REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology

Ugis Sarkans; Wah Chiu; Lucy Collinson; Michele C. Darrow; Jan Ellenberg; David Grunwald; Jean-Karim Hériché; Andrii Iudin; Gabriel G. Martins; Terry Meehan; Kedar Narayan; Ardan Patwardhan; Matthew Robert Geoffrey Russell; Helen R. Saibil; Caterina Strambio-De-Castillia; Jason R. Swedlow; Christian Tischer; Virginie Uhlmann; Paul Verkade; Mary Barlow; Omer Bayraktar; Ewan Birney; Cesare Catavitello; Christopher Cawthorne; Stephan Wagner-Conrad; Elizabeth Duke; Perrine Paul-Gilloteaux; Emmanuel Gustin; Maria Harkiolaki; Pasi Kankaanpää; Thomas Lemberger; Jo McEntyre; Josh Moore; Andrew W. Nicholls; Shuichi Onami; Helen Parkinson; Maddy Parsons; Marina Romanchikova; Nicholas Sofroniew; Jim Swoger; Nadine Utz; Lenard M. Voortman; Frances Wong; Peijun Zhang; Gerard J. Kleywegt; Alvis Brazma

doi:10.1038/s41592-021-01166-8

REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology

Ugis Sarkans (Lead / Corresponding author)
, Wah Chiu
, Lucy Collinson
, Michele C. Darrow
, Jan Ellenberg
, David Grunwald
, Jean-Karim Hériché
, Andrii Iudin
, Gabriel G. Martins
, Terry Meehan
, Kedar Narayan
, Ardan Patwardhan
, Matthew Robert Geoffrey Russell
, Helen R. Saibil
, Caterina Strambio-De-Castillia
, Jason R. Swedlow
, Christian Tischer
, Virginie Uhlmann
, Paul Verkade
, Mary Barlow

Omer Bayraktar, Ewan Birney, Cesare Catavitello, Christopher Cawthorne, Stephan Wagner-Conrad, Elizabeth Duke, Perrine Paul-Gilloteaux, Emmanuel Gustin, Maria Harkiolaki, Pasi Kankaanpää, Thomas Lemberger, Jo McEntyre, Josh Moore, Andrew W. Nicholls, Shuichi Onami, Helen Parkinson, Maddy Parsons, Marina Romanchikova, Nicholas Sofroniew, Jim Swoger, Nadine Utz, Lenard M. Voortman, Frances Wong, Peijun Zhang, Gerard J. Kleywegt (Lead / Corresponding author), Alvis Brazma (Lead / Corresponding author)

Research output: Contribution to journal › Comment/debate › peer-review

79 Citations (Scopus)

Abstract

Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

Original language	English
Pages (from-to)	1418-1422
Number of pages	5
Journal	Nature Methods
Volume	18
Early online date	21 May 2021
DOIs	https://doi.org/10.1038/s41592-021-01166-8
Publication status	Published - Dec 2021

Keywords

Data integration
Molecular imaging
Optical imaging

ASJC Scopus subject areas

Molecular Biology
Biochemistry
Biotechnology
Cell Biology

Access to Document

10.1038/s41592-021-01166-8

Connecting and Expanding RIKENs Systems Science of Biological Dynamics and OMEs Image Data Resource Databases (International Travel Award)
Swedlow, J. (Investigator)
Biotechnology and Biological Sciences Research Council
5/10/18 → 4/11/18
Project: Research
The Image Data Resource: Making Biological Imaging Data FAIR (Joint with EMBL-EBI) (Biomedical Resources Grant)
Swedlow, J. (Investigator)
1/10/18 → 1/04/22
Project: Research
BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)
Swedlow, J. (Investigator)
Biotechnology and Biological Sciences Research Council
1/07/18 → 30/06/21
Project: Research

Cite this

Sarkans, U., Chiu, W., Collinson, L., Darrow, M. C., Ellenberg, J., Grunwald, D., Hériché, J.-K., Iudin, A., Martins, G. G., Meehan, T., Narayan, K., Patwardhan, A., Russell, M. R. G., Saibil, H. R., Strambio-De-Castillia, C., Swedlow, J. R., Tischer, C., Uhlmann, V., Verkade, P., ... Brazma, A. (2021). REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nature Methods, 18, 1418-1422. https://doi.org/10.1038/s41592-021-01166-8

