tag:joss.theoj.org,2005:/papers/tagged/D3Journal of Open Source Software2024-03-04T15:38:25ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/48272024-03-04T15:38:25Z2024-03-05T01:12:22Z$hp\mathrm{3D}$: A Scalable MPI/OpenMP $hp$-Adaptive Finite Element Software Library for Complex Multiphysics Applicationsacceptedv1.0-beta2023-10-02 22:48:04 UTC952024-03-04 15:38:25 UTC920245946StefanHennekingOden Institute, The University of Texas at Austin, USA0000-0003-2177-8519SocratisPetridesLawrence Livermore National Laboratory, USA0000-0002-1284-5495FedericoFuentesInstitute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Chile0000-0002-4039-082XJacobBadgerOden Institute, The University of Texas at Austin, USA0000-0001-6482-105XLeszekDemkowiczOden Institute, The University of Texas at Austin, USA0000-0001-7839-803710.21105/joss.05946https://doi.org/10.5281/zenodo.10763375Perl, Pythonhttps://joss.theoj.org/papers/10.21105/joss.05946.pdffinite element, hp-adaptivity, DPG methodtag:joss.theoj.org,2005:Paper/47452024-03-03T08:56:11Z2024-03-09T08:34:29ZDICaugment: A Python Package for 3D Medical Imaging Augmentationacceptedv1.0.02023-09-10 23:37:02 UTC952024-03-03 08:56:11 UTC920246120J.McIntoshDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA0009-0008-2573-180XQianCaoDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USABerkmanSahinerDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USANicholasPetrickDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USAM.MehdiFarhangiDivision of Imaging, Diagnostics, and Software Reliability, CDRH, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA10.21105/joss.06120https://doi.org/10.5281/zenodo.10738855Pythonhttps://joss.theoj.org/papers/10.21105/joss.06120.pdfAugmentation, Deep Learning, Medical, tag:joss.theoj.org,2005:Paper/48132024-02-27T21:24:38Z2024-03-22T14:09:24ZDeepRank2: Mining 3D Protein Structures with Geometric Deep Learningacceptedv2.1.02023-09-22 15:36:51 UTC942024-02-27 21:24:38 UTC920245983GiuliaCrocioniNetherlands eScience Center, Amsterdam, The Netherlands0000-0002-0823-0121DaniL.BodorNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-2109-2349CoosBaakmanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4317-1566FarzanehM.PariziThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-4230-7492Daniel-T.RademakerThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0003-1959-1317GayatriRamakrishnanThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0001-8203-2783SvenA.van der BurgNetherlands eScience Center, Amsterdam, The Netherlands0000-0003-1250-6968DarioF.MarzellaThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-0043-3055JoãoM.c.TeixeiraIndependent Researcher0000-0002-9113-0622LiC.XueThe Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands0000-0002-2613-538X10.21105/joss.05983https://doi.org/10.5281/zenodo.10566809Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05983.pdfPyTorch, structural biology, geometric deep learning, 3D protein structures, protein-protein interfaces, single-residue variants, graph neural networks, convolutional neural networks, DeepRanktag:joss.theoj.org,2005:Paper/40002023-05-18T13:10:37Z2023-05-30T08:52:39ZPyBullet Industrial: A process-aware robot simulationacceptedv1.0.02022-11-11 15:27:01 UTC852023-05-18 13:10:37 UTC820235174JanBaumgärtnerwbk Institute of Production Science0000-0002-7825-3476MalteHansjostenwbk Institute of Production ScienceDominikSchönhofenIndependent ResearcherProf.Dr.-Ing. JürgenFleischerwbk Institute of Production Science0000-0003-0961-767510.21105/joss.05174https://doi.org/10.5281/zenodo.7833292https://joss.theoj.org/papers/10.21105/joss.05174.pdfPython, robotics, simulation, milling, force calculation, 3D printing, production processestag:joss.theoj.org,2005:Paper/39612023-01-30T10:25:42Z2023-01-31T12:33:59ZFijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + tacceptedv4.0.22022-10-14 14:29:38 UTC812023-01-30 10:25:42 UTC820234981RomainFernandezCIRAD, UMR AGAP Institut, F-34398 Montpellier, France, AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France.0000-0003-3670-044XCedricMoisyIFV, French Institute of Vine and Wine, UMT Géno-Vigne, UMR AGAP, F-34398 Montpellier, France.0000-0003-4637-471310.21105/joss.04981https://doi.org/10.5281/zenodo.7554691Java, MATLAB, Pythonhttps://joss.theoj.org/papers/10.21105/joss.04981.pdfFiji, Image