Literature DB >> 34654919

MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text.

Joel Ryan1,2, Thomas Pengo3, Alex Rigano4, Paula Montero Llopis5, Michelle S Itano6,7,8,9, Lisa A Cameron10, Guillermo Marqués11,12, Caterina Strambio-De-Castillia4, Mark A Sanders11,12, Claire M Brown13,14.   

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Year:  2021        PMID: 34654919      PMCID: PMC9488561          DOI: 10.1038/s41592-021-01290-5

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   47.990


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  20 in total

Review 1.  A guide to accurate reporting in digital image acquisition - can anyone replicate your microscopy data?

Authors:  John M Heddleston; Jesse S Aaron; Satya Khuon; Teng-Leong Chew
Journal:  J Cell Sci       Date:  2021-03-30       Impact factor: 5.285

2.  Replication Study: Biomechanical remodeling of the microenvironment by stromal caveolin-1 favors tumor invasion and metastasis.

Authors:  Mee Rie Sheen; Jennifer L Fields; Brian Northan; Judith Lacoste; Lay-Hong Ang; Steven Fiering
Journal:  Elife       Date:  2019-12-17       Impact factor: 8.140

3.  Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.

Authors:  Mathias Hammer; Maximiliaan Huisman; Alessandro Rigano; Ulrike Boehm; James J Chambers; Nathalie Gaudreault; Alison J North; Jaime A Pimentel; Damir Sudar; Peter Bajcsy; Claire M Brown; Alexander D Corbett; Orestis Faklaris; Judith Lacoste; Alex Laude; Glyn Nelson; Roland Nitschke; Farzin Farzam; Carlas S Smith; David Grunwald; Caterina Strambio-De-Castillia
Journal:  Nat Methods       Date:  2021-12       Impact factor: 47.990

4.  The 4D nucleome project.

Authors:  Job Dekker; Andrew S Belmont; Mitchell Guttman; Victor O Leshyk; John T Lis; Stavros Lomvardas; Leonid A Mirny; Clodagh C O'Shea; Peter J Park; Bing Ren; Joan C Ritland Politz; Jay Shendure; Sheng Zhong
Journal:  Nature       Date:  2017-09-13       Impact factor: 49.962

Review 5.  Best practices and tools for reporting reproducible fluorescence microscopy methods.

Authors:  Paula Montero Llopis; Rebecca A Senft; Tim J Ross-Elliott; Ryan Stephansky; Daniel P Keeley; Preman Koshar; Guillermo Marqués; Ya-Sheng Gao; Benjamin R Carlson; Thomas Pengo; Mark A Sanders; Lisa A Cameron; Michelle S Itano
Journal:  Nat Methods       Date:  2021-06-07       Impact factor: 28.547

6.  A beginner's guide to rigor and reproducibility in fluorescence imaging experiments.

Authors:  Jen-Yi Lee; Maiko Kitaoka
Journal:  Mol Biol Cell       Date:  2018-07-01       Impact factor: 4.138

7.  FAIRsharing as a community approach to standards, repositories and policies.

Authors:  Susanna-Assunta Sansone; Peter McQuilton; Philippe Rocca-Serra; Alejandra Gonzalez-Beltran; Massimiliano Izzo; Allyson L Lister; Milo Thurston
Journal:  Nat Biotechnol       Date:  2019-04       Impact factor: 54.908

8.  No raw data, no science: another possible source of the reproducibility crisis.

Authors:  Tsuyoshi Miyakawa
Journal:  Mol Brain       Date:  2020-02-21       Impact factor: 4.041

