tag:joss.theoj.org,2005:/papers/tagged/neuroscience?page=2Journal of Open Source Software2023-03-21T11:34:30ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/39792023-03-21T11:34:30Z2023-03-22T00:03:16ZHigh-performance neural population dynamics modeling enabled by scalable computational infrastructureacceptedv1.0.02022-10-26 06:03:04 UTC832023-03-21 11:34:30 UTC820235023AashishN.PatelDepartment of Electrical and Computer Engineering, University of California San Diego, United States of America, Institute for Neural Computation, University of California San Diego, United States of AmericaAndrewR.SedlerCenter for Machine Learning, Georgia Institute of Technology, United States of America, Department of Biomedical Engineering, Georgia Institute of Technology, United States of America0000-0001-9480-0698JingyaHuangDepartment of Electrical and Computer Engineering, University of California San Diego, United States of AmericaChethanPandarinathCenter for Machine Learning, Georgia Institute of Technology, United States of America, Department of Biomedical Engineering, Georgia Institute of Technology, United States of America, Department of Neurosurgery, Emory University, United States of America, These authors contributed equallyVikashGiljaDepartment of Electrical and Computer Engineering, University of California San Diego, United States of America, These authors contributed equally10.21105/joss.05023https://doi.org/10.5281/zenodo.7719505Python, Smartyhttps://joss.theoj.org/papers/10.21105/joss.05023.pdfautolfads, kubeflow, ray, neurosciencetag:joss.theoj.org,2005:Paper/39622023-02-21T09:47:34Z2023-02-22T00:00:50ZPyView: A general purpose tool for analyzing calcium imaging dataaccepted1.12022-10-14 16:37:22 UTC822023-02-21 09:47:34 UTC820234936AjayramaKumaraswamyUniversity of Konstanz, Department of Biology, Universitatsstr. 10, D-78457 Konstanz0000-0001-7928-877XGeorgRaiserChampalimaud Centre for the Unknown, Avenida de Brasília, 1400-038 Lisboa, Portugal0000-0002-9716-3513CGiovanniGaliziaUniversity of Konstanz, Department of Biology, Universitatsstr. 10, D-78457 Konstanz0000-0001-8292-603110.21105/joss.04936https://doi.org/10.12751/g-node.ezh5w2Jupyter Notebook, Python, IDLhttps://joss.theoj.org/papers/10.21105/joss.04936.pdfNeuroscience, Calcium imagingtag:joss.theoj.org,2005:Paper/38962022-12-13T14:47:46Z2022-12-14T00:01:30ZSpectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPUacceptedv1.0.32022-09-15 00:44:07 UTC802022-12-13 14:47:46 UTC720224840EricL.DenovellisHoward Hughes Medical Institute - University of California, San Francisco, San Francisco, California, United States of America, Departments of Physiology and Psychiatry, University of California, San Francisco, San Francisco, California, United States of America, Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, California, United States of America0000-0003-4606-087XMaxymMyroshnychenkoNational Institute of Neurological Disorders and Stroke, Bethesda, Maryland, United States of America0000-0001-7790-257XMehradSarmashghiDivision of Systems Engineering, Boston University, Boston, Massachusetts, United States of America0000-0002-7976-6636EmilyP.StephenDepartment of Mathematics and Statistics, Boston University, Boston, Massachusetts, United States of America, Center for Systems Neuroscience, Boston University, Boston, Massachusetts, United States of America0000-0003-1978-962210.21105/joss.04840https://doi.org/10.5281/zenodo.7416614Pythonhttps://joss.theoj.org/papers/10.21105/joss.04840.pdfNeuroscience, Multitaper analysis, Spectral estimation, Brain connectivity measures, Fourier