analysis, MRI, Relaxometry, Phenotypingtag:joss.theoj.org,2005:Paper/34052022-09-13T12:03:32Z2022-09-13T12:03:36ZDuoDIC: 3D Digital Image Correlation in MATLABacceptedv1.0.02022-03-01 12:05:28 UTC742022-09-13 12:03:32 UTC720224279DanaSolavFaculty of Mechanical Engineering, Technion, Haifa, Israel0000-0003-3215-0401AsafSilversteinFaculty of Mechanical Engineering, Technion, Haifa, Israel10.21105/joss.04279https://doi.org/10.5281/zenodo.6673060MATLAB, Java, C++https://joss.theoj.org/papers/10.21105/joss.04279.pdfdigital image correlation, material testing, full-field strain, full-field deformations, Ncorr, Stereo camera calibrationtag:joss.theoj.org,2005:Paper/35042022-07-30T17:54:01Z2022-07-31T17:28:51ZMyPTV: A Python Package for 3D Particle Trackingacceptedv0.22022-04-14 12:13:19 UTC752022-07-30 17:54:01 UTC720224398RonShnappSwiss Federal Institute for Forest, Snow and Landscape Research WSL, 8903 Birmensdorf, Switzerland0000-0001-7495-842010.21105/joss.04398https://doi.org/10.5281/zenodo.6846969Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.04398.pdf3D particle tracking, Fluid mechanics, Turbulence, Experimental methodstag:joss.theoj.org,2005:Paper/31032022-05-05T15:17:18Z2022-05-06T08:43:39ZThe 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical imagesaccepted1.0.02021-10-05 19:24:10 UTC732022-05-05 15:17:18 UTC720223920JonasLamyUniversité Lyon 2, LIRIS (UMR 5205) Lyon, FranceThibaultPelletierKitware SAS, Villeurbanne, FranceGuillaumeLienemannUniversité Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, F-63000, Clermont-Ferrand, FranceBenoîtMagninUniversité Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, F-63000, Clermont-Ferrand, FranceBertrandKerautretUniversité Lyon 2, LIRIS (UMR 5205) Lyon, FranceNicolasPassatUniversité de Reims Champagne Ardenne, CReSTIC, EA 3804, 51100 Reims, FranceJulienFinetKitware SAS, Villeurbanne, FranceAntoineVacavantUniversité Clermont Auvergne, CNRS, SIGMA Clermont, Institut Pascal, F-63000, Clermont-Ferrand, France10.21105/joss.03920https://doi.org/10.5281/zenodo.6513517Pythonhttps://joss.theoj.org/papers/10.21105/joss.03920.pdf3D Slicer, medical imaging, image segmentation, image processing, annotation, livertag:joss.theoj.org,2005:Paper/31362022-03-03T18:42:06Z2022-03-04T00:01:11Z3D Line Radiative Transfer & Synthetic Observations with Magritteaccepted0.0.12021-10-27 19:03:50 UTC712022-03-03 18:42:06 UTC720223905FrederikDe CeusterDepartment of Physics and Astronomy, University College London, London, UK, Institute of Astronomy, KU Leuven, Leuven, Belgium0000-0001-5887-8498ThomasCeulemansInstitute of Astronomy, KU Leuven, Leuven, BelgiumAtulitSrivastavaInstitute of Astronomy, KU Leuven, Leuven, BelgiumWardHomanInstitut d’Astronomie et d’Astrophysique, Université Libre de Bruxelles, Brussels, Belgium0000-0001-7314-5081JanBolteInstitute of Astronomy, KU Leuven, Leuven, Belgium0000-0002-7991-9663JeremyYatesDepartment of Physics and Astronomy, University College London, London, UK0000-0003-1954-8749LeenDecinInstitute of Astronomy, KU Leuven, Leuven, Belgium, School of Chemistry, University of Leeds, Leeds, UK0000-0002-5342-8612PeterBoyleSchool of Physics and Astronomy, The University of Edinburgh, Edinburgh, UK, Brookhaven National Laboratory, NY, USA0000-0002-8960-1587JamesHetheringtonDepartment of Computer Science, University College London, London, UK0000-0001-6993-031910.21105/joss.03905https://doi.org/10.5281/zenodo.6320469Python, C++https://joss.theoj.org/papers/10.21105/joss.03905.pdfastronomy, radiative transfertag:joss.theoj.org,2005:Paper/30872021-11-12T21:08:31Z2022-01-18T12:11:45Zdisksurf: Extracting the 3D Structure of Protoplanetary Disksacceptedv0.1.72021-09-29 13:29:23 UTC672021-11-12 21:08:31 UTC620213827RichardTeagueCenter for Astrophysics | Harvard & Smithsonian, 60 Garden St., Cambridge, MA 02138, USACharlesJ.LawCenter for Astrophysics | Harvard & Smithsonian, 60 Garden St., Cambridge, MA 02138, USA0000-0003-1413-1776JaneHuangDepartment of Astronomy, University of Michigan, 323 West Hall, 1085 South University Avenue, Ann Arbor, MI 48109, USA, NASA Hubble Fellowship Program Sagan Fellow0000-0001-6947-6072FeilongMengDepartment of Astronomy, University of Michigan, 323 West Hall, 1085 South University Avenue, Ann Arbor, MI 48109, USA0000-0003-0079-683010.21105/joss.03827https://doi.org/10.5281/zenodo.5670586Pythonhttps://joss.theoj.org/papers/10.21105/joss.03827.pdfastronomy, protoplanetary disks