@article{b4a481547a054483b492db86394e38fe,

title = "REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology",

abstract = "Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.",

keywords = "Data integration, Molecular imaging, Optical imaging",

author = "Ugis Sarkans and Wah Chiu and Lucy Collinson and Darrow, \{Michele C.\} and Jan Ellenberg and David Grunwald and Jean-Karim H{\'e}rich{\'e} and Andrii Iudin and Martins, \{Gabriel G.\} and Terry Meehan and Kedar Narayan and Ardan Patwardhan and Russell, \{Matthew Robert Geoffrey\} and Saibil, \{Helen R.\} and Caterina Strambio-De-Castillia and Swedlow, \{Jason R.\} and Christian Tischer and Virginie Uhlmann and Paul Verkade and Mary Barlow and Omer Bayraktar and Ewan Birney and Cesare Catavitello and Christopher Cawthorne and Stephan Wagner-Conrad and Elizabeth Duke and Perrine Paul-Gilloteaux and Emmanuel Gustin and Maria Harkiolaki and Pasi Kankaanp{\"a}{\"a} and Thomas Lemberger and Jo McEntyre and Josh Moore and Nicholls, \{Andrew W.\} and Shuichi Onami and Helen Parkinson and Maddy Parsons and Marina Romanchikova and Nicholas Sofroniew and Jim Swoger and Nadine Utz and Voortman, \{Lenard M.\} and Frances Wong and Peijun Zhang and Kleywegt, \{Gerard J.\} and Alvis Brazma",

note = "Funding Information: Work on IDR by J.R.S., F.W., A.B. and U.S. is supported by the Wellcome Trust (212962/Z/18/Z) and BBSRC (BB/ R015384/1). W.C. was supported by NIH R01GM079429. L.C. was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001999), the UK Medical Research Council (FC001999) and the Wellcome Trust (FC001999). M.C.D. would like to acknowledge the Wellcome Trust (212980/Z/18/Z) for funding. J.E. was supported by a grant from the European Commission H2020-ES-RI-INFRAEOSC “EOSC-Life” (Grant Agreement 824087). D.G. was supported by NIH 8U01DA047733-05 and NSF 1917206. Work on EMPIAR by A.P., A.I., C. Catavitello and G.J.K. is supported by UKRI-MRC (MR/P019544/1), the Wellcome Trust (221371/Z/20/Z) and EMBL-EBI. G.G.M. is supported by grant PTDCBII-BTI323752017-FCT and is part of the national Portuguese infrastructure PPBI, supported by PPBI-POCI-01-0145-FEDER-022122 from Funda{\c c}{\~a}o para a Ci{\^e}ncia e Tecnologia / FEDER. T.M. and H.P. were supported in part by NIH Common Fund Award 5UM1HG006370-10. K.N. was supported by federal funds from the National Cancer Institute, National Institutes of Health, under contract no. HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the US Government. C.S.-D.-C. was supported by the Chan Zuckerberg Initiative (Imaging Scientist award no. 2019-198155) and by NIH grant U01CA200059. V.U., M.B., E.B. and J. McEntyre are supported by EMBL internal funding. C. Cawthorne was supported by the Fonds Wetenschappelijk Onderzoek (FWO 1001719N). P.P.-G. was supported by CROCOVAL (ANR-18-CE45-0015) and is part of the national infrastructure “France BioImaging” supported by the ANR PIA1 (ANR-10-INBS-04). S.O. was supported by the Core Research for Evolutionary Science and Technology (CREST) grant no. JPMJCR1511, Japan Science and Technology Agency (JST). M.P. is supported by BBSRC Bioimaging UK community network grant (BB/S018689/1). P.Z. is supported by the Wellcome Trust (206422/Z/17/Z) and BBSRC (BB/S003339/1).",

year = "2021",

month = dec,

doi = "10.1038/s41592-021-01166-8",

language = "English",

volume = "18",

pages = "1418--1422",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Research",

}

Sarkans, U, Chiu, W, Collinson, L, Darrow, MC, Ellenberg, J, Grunwald, D, Hériché, J-K, Iudin, A, Martins, GG, Meehan, T, Narayan, K, Patwardhan, A, Russell, MRG, Saibil, HR, Strambio-De-Castillia, C, Swedlow, JR, Tischer, C, Uhlmann, V, Verkade, P, Barlow, M, Bayraktar, O, Birney, E, Catavitello, C, Cawthorne, C, Wagner-Conrad, S, Duke, E, Paul-Gilloteaux, P, Gustin, E, Harkiolaki, M, Kankaanpää, P, Lemberger, T, McEntyre, J, Moore, J, Nicholls, AW, Onami, S, Parkinson, H, Parsons, M, Romanchikova, M, Sofroniew, N, Swoger, J, Utz, N, Voortman, LM, Wong, F, Zhang, P, Kleywegt, GJ & Brazma, A 2021, 'REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology', Nature Methods, vol. 18, pp. 1418-1422. https://doi.org/10.1038/s41592-021-01166-8

TY - JOUR

T1 - REMBI

T2 - Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology

AU - Sarkans, Ugis

AU - Chiu, Wah

AU - Collinson, Lucy

AU - Darrow, Michele C.

AU - Ellenberg, Jan

AU - Grunwald, David

AU - Hériché, Jean-Karim

AU - Iudin, Andrii

AU - Martins, Gabriel G.