transformtag:joss.theoj.org,2005:Paper/34202022-12-08T21:58:29Z2022-12-09T03:31:51ZPyNM: a Lightweight Python implementation of Normative Modelingaccepted1.0.0b12022-03-11 18:20:42 UTC802022-12-08 21:58:29 UTC720224321AnnabelleHarveyCentre de Recherche de l’Institut Universitaire de Gériatrie de Montréal, Université de Montréal, QC, Canada, Centre de Recherche du CHU Sainte-Justine, Université de Montréal, QC, Canada0000-0002-9940-8799GuillaumeDumasCentre de Recherche du CHU Sainte-Justine, Université de Montréal, QC, Canada, Mila - Quebec AI Institute, Université de Montréal, QC, Canada0000-0002-2253-184410.21105/joss.04321https://doi.org/10.5281/zenodo.7396721Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04321.pdfNormative Modeling, Heterogeneity, Heteroskedasticity, Big Data, Centiles, LOESS, Gaussian Process, Stochastic Variational Gaussian Process, GAMLSS, Computational Psychiatry, Neurosciencetag:joss.theoj.org,2005:Paper/30732022-11-11T11:25:25Z2022-11-14T13:35:42ZFrites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological dataacceptedv0.4.02021-09-21 12:11:23 UTC792022-11-11 11:25:25 UTC720223842EtienneCombrissonInstitut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France0000-0002-7362-3247RuggeroBasanisiInstitut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France0000-0003-4776-596XViniciusLimaCordeiroInstitut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France, Institut de Neurosciences des Systèmes, Aix-Marseille Université, UMR 1106 Inserm, 13005, Marseille, France0000-0001-7115-9041RobinA.aInceInstitute of Neuroscience and Psychology, University of Glasgow, Glasgow, UK0000-0001-8427-0507AndreaBrovelliInstitut de Neurosciences de la Timone, Aix Marseille Université, UMR 7289 CNRS, 13005, Marseille, France0000-0002-5342-133010.21105/joss.03842https://doi.org/10.5281/zenodo.7278278Pythonhttps://joss.theoj.org/papers/10.21105/joss.03842.pdfpython, cognitive neuroscience, computational neuroscience, neuroinformatics, neurophysiology, information theory, information-based measures, statistics, functional connectivity, fixed-effect ffx, random-effect rfx, cluster-based statistics, MEG EEG sEEG LFPs, Granger causalitytag:joss.theoj.org,2005:Paper/36572022-10-13T14:56:15Z2022-10-14T00:00:26ZPycrostates: a Python library to study EEG microstatesaccepted0.1.12022-06-14 15:36:12 UTC782022-10-13 14:56:15 UTC720224564VictorFératFunctional Brain Mapping Laboratory, Department of Basic Neurosciences, Campus Biotech, University of Geneva, Geneva, Switzerland0000-0003-1952-7657MathieuScheltienneHuman Neuroscience Platform, Fondation Campus Biotech Geneva, Geneva, Switzerland0000-0001-8316-7436DenisBrunetFunctional Brain Mapping Laboratory, Department of Basic Neurosciences, Campus Biotech, University of Geneva, Geneva, Switzerland, Centre for Biomedical Imaging (CIBM) Lausanne-Geneva, Geneva, SwitzerlandTomasRosFunctional Brain Mapping Laboratory, Department of Basic Neurosciences, Campus Biotech, University of Geneva, Geneva, Switzerland, Centre for Biomedical Imaging (CIBM) Lausanne-Geneva, Geneva, Switzerland0000-0001-6952-0459ChristophMichelFunctional Brain Mapping Laboratory, Department of Basic Neurosciences, Campus Biotech, University of Geneva, Geneva, Switzerland, Centre for Biomedical Imaging (CIBM) Lausanne-Geneva, Geneva, Switzerland0000-0003-3426-573910.21105/joss.04564https://doi.org/10.5281/zenodo.7129852Python, Jinjahttps://joss.theoj.org/papers/10.21105/joss.04564.pdfneuroscience, neuroimaging, EEG, microstates, braintag:joss.theoj.org,2005:Paper/37382022-10-09T08:04:24Z2022-10-10T00:01:29ZPatchView: A Python Package for Patch-clamp Data Analysis and Visualizationacceptedv0.2.22022-07-22 