tag:joss.theoj.org,2005:/papers/tagged/microscopy?page=2Journal of Open Source Software2021-05-03T08:46:12ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/22462021-05-03T08:46:12Z2021-05-04T00:01:23ZfastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLIacceptedv1.0.02020-12-18 14:43:24 UTC612021-05-03 08:46:12 UTC620213042FelixMatuschkeInstitute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany0000-0001-6435-5351KatrinAmuntsInstitute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany, Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, University of Düsseldorf, 40204, Düsseldorf, Germany.0000-0001-5828-0867MarkusAxerInstitute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany0000-0001-5871-933110.21105/joss.03042https://doi.org/10.5281/zenodo.4720075Python, C++https://joss.theoj.org/papers/10.21105/joss.03042.pdf3D-PLI, microscopy, simulationtag:joss.theoj.org,2005:Paper/21342021-01-28T13:56:25Z2021-02-15T11:29:48ZCellocity: A Python package for analysis of confluent cell layer dynamicsaccepted1.0.02020-10-28 10:09:34 UTC572021-01-28 13:56:25 UTC620212818JensErikssonScience for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University0000-0002-8945-2665DanielStyrströmDaniel Styrström ConsultingMikaelE.SellinScience for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University0000-0002-8355-080310.21105/joss.02818https://doi.org/10.5281/zenodo.4475442Pythonhttps://joss.theoj.org/papers/10.21105/joss.02818.pdfmicroscopy, dynamics, confluent cell layertag:joss.theoj.org,2005:Paper/20032020-10-26T00:05:14Z2021-02-15T11:30:02ZSLIX: A Python package for fully automated evaluation of Scattered Light Imaging measurements on brain tissueacceptedv1.12020-08-31 19:48:33 UTC542020-10-26 00:05:14 UTC520202675JanA.ReuterInstitute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany0000-0002-1219-0310MiriamMenzelInstitute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany0000-0002-6042-749010.21105/joss.02675https://doi.org/10.5281/zenodo.4121953Pythonhttps://joss.theoj.org/papers/10.21105/joss.02675.pdflight scattering, dark-field microscopy, brain architecture, connectivity, nerve fiber crossingstag:joss.theoj.org,2005:Paper/20142020-10-05T11:38:32Z2021-02-15T11:29:59ZBrainGlobe Atlas API: a common interface for neuroanatomical atlasesaccepted0.2.02020-09-04 08:32:31 UTC542020-10-05 11:38:32 UTC520202668FedericoClaudiSainsbury Wellcome Centre, University College London, London, U.K.LuigiPetruccoInstitute of Neuroscience, Technical University of Munich, Munich, Germany, Max Planck Institute of Neurobiology, Research Group of Sensorimotor Control, Martinsried, GermanyAdamL.TysonSainsbury Wellcome Centre, University College London, London, U.K.0000-0003-3225-1130TiagoBrancoSainsbury Wellcome Centre, University College London, London, U.K.TroyW.MargrieSainsbury Wellcome Centre, University College London, London, U.K.RubenPortuguesInstitute of Neuroscience, Technical University of Munich, Munich, Germany, Max Planck Institute of Neurobiology, Research Group of Sensorimotor Control, Martinsried, Germany, Munich Cluster for Systems Neurology (SyNergy), Munich, Germany10.21105/joss.02668https://doi.org/10.5281/zenodo.4065389Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.02668.pdfneuroscience, neuroanatomy, microscopytag:joss.theoj.org,2005:Paper/14062020-06-20T19:32:38Z2021-02-15T11:31:14ZLiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopyacceptedv0.3.02019-12-16 10:10:42 UTC502020-06-20 19:32:38 UTC520202006AlexanderClausenForschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons0000-0002-9555-7455DieterWeberForschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons0000-0001-6635-9567KarinaRuzaevaForschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons0000-0003-3610-0989VadimMigunovForschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Central Facility for Electron Microscopy (GFE), RWTH Aachen University0000-0002-6296-4492AnandBaburajanGovernment Engineering College Sreekrishnapuram0000-0002-2870-366XAbijithBahuleyanGovernment Engineering College Sreekrishnapuram0000-0001-5045-5650JanCaronForschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons0000-0002-0873-889XRahulChandraChandigarh University0000-0003-2079-5368SayandipHalderJadavpur University0000-0003-0224-3746MagnusNordUniversity of Antwerp, EMAT0000-0001-7981-5293KnutMüller-CasparyForschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons0000-0002-2588-7993RafalE.Dunin-BorkowskiForschungszentrum Jülich, Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons0000-0001-8082-064710.21105/joss.02006https://doi.org/10.5281/zenodo.3763313C, Python, Scalahttps://joss.theoj.org/papers/10.21105/joss.02006.pdftransmission electron microscopy, distributed, big data, MapReducetag:joss.theoj.org,2005:Paper/14342020-02-09T17:12:24Z2021-02-15T11:31:09ZExTemp: A computational and image-processing suite for extracting temporal barcodesaccepted1.02020-01-09 21:44:26 UTC462020-02-09 17:12:24 UTC520202026ShalinShahDepartment of Electrical & Computer Engineering, Duke University, Durham, NC 27708, USA0000-0002-1406-3577AbhishekDubeyDepartment of Electrical & Computer Engineering, Duke University, Durham, NC 27708, USA, Computational Sciences and Engineering Division, Health Data Sciences Institute, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States0000-0001-8052-7416JohnReifDepartment of Electrical & Computer Engineering, Duke University, Durham, NC 27708, USA, Department of Computer Science, Duke University, Durham, NC 27708, USA10.21105/joss.02026https://doi.org/10.5281/zenodo.3660411Matlabhttps://joss.theoj.org/papers/10.21105/joss.02026.pdfobject detection, signal processing, drift correction, object tracking, microscopy image analysis, computer vision, TIRF, MATLAB