tag:joss.theoj.org,2005:/papers/tagged/neuroscienceJournal of Open Source Software2024-01-11T22:46:25ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/47432024-01-11T22:46:25Z2024-01-12T00:05:23ZPhysioLabXR: A Python Platform for Real-Time, Multi-modal, Brain–Computer Interfaces and Extended Reality Experimentsacceptedv1.0.02023-09-09 02:37:52 UTC932024-01-11 22:46:25 UTC920245854Ziheng'Leo'LiColumbia University, New York, New York, United States of America0000-0001-5187-200XHaowen'John'WeiColumbia University, New York, New York, United States of America0000-0003-1856-5627ZiwenXieColumbia University, New York, New York, United States of America0009-0006-2304-7591YunxiangPengColumbia University, New York, New York, United States of America0009-0000-1824-970XJunePyoSuhColumbia University, New York, New York, United States of America0009-0005-1211-6101StevenFeinerColumbia University, New York, New York, United States of America0000-0001-9978-7090PaulSajdaColumbia University, New York, New York, United States of America0000-0002-9738-134210.21105/joss.05854https://doi.org/10.5281/zenodo.10471500Python, C++, Cythonhttps://joss.theoj.org/papers/10.21105/joss.05854.pdfneuroscience, human–computer interaction, brain-computer interface, multi-modality, virtual augmented realitytag:joss.theoj.org,2005:Paper/47162023-12-15T17:51:50Z2023-12-16T20:57:44ZHNN-core: A Python software for cellular and circuit-level interpretation of human MEG/EEGaccepted0.32023-08-23 18:15:30 UTC922023-12-15 17:51:50 UTC820235848MainakJasAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA0000-0002-3199-9027RyanThorpeDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0003-2491-8599NicholasTolleyDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0003-0358-0074ChristopherBaileyDepartment of Clinical Medicine, Aarhus University, Aarhus, Denmark0000-0003-3318-3344StevenBrandtDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USABlakeCaldwellBassett Medical Center, Cooperstown, NY, USA0000-0002-6882-6998HuziChengDepartment of Psychological and Brain Sciences, Indiana University Bloomington, Bloomington, IN, USADylanDanielsRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0009-0008-1958-353XCarolinaFernandezPujolDepartment of Biomedical Engineering, University of Miami, Coral Gables, FL, USA0009-0003-0611-1270MostafaKhalilDepartment of Psychiatry and Behavioral Health, Penn State Milton S. Hershey Medical Center, Penn State College of Medicine, Hershey, PA, USASamikaKanekarWarren Alpert Medical, Brown University, Providence, RI0000-0002-6111-4461CarmenKohlRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0001-7585-595XOrsolyaKolozsváriDepartment of Psychology, University of Jyväskylä, Jyväskylä, Finland, Jyväskylä Centre for Interdisciplinary Brain Research, University of Jyväskylä, Jyväskylä, Finland0000-0002-1619-6314KaisuLankinenAthinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, USA, Department of Radiology, Harvard Medical School, Boston, MA, USA0000-0003-2210-2385KennethLoiRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA, Department of Molecular and Cell Biology; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USASamNeymotinCenter for Biomedical Imaging and Neuromodulation, Nathan S. Kline Institute for Psychiatric Research, Orangeburg, NY, USA, Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA0000-0003-3646-5195RajatPartaniDepartment of Computer Science and Engineering, National Institute of Technology Karnataka, Karnataka, India0000-0002-6863-7046MattanPelahRobert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA, Florida State University, Tallahassee, FL, USAAlexRockhillDepartment of Human Physiology, University of Oregon, Eugene, OR, USA0000-0003-3868-7453MohamedSherifDepartment of Psychiatry and Human Behavior, Brown University, Providence, RI, USA, Rhode Island Hospital, Providence, RI, USA0000-0002-8951-1645MattiHamalainenDepartment of Neuroscience and Biomedical Engineering, Aalto University, Espoo, Finland0000-0001-6841-112XStephanieJonesDepartment of Neuroscience, Brown University, Providence, RI, USA, Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI, USA0000-0001-6760-530110.21105/joss.05848https://doi.org/10.5281/zenodo.10289164Python, Jupyter Notebook, AMPLhttps://joss.theoj.org/papers/10.21105/joss.05848.pdfneuroscience, EEG, MEG, modeling, neocortextag:joss.theoj.org,2005:Paper/42642023-11-14T13:13:20Z2023-11-21T14:12:33Zspiketools: a Python package for analyzing single-unit neural activityacceptedv0.0.02023-02-26 05:10:56 UTC912023-11-14 13:13:20 UTC820235268ThomasDonoghueDepartment of Biomedical Engineering, Columbia University, New York, United States of America0000-0001-5911-0472SandraMaesta-PereiraDepartment of Biomedical Engineering, Columbia University, New York, United States of America0000-0001-6522-8311ClaireZhixianHanDepartment of Biomedical Engineering, Columbia University, New York, United States of America0000-0001-9710-8381SalmanEhteshamQasimDepartment