Literature DB >> 34862501

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

Mathias Hammer1,2, Maximiliaan Huisman1, Alessandro Rigano3, Ulrike Boehm4, James J Chambers5, Nathalie Gaudreault6, Alison J North7, Jaime A Pimentel8, Damir Sudar9, Peter Bajcsy10, Claire M Brown11, Alexander D Corbett12, Orestis Faklaris13, Judith Lacoste14, Alex Laude15, Glyn Nelson15, Roland Nitschke16, Farzin Farzam1, Carlas S Smith17, David Grunwald1, Caterina Strambio-De-Castillia18.   

Abstract

Entities:  

Mesh:

Year:  2021        PMID: 34862501      PMCID: PMC9271325          DOI: 10.1038/s41592-021-01327-9

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


× No keyword cloud information.
  42 in total

1.  Informatics and quantitative analysis in biological imaging.

Authors:  Jason R Swedlow; Ilya Goldberg; Erik Brauner; Peter K Sorger
Journal:  Science       Date:  2003-04-04       Impact factor: 47.728

2.  Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE).

Authors:  Eric W Deutsch; Catherine A Ball; Jules J Berman; G Steven Bova; Alvis Brazma; Roger E Bumgarner; David Campbell; Helen C Causton; Jeffrey H Christiansen; Fabrice Daian; Delphine Dauga; Duncan R Davidson; Gregory Gimenez; Young Ah Goo; Sean Grimmond; Thorsten Henrich; Bernhard G Herrmann; Michael H Johnson; Martin Korb; Jason C Mills; Asa J Oudes; Helen E Parkinson; Laura E Pascal; Nicolas Pollet; John Quackenbush; Mirana Ramialison; Martin Ringwald; David Salgado; Susanna-Assunta Sansone; Gavin Sherlock; Christian J Stoeckert; Jason Swedlow; Ronald C Taylor; Laura Walashek; Anthony Warford; David G Wilkinson; Yi Zhou; Leonard I Zon; Alvin Y Liu; Lawrence D True
Journal:  Nat Biotechnol       Date:  2008-03       Impact factor: 54.908

Review 3.  A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis?

Authors:  Jesse Aaron; Teng-Leong Chew
Journal:  J Cell Sci       Date:  2021-03-30       Impact factor: 5.285

Review 4.  Reproducibility in light microscopy: Maintenance, standards and SOPs.

Authors:  Rebecca C Deagle; Tse-Luen Erika Wee; Claire M Brown
Journal:  Int J Biochem Cell Biol       Date:  2017-06-09       Impact factor: 5.085

5.  1,500 scientists lift the lid on reproducibility.

Authors:  Monya Baker
Journal:  Nature       Date:  2016-05-26       Impact factor: 49.962

6.  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 7.  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

8.  QUAREP-LiMi: a community endeavor to advance quality assessment and reproducibility in light microscopy.

Authors:  Ulrike Boehm; Glyn Nelson; Claire M Brown; Steve Bagley; Peter Bajcsy; Johanna Bischof; Aurelien Dauphin; Ian M Dobbie; John E Eriksson; Orestis Faklaris; Julia Fernandez-Rodriguez; Alexia Ferrand; Laurent Gelman; Ali Gheisari; Hella Hartmann; Christian Kukat; Alex Laude; Miso Mitkovski; Sebastian Munck; Alison J North; Tobias M Rasse; Ute Resch-Genger; Lucas C Schuetz; Arne Seitz; Caterina Strambio-De-Castillia; Jason R Swedlow; Roland Nitschke
Journal:  Nat Methods       Date:  2021-12       Impact factor: 47.990

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.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

View more
  6 in total

1.  Quality assessment in light microscopy for routine use through simple tools and robust metrics.

Authors:  Orestis Faklaris; Leslie Bancel-Vallée; Aurélien Dauphin; Baptiste Monterroso; Perrine Frère; David Geny; Tudor Manoliu; Sylvain de Rossi; Fabrice P Cordelières; Damien Schapman; Roland Nitschke; Julien Cau; Thomas Guilbert
Journal:  J Cell Biol       Date:  2022-09-29       Impact factor: 8.077

2.  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

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 European Bioinformatics Institute (EMBL-EBI) in 2021.

Authors:  Gaia Cantelli; Alex Bateman; Cath Brooksbank; Anton I Petrov; Rahuman S Malik-Sheriff; Michele Ide-Smith; Henning Hermjakob; Paul Flicek; Rolf Apweiler; Ewan Birney; Johanna McEntyre
Journal:  Nucleic Acids Res       Date:  2022-01-07       Impact factor: 16.971

5.  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

6.  Standard metadata for 3D microscopy.

Authors:  Alexander J Ropelewski; Megan A Rizzo; Jason R Swedlow; Jan Huisken; Pavel Osten; Neda Khanjani; Kurt Weiss; Vesselina Bakalov; Michelle Engle; Lauren Gridley; Michelle Krzyzanowski; Tom Madden; Deborah Maiese; Meisha Mandal; Justin Waterfield; David Williams; Carol M Hamilton; Wayne Huggins
Journal:  Sci Data       Date:  2022-07-27       Impact factor: 8.501

  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.