NEUBIAS - the Bioimage Analysts Network

NEUBIAS - the Bioimage Analysts Network

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1-20 of 29 ARTICLES
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Featured Article
https://doi.org/10.12688/f1000research.27395.2
Software Tool Article metrics
Revised
GeNePy3D: a quantitative geometry python toolbox for bioimaging
[version 2; peer review: 2 approved]
Minh-Son Phan, Anatole Chessel
Peer Reviewers Virginie Uhlmann; Yizhi Wang
  • Funder
  • Agence Nationale de la Recherche
LATEST VERSION PUBLISHED 17 Jun 2021
https://doi.org/10.12688/f1000research.143062.1
Software Tool Article metrics
COverlap: a Fiji toolset for the 3D co-localization of two fluorescent nuclear markers in confocal images
[version 1; peer review: 3 approved with reservations]
Mélodie Ambroset, Bruno Bontempi, Jean-Luc Morel
Peer Reviewers Thomas Boudier; Jean-Karim Heriche; Bijie Bai
  • Funders
  • Agence Nationale de la Recherche
  • Université de Bordeaux
  • Centre National de la Recherche Scientifique
  • Centre National d’Etudes Spatiales
PUBLISHED 03 Jan 2024
https://doi.org/10.12688/f1000research.27158.3
Software Tool Article metrics
Revised
DeepCLEM: automated registration for correlative light and electron microscopy using deep learning
[version 3; peer review: 1 approved, 2 approved with reservations]
Rick Seifert, Sebastian M. Markert, Sebastian Britz, Veronika Perschin, Christoph Erbacher, Christian Stigloher, Philip Kollmannsberger
Peer Reviewers Martin L. Jones; Reinhard Rachel; Christopher Schmied
  • Funders
  • Studienstiftung des Deutschen Volkes
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 28 Dec 2023
https://doi.org/10.12688/f1000research.27139.4
Software Tool Article metrics
Revised
A multi-spectral myelin annotation tool for machine learning based myelin quantification
[version 4; peer review: 2 approved]
Abdulkerim Çapar, Sibel Çimen, Zeynep Aladağ, Dursun Ali Ekinci, Umut Engin Ayten, Bilal Ersen Kerman, Behçet Uğur Töreyin
Peer Reviewers Predrag Janjic; Mustafa Ozuysal
  • Funder
  • Türkiye Bilimsel ve Teknolojik Araştirma Kurumu
LATEST VERSION PUBLISHED 15 Nov 2023
https://doi.org/10.12688/f1000research.124990.1
Software Tool Article metrics
A flexible open-source processing workflow for multiplexed fluorescence imaging based on cycles
[version 1; peer review: 1 approved, 2 approved with reservations]
Guillaume Potier, Aurélie Doméné, Perrine Paul-Gilloteaux
Peer Reviewers Anna H. Klemm; Mark Zaidi; Asier Antoranz
  • Funders
  • Labex IGO
  • France Bio Imaging
PUBLISHED 29 Sep 2022
https://doi.org/10.12688/f1000research.110385.2
Software Tool Article metrics
Revised
Easing batch image processing from OMERO: a new toolbox for ImageJ
[version 2; peer review: 2 approved]
Pierre Pouchin, Rayan Zoghlami, Rémi Valarcher, Maxence Delannoy, Manon Carvalho, Clémence Belle, Marc Mongy, Sophie Desset, Frédéric Brau
Peer Reviewers Jason R. Swedlow; Caterina Strambio-De-Castillia
  • Funders
  • Université Clermont Auvergne
  • Agence Nationale de la Recherche
  • Pack Ambition Recherche project Noyau-HD
  • COST-Action INDEPTH
LATEST VERSION PUBLISHED 12 Sep 2022
https://doi.org/10.12688/f1000research.51868.3
Method Article metrics
Revised
Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo
[version 3; peer review: 2 approved]
Benjamin Mayer, Meike Schwan, Kai M. Thormann, Peter L. Graumann
Peer Reviewers Massimiliano Lucidi; Janos Kriston-Vizi and Qing Hsuan Ong
  • Funder
  • Deutsche Forschungsgemeinschaft
LATEST VERSION PUBLISHED 17 May 2022
https://doi.org/10.12688/f1000research.51900.2
Software Tool Article metrics
Revised
ContactJ: Characterization of lipid droplet-mitochondrial contacts using fluorescence microscopy and image analysis
[version 2; peer review: 2 approved]
Gemma Martín, Marta Bosch, Elisenda Coll, Robert G. Parton, Albert Pol, Maria Calvo
Peer Reviewers Mafalda Sousa and Maria Azevedo; Gadea Mata Martinez
  • Funder
  • European Cooperation in Science and Technology
LATEST VERSION PUBLISHED 18 Jan 2022
https://doi.org/10.12688/f1000research.52026.2
Method Article metrics
Revised
A deep learning segmentation strategy that minimizes the amount of manually annotated images
[version 2; peer review: 2 approved]
Thierry Pécot, Alexander Alekseyenko, Kristin Wallace
Peer Reviewers Alice Lucas; Romain F Laine
  • Funder
  • Chan Zuckerberg Initiative
LATEST VERSION PUBLISHED 17 Jan 2022
https://doi.org/10.12688/f1000research.51755.2
Review metrics
Revised
Calcium imaging analysis – how far have we come?