of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America0000-0001-8739-5962JoshuaJacobsDepartment of Biomedical Engineering, Columbia University, New York, United States of America, Department of Neurological Surgery, Columbia University, New York, United States of America0000-0003-1807-688210.21105/joss.05268https://doi.org/10.5281/zenodo.10076024Pythonhttps://joss.theoj.org/papers/10.21105/joss.05268.pdfneuroscience, electrophysiology, single unit activitytag:joss.theoj.org,2005:Paper/44482023-10-27T15:27:51Z2023-10-28T00:00:39Zbayes-toolbox: A Python package for Bayesian statisticsacceptedv0.1.02023-04-22 21:43:52 UTC902023-10-27 15:27:51 UTC820235526HyosubE.KimSchool of Kinesiology, The University of British Columbia, Canada, Department of Physical Therapy, University of Delaware, United States0000-0003-0109-593X10.21105/joss.05526https://doi.org/10.5281/zenodo.7849408Pythonhttps://joss.theoj.org/papers/10.21105/joss.05526.pdfBayesian statistics, psychology, neurosciencetag:joss.theoj.org,2005:Paper/42602023-09-20T00:32:03Z2023-09-21T00:01:17ZSpikeometric: Linear Non-Linear Cascade Spiking Neural Networks with Pytorch Geometricacceptedv1.0.02023-02-23 16:23:51 UTC892023-09-20 00:32:03 UTC820235451JakobL.SønstebøDepartment of Numerical Analysis and Scientific Computing, Simula Research Laboratory, Oslo, Norway0009-0009-0584-9293HermanBrunborgDepartment of Physics, University of Oslo, Oslo, NorwayMikkelElleLepperødDepartment of Numerical Analysis and Scientific Computing, Simula Research Laboratory, Oslo, Norway, Department of Physics, University of Oslo, Oslo, Norway0000-0002-4262-554910.21105/joss.05451https://doi.org/10.5281/zenodo.8358903Pythonhttps://joss.theoj.org/papers/10.21105/joss.05451.pdfpython, computational neuroscience, machine learning, spiking neural networks, generalized linear models, linear non-linear poisson modelstag:joss.theoj.org,2005:Paper/44692023-09-12T03:11:54Z2023-09-14T02:59:51ZmTRFpy: A Python package for temporal response function analysisaccepted1.2.12023-05-03 15:17:43 UTC892023-09-12 03:11:54 UTC820235657OleBialasDepartment of Biomedical Engineering, University of Rochester, USA0000-0003-4472-7626JinDouDepartment of Biomedical Engineering, University of Rochester, USA0009-0000-0539-5951EdmundC.LalorDepartment of Biomedical Engineering, University of Rochester, USA, Department of Neuroscience, University of Rochester, USA0000-0002-2498-663110.21105/joss.05657https://doi.org/10.5281/zenodo.8321912Pythonhttps://joss.theoj.org/papers/10.21105/joss.05657.pdfelectrophysiology, temporal response function, cognitive neuroscience, computational neuroscience, TRFtag:joss.theoj.org,2005:Paper/43962023-06-12T08:03:36Z2023-06-20T20:35:26ZDeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking dataacceptedv0.22023-04-12 15:39:51 UTC862023-06-12 08:03:36 UTC820235394LucasMirandaResearch Group Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany0000-0002-5484-6744JoeriBordesResearch Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany0000-0003-2909-2976BennoPützResearch Group Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany0000-0002-2208-209XMathiasV.SchmidtResearch Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany0000-0002-3788-2268BertramMüller-MyhsokResearch Group Statistical Genetics, Max Planck Institute of Psychiatry, Munich, Germany0000-0002-0719-101X10.21105/joss.05394https://doi.org/10.5281/zenodo.8013401Pythonhttps://joss.theoj.org/papers/10.21105/joss.05394.pdfbiology, neuroscience, behavioral annotationtag:joss.theoj.org,2005:Paper/42622023-05-11T08:31:02Z2023-05-12T00:01:06ZfRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging dataaccepted1.0.02023-02-24 14:54:52 UTC852023-05-11 08:31:02 UTC820235200ElliotHowleySchool of Psychology, University of Nottingham, Nottingham, United Kingdom0000-0002-3868-2516SusanFrancisSir Peter Mansfield Imaging Centre, University of Nottingham, Nottingham, United Kingdom, NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom0000-0003-0903-7507DenisSchluppeckSchool of Psychology, University of Nottingham, Nottingham, United Kingdom0000-0002-0634-771310.21105/joss.05200https://doi.org/10.5281/zenodo.7877605Python, JavaScripthttps://joss.theoj.org/papers/10.21105/joss.05200.pdffMRI, Neuroscience, Nipype, Pipelinetag:joss.theoj.org,2005:Paper/40972023-04-05T14:27:49Z2023-04-06T00:03:27ZOpenseize: A digital signal processing package for large EEG datasets in Pythonacceptedv1.0.02022-12-20 15:34:56 UTC842023-04-05 14:27:49 UTC820235126MatthewS.CaudillDepartment of Neuroscience, Baylor College of Medicine, Houston, TX, United States of America, Jan and Dan Duncan Neurological Research Institute at Texas Childrens Hospital, Houston, TX, United States of America0000-0002-3656-926110.21105/joss.05126https://doi.org/10.5281/zenodo.7760376Pythonhttps://joss.theoj.org/papers/10.21105/joss.05126.pdfEEG, neuroscience, signal processing, local field potentials, time series analysistag: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, neuroscience