MITI minimum information guidelines for highly multiplexed tissue images

Denis Schapiro; Clarence Yapp; Artem Sokolov; Sheila M. Reynolds; Yu-An Chen; Damir Sudar; Yubin Xie; Jeremy Muhlich; Raquel Arias-Camison; Sarah Arena; Adam J. Taylor; Milen Nikolov; Madison Tyler; Jia-Ren Lin; Erik A. Burlingame; Young H. Chang; Samouil L. Farhi; Vésteinn Thorsson; Nithya Venkatamohan; Julia L. Drewes; Dana Pe'er; David A. Gutman; Markus D. Herrmann; Nils Gehlenborg; Peter Bankhead; Joseph T. Roland; John M Herndon; Michael P Snyder; Michael Angelo; Garry Nolan; Jason R. Swedlow; Nikolaus Schultz; Daniel T. Merrick; Sarah A. Mazzili; Ethan Cerami; Scott J. Rodig; Sandro Santagata; Peter K. Sorger

doi:10.1038/s41592-022-01415-4

MITI minimum information guidelines for highly multiplexed tissue images

, Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy Muhlich, Raquel Arias-Camison, Sarah Arena, Adam J. Taylor, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Young H. Chang, Samouil L. Farhi, Vésteinn Thorsson, Nithya VenkatamohanJulia L. Drewes, Dana Pe'er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M Herndon, Michael P Snyder, Michael Angelo, Garry Nolan, Jason R. Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzili, Ethan Cerami, Scott J. Rodig, Sandro Santagata (Lead / Corresponding author), Peter K. Sorger (Lead / Corresponding author)

Gene Regulation and Expression

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Abstract

The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards to guide data deposition, curation and release. We describe a Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.

Original language	English
Pages (from-to)	262-267
Number of pages	6
Journal	Nature Methods
Volume	19
Issue number	3
Early online date	11 Mar 2022
DOIs	https://doi.org/10.1038/s41592-022-01415-4
Publication status	Published - 21 Mar 2022

Keywords

Data publication and archiving
Databases
Image processing
Standards

ASJC Scopus subject areas

Molecular Biology
Biochemistry
Biotechnology
Cell Biology

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10.1038/s41592-022-01415-4

Author Accepted ManuscriptAccepted author manuscript, 889 KB

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, Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S. M., Chen, Y-A., Sudar, D., Xie, Y., Muhlich, J., Arias-Camison, R., Arena, S., Taylor, A. J., Nikolov, M., Tyler, M., Lin, J-R., Burlingame, E. A., Chang, Y. H., Farhi, S. L., Thorsson, V., ... Sorger, P. K. (2022). MITI minimum information guidelines for highly multiplexed tissue images. Nature Methods, 19(3), 262-267. https://doi.org/10.1038/s41592-022-01415-4

@article{ffde6e1b13c547488e2ba50f0a61b174,

title = "MITI minimum information guidelines for highly multiplexed tissue images",

abstract = "The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards to guide data deposition, curation and release. We describe a Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.",

keywords = "Data publication and archiving, Databases, Image processing, Standards",

author = "Denis Schapiro and Clarence Yapp and Artem Sokolov and Reynolds, {Sheila M.} and Yu-An Chen and Damir Sudar and Yubin Xie and Jeremy Muhlich and Raquel Arias-Camison and Sarah Arena and Taylor, {Adam J.} and Milen Nikolov and Madison Tyler and Jia-Ren Lin and Burlingame, {Erik A.} and Chang, {Young H.} and Farhi, {Samouil L.} and V{\'e}steinn Thorsson and Nithya Venkatamohan and Drewes, {Julia L.} and Dana Pe'er and Gutman, {David A.} and Herrmann, {Markus D.} and Nils Gehlenborg and Peter Bankhead and Roland, {Joseph T.} and Herndon, {John M} and Snyder, {Michael P} and Michael Angelo and Garry Nolan and Swedlow, {Jason R.} and Nikolaus Schultz and Merrick, {Daniel T.} and Mazzili, {Sarah A.} and Ethan Cerami and Rodig, {Scott J.} and Sandro Santagata and Sorger, {Peter K.}",

note = "This work was supported by the following grants from the US National Cancer Institute under the Human Tumor Atlas Network (HTAN): U2C CA233262 (Harvard Medical School), U2C CA233280 (OHSU), U2C CA233195 (Boston DFCI Broad), U2C CA233291 (Vanderbilt University Medical Center), U2C CA233311 (Stanford University), U2C CA233238 (Boston University Medical Campus), U2C CA233285 (Children{\textquoteright}s Hospital of Philadelphia), U2C CA233303 (Washington University St. Louis), U2C CA233280 (Oregon Health and Science University), U2C CA233284 (Memorial Sloan Kettering Cancer Center) and U2C CA233254 (Duke University Medical Center), and by other public support including U54 CA225088 (S.S., P.K.S.) and U24 CA233243 (Dana-Farber Cancer Institute, Emory University, Institute for Systems Biology, Memorial Sloan Kettering Cancer Center, Sage Bionetworks). D. Schapiro was funded by an Early Postdoc Mobility fellowship (no. P2ZHP3_181475) from the Swiss National Science Foundation and was a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRQ-03-20); D. Schapiro is currently supported by the BMBF (01ZZ2004). N.G. was funded by the US National Institutes of Health Human BioMolecular Atlas Program (HuBMAP) OT2 OD026677 and M.D.H. by NCI/NIH Task Order No. HHSN26110071 under Contract No. HHSN2612015000031.",