9.  Variability in the analysis of a single neuroimaging dataset by many teams.

Authors:  Rotem Botvinik-Nezer; Felix Holzmeister; Colin F Camerer; Anna Dreber; Juergen Huber; Magnus Johannesson; Michael Kirchler; Roni Iwanir; Jeanette A Mumford; R Alison Adcock; Paolo Avesani; Blazej M Baczkowski; Aahana Bajracharya; Leah Bakst; Sheryl Ball; Marco Barilari; Nadège Bault; Derek Beaton; Julia Beitner; Roland G Benoit; Ruud M W J Berkers; Jamil P Bhanji; Bharat B Biswal; Sebastian Bobadilla-Suarez; Tiago Bortolini; Katherine L Bottenhorn; Alexander Bowring; Senne Braem; Hayley R Brooks; Emily G Brudner; Cristian B Calderon; Julia A Camilleri; Jaime J Castrellon; Luca Cecchetti; Edna C Cieslik; Zachary J Cole; Olivier Collignon; Robert W Cox; William A Cunningham; Stefan Czoschke; Kamalaker Dadi; Charles P Davis; Alberto De Luca; Mauricio R Delgado; Lysia Demetriou; Jeffrey B Dennison; Xin Di; Erin W Dickie; Ekaterina Dobryakova; Claire L Donnat; Juergen Dukart; Niall W Duncan; Joke Durnez; Amr Eed; Simon B Eickhoff; Andrew Erhart; Laura Fontanesi; G Matthew Fricke; Shiguang Fu; Adriana Galván; Remi Gau; Sarah Genon; Tristan Glatard; Enrico Glerean; Jelle J Goeman; Sergej A E Golowin; Carlos González-García; Krzysztof J Gorgolewski; Cheryl L Grady; Mikella A Green; João F Guassi Moreira; Olivia Guest; Shabnam Hakimi; J Paul Hamilton; Roeland Hancock; Giacomo Handjaras; Bronson B Harry; Colin Hawco; Peer Herholz; Gabrielle Herman; Stephan Heunis; Felix Hoffstaedter; Jeremy Hogeveen; Susan Holmes; Chuan-Peng Hu; Scott A Huettel; Matthew E Hughes; Vittorio Iacovella; Alexandru D Iordan; Peder M Isager; Ayse I Isik; Andrew Jahn; Matthew R Johnson; Tom Johnstone; Michael J E Joseph; Anthony C Juliano; Joseph W Kable; Michalis Kassinopoulos; Cemal Koba; Xiang-Zhen Kong; Timothy R Koscik; Nuri Erkut Kucukboyaci; Brice A Kuhl; Sebastian Kupek; Angela R Laird; Claus Lamm; Robert Langner; Nina Lauharatanahirun; Hongmi Lee; Sangil Lee; Alexander Leemans; Andrea Leo; Elise Lesage; Flora Li; Monica Y C Li; Phui Cheng Lim; Evan N Lintz; Schuyler W Liphardt; Annabel B Losecaat Vermeer; Bradley C Love; Michael L Mack; Norberto Malpica; Theo Marins; Camille Maumet; Kelsey McDonald; Joseph T McGuire; Helena Melero; Adriana S Méndez Leal; Benjamin Meyer; Kristin N Meyer; Glad Mihai; Georgios D Mitsis; Jorge Moll; Dylan M Nielson; Gustav Nilsonne; Michael P Notter; Emanuele Olivetti; Adrian I Onicas; Paolo Papale; Kaustubh R Patil; Jonathan E Peelle; Alexandre Pérez; Doris Pischedda; Jean-Baptiste Poline; Yanina Prystauka; Shruti Ray; Patricia A Reuter-Lorenz; Richard C Reynolds; Emiliano Ricciardi; Jenny R Rieck; Anais M Rodriguez-Thompson; Anthony Romyn; Taylor Salo; Gregory R Samanez-Larkin; Emilio Sanz-Morales; Margaret L Schlichting; Douglas H Schultz; Qiang Shen; Margaret A Sheridan; Jennifer A Silvers; Kenny Skagerlund; Alec Smith; David V Smith; Peter Sokol-Hessner; Simon R Steinkamp; Sarah M Tashjian; Bertrand Thirion; John N Thorp; Gustav Tinghög; Loreen Tisdall; Steven H Tompson; Claudio Toro-Serey; Juan Jesus Torre Tresols; Leonardo Tozzi; Vuong Truong; Luca Turella; Anna E van 't Veer; Tom Verguts; Jean M Vettel; Sagana Vijayarajah; Khoi Vo; Matthew B Wall; Wouter D Weeda; Susanne Weis; David J White; David Wisniewski; Alba Xifra-Porxas; Emily A Yearling; Sangsuk Yoon; Rui Yuan; Kenneth S L Yuen; Lei Zhang; Xu Zhang; Joshua E Zosky; Thomas E Nichols; Russell A Poldrack; Tom Schonberg
Journal:  Nature       Date:  2020-05-20       Impact factor: 69.504

10.  A call for public archives for biological image data.

Authors:  Jan Ellenberg; Jason R Swedlow; Mary Barlow; Charles E Cook; Ugis Sarkans; Ardan Patwardhan; Alvis Brazma; Ewan Birney
Journal:  Nat Methods       Date:  2018-11       Impact factor: 28.547

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  3 in total

1.  MethodsJ2: a software tool to capture metadata and generate comprehensive microscopy methods text.

Authors:  Joel Ryan; Thomas Pengo; Alex Rigano; Paula Montero Llopis; Michelle S Itano; Lisa A Cameron; Guillermo Marqués; Caterina Strambio-De-Castillia; Mark A Sanders; Claire M Brown
Journal:  Nat Methods       Date:  2021-12       Impact factor: 47.990

2.  Towards community-driven metadata standards for light microscopy: tiered specifications extending the OME model.

Authors:  Mathias Hammer; Maximiliaan Huisman; Alessandro Rigano; Ulrike Boehm; James J Chambers; Nathalie Gaudreault; Alison J North; Jaime A Pimentel; Damir Sudar; Peter Bajcsy; Claire M Brown; Alexander D Corbett; Orestis Faklaris; Judith Lacoste; Alex Laude; Glyn Nelson; Roland Nitschke; Farzin Farzam; Carlas S Smith; David Grunwald; Caterina Strambio-De-Castillia
Journal:  Nat Methods       Date:  2021-12       Impact factor: 47.990

3.  Microscopy-BIDS: An Extension to the Brain Imaging Data Structure for Microscopy Data.

Authors:  Marie-Hélène Bourget; Lee Kamentsky; Satrajit S Ghosh; Giacomo Mazzamuto; Alberto Lazari; Christopher J Markiewicz; Robert Oostenveld; Guiomar Niso; Yaroslav O Halchenko; Ilona Lipp; Sylvain Takerkart; Paule-Joanne Toussaint; Ali R Khan; Gustav Nilsonne; Filippo Maria Castelli; Julien Cohen-Adad
Journal:  Front Neurosci       Date:  2022-04-19       Impact factor: 5.152

  3 in total

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