{"title":"QSOnic: fast quasar continuum fitting","authors":"Naim Göksel Karaçaylı","doi":"10.21105/joss.06373","DOIUrl":"https://doi.org/10.21105/joss.06373","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141001378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oliver R. A. Dunbar, Melanie Bieli, A. Garbuno-Iñigo, Michael Howland, Andre Nogueira de Souza, Laura A. Mansfield, G. L. Wagner, N. Efrat-Henrici
{"title":"CalibrateEmulateSample.jl: Accelerated Parametric\u0000Uncertainty Quantification","authors":"Oliver R. A. Dunbar, Melanie Bieli, A. Garbuno-Iñigo, Michael Howland, Andre Nogueira de Souza, Laura A. Mansfield, G. L. Wagner, N. Efrat-Henrici","doi":"10.21105/joss.06372","DOIUrl":"https://doi.org/10.21105/joss.06372","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141008795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Arabica: A Python package for exploratory analysis of\u0000text data","authors":"Petr Koráb, J. Poměnková","doi":"10.21105/joss.06186","DOIUrl":"https://doi.org/10.21105/joss.06186","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141011737","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Brain extraction and segmentation are the first step for most neuroimaging analyses. Automatic methods work well in adult human brains, but produce unreliable results in non-human data, due to muscle tissue, skull, and luminosity gradients. Thresholdmann (https://neuroanatomy. github.io/thresholdmann) is an open source Web tool for the interactive application of space-varying thresholds to Nifti volumes. No download or installation are required and all processing is done on the user’s computer. Nifti volumes are dragged and dropped onto the Web app and become available for visual exploration in a stereotaxic viewer. A space-varying threshold is then created by setting control points, each with their own local threshold. Each point can be repositioned or removed, and each local threshold can be adjusted in real time using sliders or entering their values numerically. The threshold direction can be switched to allow segmentation of the structure of interest in different imaging modalities, such as T1 and T2 weighted contrasts. The opacity of the mask and the brightness and contrast of the MRI image can be adjusted via sliders. A 3D model of the thresholded mask can be computed to inspect the result in an interactive 3D render. Finally, the thresholded mask, the space varying threshold and the list of control points can be saved for later use in scripted workflows, able to reproduce the thresholded volume from the original data.
{"title":"Thresholdmann: A Web tool for interactively creating\u0000adaptive thresholds to segment MRI data.","authors":"K. Heuer, N. Traut, Roberto Toro","doi":"10.21105/joss.06336","DOIUrl":"https://doi.org/10.21105/joss.06336","url":null,"abstract":"Brain extraction and segmentation are the first step for most neuroimaging analyses. Automatic methods work well in adult human brains, but produce unreliable results in non-human data, due to muscle tissue, skull, and luminosity gradients. Thresholdmann (https://neuroanatomy. github.io/thresholdmann) is an open source Web tool for the interactive application of space-varying thresholds to Nifti volumes. No download or installation are required and all processing is done on the user’s computer. Nifti volumes are dragged and dropped onto the Web app and become available for visual exploration in a stereotaxic viewer. A space-varying threshold is then created by setting control points, each with their own local threshold. Each point can be repositioned or removed, and each local threshold can be adjusted in real time using sliders or entering their values numerically. The threshold direction can be switched to allow segmentation of the structure of interest in different imaging modalities, such as T1 and T2 weighted contrasts. The opacity of the mask and the brightness and contrast of the MRI image can be adjusted via sliders. A 3D model of the thresholded mask can be computed to inspect the result in an interactive 3D render. Finally, the thresholded mask, the space varying threshold and the list of control points can be saved for later use in scripted workflows, able to reproduce the thresholded volume from the original data.","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141016318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Alexander Jaffray, Zhe Wu, S. Vannesjo, K. Uludağ, Lars Kasper
{"title":"GIRFReco.jl: An Open-Source Pipeline for Spiral\u0000Magnetic Resonance Image (MRI) Reconstruction in Julia","authors":"Alexander Jaffray, Zhe Wu, S. Vannesjo, K. Uludağ, Lars Kasper","doi":"10.21105/joss.05877","DOIUrl":"https://doi.org/10.21105/joss.05877","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141021178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hongyang Cheng, Luisa Orozco, Retief Lubbe, Aron Jansen, Philipp Hartmann, K. Thoeni
{"title":"GrainLearning: A Bayesian uncertainty quantification\u0000toolbox for discrete and continuum numerical models of granular\u0000materials","authors":"Hongyang Cheng, Luisa Orozco, Retief Lubbe, Aron Jansen, Philipp Hartmann, K. Thoeni","doi":"10.21105/joss.06338","DOIUrl":"https://doi.org/10.21105/joss.06338","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141017661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Julia Wind, Asbjørn Ulvestad, Muhammad Abdelhamid, J. P. Mæhlen
{"title":"Cellpy – an open-source library for processing and\u0000analysis of battery testing data","authors":"Julia Wind, Asbjørn Ulvestad, Muhammad Abdelhamid, J. P. Mæhlen","doi":"10.21105/joss.06236","DOIUrl":"https://doi.org/10.21105/joss.06236","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141021356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"ETHOS.PeNALPS: A Tool for the Load Profile Simulation\u0000of Industrial Processes Based on a Material Flow Simulation","authors":"Julian Belina, N. Pflugradt, Detlef Stolten","doi":"10.21105/joss.06358","DOIUrl":"https://doi.org/10.21105/joss.06358","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141021853","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The plebeian Graph Library: A WebGL based network\u0000visualisation and diagnostics package","authors":"Indrajeet Haldar","doi":"10.21105/joss.05887","DOIUrl":"https://doi.org/10.21105/joss.05887","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140653687","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rohini S. Gupta, Chris R. Vernon, Travis B. Thurber, D. Gold, Zachary M. Hirsch, A. Hadjimichael, P. Reed
{"title":"statemodify: a Python framework to facilitate\u0000accessible exploratory modeling for discovering drought\u0000vulnerabilities","authors":"Rohini S. Gupta, Chris R. Vernon, Travis B. Thurber, D. Gold, Zachary M. Hirsch, A. Hadjimichael, P. Reed","doi":"10.21105/joss.06325","DOIUrl":"https://doi.org/10.21105/joss.06325","url":null,"abstract":"","PeriodicalId":16635,"journal":{"name":"Journal of open source software","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140658888","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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