year = "2022",

month = mar,

day = "21",

doi = "10.1038/s41592-022-01415-4",

language = "English",

volume = "19",

pages = "262--267",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "3",

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Schapiro, D, Yapp, C, Sokolov, A, Reynolds, SM, Chen, Y-A, Sudar, D, Xie, Y, Muhlich, J, Arias-Camison, R, Arena, S, Taylor, AJ, Nikolov, M, Tyler, M, Lin, J-R, Burlingame, EA, Chang, YH, Farhi, SL, Thorsson, V, Venkatamohan, N, Drewes, JL, Pe'er, D, Gutman, DA, Herrmann, MD, Gehlenborg, N, Bankhead, P, Roland, JT, Herndon, JM, Snyder, MP, Angelo, M, Nolan, G, Swedlow, JR, Schultz, N, Merrick, DT, Mazzili, SA, Cerami, E, Rodig, SJ & Santagata, S & Sorger, PK 2022, 'MITI minimum information guidelines for highly multiplexed tissue images', Nature Methods, vol. 19, no. 3, pp. 262-267. https://doi.org/10.1038/s41592-022-01415-4

TY - JOUR

T1 - MITI minimum information guidelines for highly multiplexed tissue images

AU - Schapiro, Denis

AU - Yapp, Clarence

AU - Sokolov, Artem

AU - Reynolds, Sheila M.

AU - Chen, Yu-An

AU - Sudar, Damir

AU - Xie, Yubin

AU - Muhlich, Jeremy

AU - Arias-Camison, Raquel

AU - Arena, Sarah

AU - Taylor, Adam J.

AU - Nikolov, Milen

AU - Tyler, Madison

AU - Lin, Jia-Ren

AU - Burlingame, Erik A.

AU - Chang, Young H.

AU - Farhi, Samouil L.

AU - Thorsson, Vésteinn

AU - Venkatamohan, Nithya

AU - Drewes, Julia L.

AU - Pe'er, Dana

AU - Gutman, David A.

AU - Herrmann, Markus D.

AU - Gehlenborg, Nils

AU - Bankhead, Peter

AU - Roland, Joseph T.

AU - Herndon, John M

AU - Snyder, Michael P

AU - Angelo, Michael

AU - Nolan, Garry

AU - Swedlow, Jason R.

AU - Schultz, Nikolaus

AU - Merrick, Daniel T.

AU - Mazzili, Sarah A.

AU - Cerami, Ethan

AU - Rodig, Scott J.

AU - Santagata, Sandro

AU - Sorger, Peter K.

N1 - This work was supported by the following grants from the US National Cancer Institute under the Human Tumor Atlas Network (HTAN): U2C CA233262 (Harvard Medical School), U2C CA233280 (OHSU), U2C CA233195 (Boston DFCI Broad), U2C CA233291 (Vanderbilt University Medical Center), U2C CA233311 (Stanford University), U2C CA233238 (Boston University Medical Campus), U2C CA233285 (Children’s Hospital of Philadelphia), U2C CA233303 (Washington University St. Louis), U2C CA233280 (Oregon Health and Science University), U2C CA233284 (Memorial Sloan Kettering Cancer Center) and U2C CA233254 (Duke University Medical Center), and by other public support including U54 CA225088 (S.S., P.K.S.) and U24 CA233243 (Dana-Farber Cancer Institute, Emory University, Institute for Systems Biology, Memorial Sloan Kettering Cancer Center, Sage Bionetworks). D. Schapiro was funded by an Early Postdoc Mobility fellowship (no. P2ZHP3_181475) from the Swiss National Science Foundation and was a Damon Runyon Fellow supported by the Damon Runyon Cancer Research Foundation (DRQ-03-20); D. Schapiro is currently supported by the BMBF (01ZZ2004). N.G. was funded by the US National Institutes of Health Human BioMolecular Atlas Program (HuBMAP) OT2 OD026677 and M.D.H. by NCI/NIH Task Order No. HHSN26110071 under Contract No. HHSN2612015000031.

PY - 2022/3/21

Y1 - 2022/3/21

N2 - The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards to guide data deposition, curation and release. We describe a Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.

AB - The imminent release of tissue atlases combining multichannel microscopy with single-cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards to guide data deposition, curation and release. We describe a Minimum Information about Highly Multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and for other microscopy data to highly multiplexed tissue images and traditional histology.

KW - Data publication and archiving

KW - Databases

KW - Image processing

KW - Standards

UR - https://arxiv.org/abs/2108.09499v2

UR - http://www.scopus.com/inward/record.url?scp=85126388877&partnerID=8YFLogxK

U2 - 10.1038/s41592-022-01415-4

DO - 10.1038/s41592-022-01415-4

M3 - Comment/debate

C2 - 35277708

SN - 1548-7091

VL - 19

SP - 262

EP - 267

JO - Nature Methods

JF - Nature Methods

IS - 3

ER -

MITI minimum information guidelines for highly multiplexed tissue images

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