AU - Meehan, Terry

AU - Narayan, Kedar

AU - Patwardhan, Ardan

AU - Russell, Matthew Robert Geoffrey

AU - Saibil, Helen R.

AU - Strambio-De-Castillia, Caterina

AU - Swedlow, Jason R.

AU - Tischer, Christian

AU - Uhlmann, Virginie

AU - Verkade, Paul

AU - Barlow, Mary

AU - Bayraktar, Omer

AU - Birney, Ewan

AU - Catavitello, Cesare

AU - Cawthorne, Christopher

AU - Wagner-Conrad, Stephan

AU - Duke, Elizabeth

AU - Paul-Gilloteaux, Perrine

AU - Gustin, Emmanuel

AU - Harkiolaki, Maria

AU - Kankaanpää, Pasi

AU - Lemberger, Thomas

AU - McEntyre, Jo

AU - Moore, Josh

AU - Nicholls, Andrew W.

AU - Onami, Shuichi

AU - Parkinson, Helen

AU - Parsons, Maddy

AU - Romanchikova, Marina

AU - Sofroniew, Nicholas

AU - Swoger, Jim

AU - Utz, Nadine

AU - Voortman, Lenard M.

AU - Wong, Frances

AU - Zhang, Peijun

AU - Kleywegt, Gerard J.

AU - Brazma, Alvis

N1 - Funding Information: Work on IDR by J.R.S., F.W., A.B. and U.S. is supported by the Wellcome Trust (212962/Z/18/Z) and BBSRC (BB/ R015384/1). W.C. was supported by NIH R01GM079429. L.C. was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001999), the UK Medical Research Council (FC001999) and the Wellcome Trust (FC001999). M.C.D. would like to acknowledge the Wellcome Trust (212980/Z/18/Z) for funding. J.E. was supported by a grant from the European Commission H2020-ES-RI-INFRAEOSC “EOSC-Life” (Grant Agreement 824087). D.G. was supported by NIH 8U01DA047733-05 and NSF 1917206. Work on EMPIAR by A.P., A.I., C. Catavitello and G.J.K. is supported by UKRI-MRC (MR/P019544/1), the Wellcome Trust (221371/Z/20/Z) and EMBL-EBI. G.G.M. is supported by grant PTDCBII-BTI323752017-FCT and is part of the national Portuguese infrastructure PPBI, supported by PPBI-POCI-01-0145-FEDER-022122 from Fundação para a Ciência e Tecnologia / FEDER. T.M. and H.P. were supported in part by NIH Common Fund Award 5UM1HG006370-10. K.N. was supported by federal funds from the National Cancer Institute, National Institutes of Health, under contract no. HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the US Government. C.S.-D.-C. was supported by the Chan Zuckerberg Initiative (Imaging Scientist award no. 2019-198155) and by NIH grant U01CA200059. V.U., M.B., E.B. and J. McEntyre are supported by EMBL internal funding. C. Cawthorne was supported by the Fonds Wetenschappelijk Onderzoek (FWO 1001719N). P.P.-G. was supported by CROCOVAL (ANR-18-CE45-0015) and is part of the national infrastructure “France BioImaging” supported by the ANR PIA1 (ANR-10-INBS-04). S.O. was supported by the Core Research for Evolutionary Science and Technology (CREST) grant no. JPMJCR1511, Japan Science and Technology Agency (JST). M.P. is supported by BBSRC Bioimaging UK community network grant (BB/S018689/1). P.Z. is supported by the Wellcome Trust (206422/Z/17/Z) and BBSRC (BB/S003339/1).

PY - 2021/12

Y1 - 2021/12

N2 - Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

AB - Bioimaging data have significant potential for reuse, but unlocking this potential requires systematic archiving of data and metadata in public databases. We propose draft metadata guidelines to begin addressing the needs of diverse communities within light and electron microscopy. We hope this publication and the proposed Recommended Metadata for Biological Images (REMBI) will stimulate discussions about their implementation and future extension.

KW - Data integration

KW - Molecular imaging

KW - Optical imaging

U2 - 10.1038/s41592-021-01166-8

DO - 10.1038/s41592-021-01166-8

M3 - Comment/debate

C2 - 34021280

SN - 1548-7091

VL - 18

SP - 1418

EP - 1422

JO - Nature Methods

JF - Nature Methods

ER -

REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Fingerprint

Projects

Connecting and Expanding RIKENs Systems Science of Biological Dynamics and OMEs Image Data Resource Databases (International Travel Award)

The Image Data Resource: Making Biological Imaging Data FAIR (Joint with EMBL-EBI) (Biomedical Resources Grant)

BioStudies and the Image Data Resource: Expanding Imaging Datasets, Linkage, Metadata and Value (Joint with EMBL-EBI) (Bioinformatics and Biological Resources Fund - BBR)

Cite this