MITI minimum information guidelines for highly multiplexed tissue images

Human Tumor Atlas Network; 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; Daniel L. Abravanel; Samuel Achilefu; Foluso O. Ademuyiwa; Andrew C. Adey; Rebecca Aft; Khung Jun Ahn; Fatemeh Alikarami; Shahar Alon; Orr Ashenberg; Ethan Baker; Gregory J. Baker; Shovik Bandyopadhyay; Peter Bayguinov; Jennifer Beane; Winston Becker; Kathrin Bernt; Courtney B. Betts; Julie Bletz; Tim Blosser; Adrienne Boire; Genevieve M. Boland; Edward S. Boyden; Elmar Bucher; Raphael Bueno; Qiuyin Cai; Francesco Cambuli; Joshua Campbell; Song Cao; Wagma Caravan; Ronan Chaligné; Joseph M. Chan; Sara Chasnoff; Deyali Chatterjee; Alyce A. Chen; Hayan Lee

doi:10.1038/s41592-022-01415-4

MITI minimum information guidelines for highly multiplexed tissue images

Human Tumor Atlas Network, 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, Daniel L. Abravanel, Samuel Achilefu, Foluso O. Ademuyiwa, Andrew C. AdeyRebecca Aft, Khung Jun Ahn, Fatemeh Alikarami, Shahar Alon, Orr Ashenberg, Ethan Baker, Gregory J. Baker, Shovik Bandyopadhyay, Peter Bayguinov, Jennifer Beane, Winston Becker, Kathrin Bernt, Courtney B. Betts, Julie Bletz, Tim Blosser, Adrienne Boire, Genevieve M. Boland, Edward S. Boyden, Elmar Bucher, Raphael Bueno, Qiuyin Cai, Francesco Cambuli, Joshua Campbell, Song Cao, Wagma Caravan, Ronan Chaligné, Joseph M. Chan, Sara Chasnoff, Deyali Chatterjee, Alyce A. Chen, Hayan Lee

Research output: Contribution to journal › Comment/debate

29 Scopus citations

Abstract

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that 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 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
DOIs	https://doi.org/10.1038/s41592-022-01415-4
State	Published - Mar 2022

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Human Tumor Atlas Network, 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., Abravanel, D. L., Achilefu, S., Ademuyiwa, F. O., ... Lee, H. (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{1205aee9fed449089e426c8bcc661dc3,

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

abstract = "The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that 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 other microscopy data to highly multiplexed tissue images and traditional histology.",

author = "{Human Tumor Atlas Network} and Denis Schapiro and Clarence Yapp and Artem Sokolov and Reynolds, {Sheila M.} and Chen, {Yu An} 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 Lin, {Jia Ren} and Burlingame, {Erik A.} and Abravanel, {Daniel L.} and Samuel Achilefu and Ademuyiwa, {Foluso O.} and Adey, {Andrew C.} and Rebecca Aft and Ahn, {Khung Jun} and Fatemeh Alikarami and Shahar Alon and Orr Ashenberg and Ethan Baker and Baker, {Gregory J.} and Shovik Bandyopadhyay and Peter Bayguinov and Jennifer Beane and Winston Becker and Kathrin Bernt and Betts, {Courtney B.} and Julie Bletz and Tim Blosser and Adrienne Boire and Boland, {Genevieve M.} and Boyden, {Edward S.} and Elmar Bucher and Raphael Bueno and Qiuyin Cai and Francesco Cambuli and Joshua Campbell and Song Cao and Wagma Caravan and Ronan Chalign{\'e} and Chan, {Joseph M.} and Sara Chasnoff and Deyali Chatterjee and Chen, {Alyce A.} and Hayan Lee",

year = "2022",

month = mar,

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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Human Tumor Atlas Network, Schapiro, D, Yapp, C, Sokolov, A, Reynolds, SM, Chen, YA, Sudar, D, Xie, Y, Muhlich, J, Arias-Camison, R, Arena, S, Taylor, AJ, Nikolov, M, Tyler, M, Lin, JR, Burlingame, EA, Abravanel, DL, Achilefu, S, Ademuyiwa, FO, Adey, AC, Aft, R, Ahn, KJ, Alikarami, F, Alon, S, Ashenberg, O, Baker, E, Baker, GJ, Bandyopadhyay, S, Bayguinov, P, Beane, J, Becker, W, Bernt, K, Betts, CB, Bletz, J, Blosser, T, Boire, A, Boland, GM, Boyden, ES, Bucher, E, Bueno, R, Cai, Q, Cambuli, F, Campbell, J, Cao, S, Caravan, W, Chaligné, R, Chan, JM, Chasnoff, S, Chatterjee, D, Chen, AA & Lee, H 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 - Human Tumor Atlas Network

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 - Abravanel, Daniel L.

AU - Achilefu, Samuel

AU - Ademuyiwa, Foluso O.

AU - Adey, Andrew C.

AU - Aft, Rebecca

AU - Ahn, Khung Jun

AU - Alikarami, Fatemeh

AU - Alon, Shahar

AU - Ashenberg, Orr

AU - Baker, Ethan

AU - Baker, Gregory J.

AU - Bandyopadhyay, Shovik

AU - Bayguinov, Peter

AU - Beane, Jennifer

AU - Becker, Winston

AU - Bernt, Kathrin

AU - Betts, Courtney B.

AU - Bletz, Julie

AU - Blosser, Tim

AU - Boire, Adrienne

AU - Boland, Genevieve M.

AU - Boyden, Edward S.

AU - Bucher, Elmar

AU - Bueno, Raphael

AU - Cai, Qiuyin

AU - Cambuli, Francesco

AU - Campbell, Joshua

AU - Cao, Song

AU - Caravan, Wagma

AU - Chaligné, Ronan

AU - Chan, Joseph M.

AU - Chasnoff, Sara

AU - Chatterjee, Deyali

AU - Chen, Alyce A.

AU - Lee, Hayan

PY - 2022/3

Y1 - 2022/3

N2 - The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that 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 other microscopy data to highly multiplexed tissue images and traditional histology.

AB - The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that 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 other microscopy data to highly multiplexed tissue images and traditional histology.

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

AN - SCOPUS:85126388877

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

Abstract

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