[version 2; peer review: 3 approved]
Miranda Robbins, Charles N. Christensen, Clemens F. Kaminski, Marta Zlatic
Peer Reviewers Christopher Rowlands and Isabell Whiteley; William Zeiger; Anubhuti Goel
LATEST VERSION PUBLISHED 26 Aug 2021
https://doi.org/10.12688/f1000research.26977.2
Research Article metrics
Revised
TAPAS: Towards Automated Processing and Analysis of multi-dimensional bioimage data
[version 2; peer review: 2 approved]
Jean-François Gilles, Thomas Boudier
Peer Reviewers Robert Haase; Lit-Hsin Loo
LATEST VERSION PUBLISHED 02 Jul 2021
https://doi.org/10.12688/f1000research.26888.3
Research Article metrics
Revised
A new analysis approach for single nephron GFR in intravital microscopy of mice
[version 3; peer review: 2 approved, 2 not approved]
Friederike Kessel, Hannah Kröger, Michael Gerlach, Jan Sradnick, Florian Gembardt, Vladimir Todorov, Christian Hugo
Peer Reviewers Bruce A. Molitoris; Christopher Schmied; Georgina Gyarmati; Anna Schueth
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Boehringer Ingelheim
  • European Cooperation in Science and Technology
LATEST VERSION PUBLISHED 10 Jun 2021
https://doi.org/10.12688/f1000research.25485.1
Opinion Article metrics
Highlights from the 2016-2020 NEUBIAS training schools for Bioimage Analysts: a success story and key asset for analysts and life scientists
[version 1; peer review: 2 approved]
Gabriel G. Martins, Fabrice P. Cordelières, Julien Colombelli, Rocco D’Antuono, Ofra Golani, Romain Guiet, Robert Haase, Anna H. Klemm, Marion Louveaux, Perrine Paul-Gilloteaux, Jean-Yves Tinevez, Kota Miura
Peer Reviewers Thorsten Wohland; Kevin Eliceiri
  • Funders
  • Swedish Foundation for Strategic Research
  • Fundação para a Ciência e a Tecnologia
  • COST
  • Luxembourg National Research Fund
  • Cancer Research UK
  • Deutsche Forschungsgemeinschaft
  • Swedish National Microscopy infrastructure
  • UK Medical Research Council
  • France BioImaging national infrastructure
  • Wellcome Trust
PUBLISHED 30 Apr 2021
https://doi.org/10.12688/f1000research.51732.1
Software Tool Article metrics
ImageM: a user-friendly interface for the processing of multi-dimensional images with Matlab
[version 1; peer review: 2 approved with reservations]
David Legland, Marie-Françoise Devaux
Peer Reviewers John Anthony Jose and Janos Lance Tiberio; Curtis Rueden
PUBLISHED 30 Apr 2021
https://doi.org/10.12688/f1000research.52569.1
Opinion Article metrics
Bioimage analysis workflows: community resources to navigate through a complex ecosystem
[version 1; peer review: 2 approved]
Perrine Paul-Gilloteaux, Sébastien Tosi, Jean-Karim Hériché, Alban Gaignard, Hervé Ménager, Raphaël Marée, Volker Baecker, Anna Klemm, Matúš Kalaš, Chong Zhang, Kota Miura, Julien Colombelli
Peer Reviewers Katy Wolstencroft; Assaf Zaritsky
  • Funder
  • Agence Nationale de la Recherche
PUBLISHED 26 Apr 2021
https://doi.org/10.12688/f1000research.52531.1
Opinion Article metrics
Developing open-source software for bioimage analysis: opportunities and challenges
[version 1; peer review: 2 approved]
Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
Peer Reviewers Loïc A. Royer; Nico Stuurman
  • Funders
  • Deutsche Forschungsgemeinschaft
  • Institut National de la Santé et de la Recherche Médicale
  • National Institutes of Health
  • Chan Zuckerberg Initiative
PUBLISHED 19 Apr 2021
https://doi.org/10.12688/f1000research.27372.2
Brief Report metrics
Revised
Image analysis method for heterogeneity and porosity characterization of biomimetic hydrogels
[version 2; peer review: 2 approved]
Maryam Jamshidi, Cavus Falamaki
Peer Reviewers Miroslava Dušková-Smrčková; Susana Rocha
LATEST VERSION PUBLISHED 12 Apr 2021
https://doi.org/10.12688/f1000research.27062.2
Software Tool Article metrics
Revised
SAPHIR: a Shiny application to analyze tissue section images
[version 2; peer review: 2 approved]
Elodie Germani, Hugues Lelouard, Mathieu Fallet
Peer Reviewers Mahmoud Ahmed; Seth Winfree
  • Funders
  • Agence Nationale de la Recherche
  • Aix-Marseille University
  • Fondation pour la Recherche Médicale
  • Centre National de la Recherche Scientifique and Institut National de la Santé et de la Recherche Médicale
LATEST VERSION PUBLISHED 08 Apr 2021
https://doi.org/10.12688/f1000research.51794.1
Research Article metrics
Summary of two questionnaires designed to understand the research climate for Bioimage Analysts in the UK between 2016-2019
[version 1; peer review: 1 approved, 2 approved with reservations]
Dominic Waithe
Peer Reviewers Julien Colombelli; Julia Fernandez-Rodriguez; Martin L. Jones
  • Funder
  • UKRI MRC
PUBLISHED 06 Apr 2021
https://doi.org/10.12688/f1000research.25447.2
Software Tool Article metrics
Revised
DEVILS: a tool for the visualization of large datasets with a high dynamic range
[version 2; peer review: 2 approved]
Romain Guiet, Olivier Burri, Nicolas Chiaruttini, Olivier Hagens, Arne Seitz
Peer Reviewers Sebastien Tosi; Mehedi Masud
  • Funder
  • Norges Forskningsråd
LATEST VERSION PUBLISHED 22 Mar 2021
1-20 of 29 ARTICLES
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