibility while minimizing implementation costs. A free VR engine (Unreal 3) has been customized to interface with any control software via text commands, allowing seamless introduction into pre-existing laboratory data acquisition frameworks. Furthermore, control functions are provided for the two most common programming languages used in visual neuroscience: Matlab and Python. RESULTS The toolbox offers milliseconds time resolution necessary for electrophysiological recordings and is flexible enough to support cross-species usage across a wide range of paradigms. COMPARISON WITH EXISTING METHODS Unlike previously proposed VR solutions whose implementation is complex and time-consuming, our toolbox requires minimal customization or technical expertise to interface with pre-existing data acquisition frameworks as it relies on already familiar programming environments. Moreover, as it is compatible with a variety of display and input devices, identical VR testing paradigms can be used across species, from rodents to humans. CONCLUSIONS This toolbox facilitates the addition of VR capabilities to any laboratory without perturbing pre-existing data acquisition frameworks, or requiring any major hardware changes.
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Affiliation(s)
- Guillaume Doucet
- Department of Physiology, McGill University, 3655 Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada; Robarts Research Institute, Brain and Mind Institute, Department of Physiology and Pharmacology, Department of Psychiatry, Western University, 1151 Richmond St. N., Room 7239, London, ON N6A 5B7, Canada.
| | - Roberto A Gulli
- Integrated Program in Neuroscience, McGill University, 3801 University Street, Room 141, Montreal, QC H3A 2B4, Canada; Robarts Research Institute, Brain and Mind Institute, Department of Physiology and Pharmacology, Department of Psychiatry, Western University, 1151 Richmond St. N., Room 7239, London, ON N6A 5B7, Canada.
| | - Julio C Martinez-Trujillo
- Robarts Research Institute, Brain and Mind Institute, Department of Physiology and Pharmacology, Department of Psychiatry, Western University, 1151 Richmond St. N., Room 7239, London, ON N6A 5B7, Canada.
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Evans BD, Jarvis S, Schultz SR, Nikolic K. PyRhO: A Multiscale Optogenetics Simulation Platform. Front Neuroinform 2016; 10:8. [PMID: 27148037 PMCID: PMC4834562 DOI: 10.3389/fninf.2016.00008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/19/2016] [Indexed: 01/07/2023] Open
Abstract
Optogenetics has become a key tool for understanding the function of neural circuits and controlling their behavior. An array of directly light driven opsins have been genetically isolated from several families of organisms, with a wide range of temporal and spectral properties. In order to characterize, understand and apply these opsins, we present an integrated suite of open-source, multi-scale computational tools called PyRhO. The purpose of developing PyRhO is three-fold: (i) to characterize new (and existing) opsins by automatically fitting a minimal set of experimental data to three-, four-, or six-state kinetic models, (ii) to simulate these models at the channel, neuron and network levels, and (iii) provide functional insights through model selection and virtual experiments in silico. The module is written in Python with an additional IPython/Jupyter notebook based GUI, allowing models to be fit, simulations to be run and results to be shared through simply interacting with a webpage. The seamless integration of model fitting algorithms with simulation environments (including NEURON and Brian2) for these virtual opsins will enable neuroscientists to gain a comprehensive understanding of their behavior and rapidly identify the most suitable variant for application in a particular biological system. This process may thereby guide not only experimental design and opsin choice but also alterations of the opsin genetic code in a neuro-engineering feed-back loop. In this way, we expect PyRhO will help to significantly advance optogenetics as a tool for transforming biological sciences.
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Affiliation(s)
- Benjamin D Evans
- Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK
| | - Sarah Jarvis
- Centre for Neurotechnology, Institute of Biomedical Engineering, Department of Bioengineering, Imperial College London London, UK
| | - Simon R Schultz
- Centre for Neurotechnology, Institute of Biomedical Engineering, Department of Bioengineering, Imperial College London London, UK
| | - Konstantin Nikolic
- Centre for Bio-Inspired Technology, Institute of Biomedical Engineering, Department of Electrical and Electronic Engineering, Imperial College London London, UK
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