00:03:39 UTC782022-10-09 08:04:24 UTC720224706MingHuDepartment of Neuroscience, Baylor College of Medicine, Houston, TX, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston,TX, USA0000-0002-5254-5315XiaolongJiangDepartment of Neuroscience, Baylor College of Medicine, Houston, TX, Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston,TX, USA, Department of Ophthalmology, Baylor College of Medicine, Houston, TX10.21105/joss.04706https://doi.org/10.5281/zenodo.7149877Python, AGS Scripthttps://joss.theoj.org/papers/10.21105/joss.04706.pdfneuroscience, patch-clamp, mini-event, Heka, Axon instrumentstag:joss.theoj.org,2005:Paper/31512022-07-04T16:37:30Z2022-07-05T00:00:36ZNeuralFieldEq.jl: A flexible solver to compute Neural Field Equations in several scenariosacceptedv0.1.22021-11-02 22:16:16 UTC752022-07-04 16:37:30 UTC720223974TiagoSequeiraInstituto Superior Técnico - University of Lisbon0000-0001-8579-367610.21105/joss.03974https://doi.org/10.5281/zenodo.6226695Juliahttps://joss.theoj.org/papers/10.21105/joss.03974.pdfComputational Neuroscience, Neural Field Equations, Stochastic Processes, Delayed Equations, Fast Fourier Transformstag:joss.theoj.org,2005:Paper/33882022-06-27T08:46:45Z2022-06-28T00:00:45ZConnectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mappingacceptedv3.0.32022-02-22 08:28:10 UTC742022-06-27 08:46:45 UTC720224248SebastienTourbierRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-4441-899XJoanRue-QueraltRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-9595-4557KatharinaGlombBerlin Institute of Health at Charité; Department of Neurology with Experimental Neurology, Brain Simulation Section, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany0000-0002-4596-4386YasserAleman-GomezRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0001-6067-8639EmelineMullierRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0001-6209-0791AlessandraGriffaDepartment of Clinical Neurosciences, Division of Neurology, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland, Institute of Bioengineering, Center of Neuroprosthetics, École Polytechnique Fédérale De Lausanne (EPFL), Geneva, Switzerland0000-0003-1923-1653MikkelSchöttnerRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-4521-9837JonathanWirsichEEG and Epilepsy Unit, University Hospitals and Faculty of Medicine of Geneva, University of Geneva, Geneva, Switzerland0000-0003-0588-9710M.AnılTuncelBlue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland0000-0003-0317-2556JakubJancovicFoxight, Geneva, Switzerland0000-0002-3312-3918MeritxellBachCuadraCIBM Center for Biomedical Imaging, Lausanne, Switzerland, Radiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0003-2730-4285PatricHagmannRadiology Department, Centre Hospitalier Universitaire Vaudois and University of Lausanne (CHUV-UNIL), Switzerland0000-0002-2854-656110.21105/joss.04248https://doi.org/10.5281/zenodo.6645256Pythonhttps://joss.theoj.org/papers/10.21105/joss.04248.pdfneuroscience, pipeline, workflow, connectome, multi-scale, MRI, BIDS, BIDS App, containerized workflows, nipypetag:joss.theoj.org,2005:Paper/31482022-05-15T17:05:53Z2022-05-16T00:00:45ZSinaps: A Python library to simulate voltage dynamics and ionic electrodiffusion in neuronsaccepted0.22021-11-02 02:28:11 UTC732022-05-15 17:05:53 UTC720224012NicolasGaltierIndependent ResearcherClaireGuerrierCRM - IRL3457, LJAD Université Côte d'Azur0000-0002-1128-106910.21105/joss.04012https://doi.org/10.5281/zenodo.6540844Pythonhttps://joss.theoj.org/papers/10.21105/joss.04012.pdfneuroscience, voltage propagation, calcium electrodiffusion, cable theory, Nernst-Planck equations