MITI minimum information guidelines for highly multiplexed tissue images

Human Tumor Atlas Network; Foluso O. Ademuyiwa; Rebecca Aft; Peter Bayguinov; Song Cao; Wagma Caravan; Sara Chasnoff; Deyali Chatterjee; Feng Chen; Siqi Chen; Milan G. Chheda; Graham A. Colditz; Daniel Cui Zhou; Sherri R. Davies; David Denardo; Li Ding; John DiPersio; Timothy J. Eberlein; Ryan C. Fields; James Fitzpatrick; Bob Fulton; William E. Gillanders; William G. Hawkins; James J. Hsieh; Michael D. Iglesia; Reyka G. Jayasinghe; Tao Ju; Albert H. Kim; Praveen Krishnamoorthy; Yize Li; Wen Wen Liang; Kian Huat Lim; Ruiyang Liu; Cynthia Ma; Chris Maher; Jay Mashl; Joshua McMichael; Jacqueline Mudd; Nataly Naser Al Deen; Stephen T. Oh; Gary J. Patti; Sidharth V. Puram; Kooresh I. Shoghi; Sheng Kwei Song; Deborah J. Veis; Richard Wahl; Michael C. Wendl; Matthew A. Wyczalkowski

doi:10.1038/s41592-022-01415-4

MITI minimum information guidelines for highly multiplexed tissue images

Human Tumor Atlas Network, Foluso O. Ademuyiwa, Rebecca Aft, Peter Bayguinov, Song Cao, Wagma Caravan, Sara Chasnoff, Deyali Chatterjee, Feng Chen, Siqi Chen, Milan G. Chheda, Graham A. Colditz, Daniel Cui Zhou, Sherri R. Davies, David Denardo, Li Ding, John DiPersio, Timothy J. Eberlein, Ryan C. Fields, James FitzpatrickBob Fulton, William E. Gillanders, William G. Hawkins, James J. Hsieh, Michael D. Iglesia, Reyka G. Jayasinghe, Tao Ju, Albert H. Kim, Praveen Krishnamoorthy, Yize Li, Wen Wen Liang, Kian Huat Lim, Ruiyang Liu, Cynthia Ma, Chris Maher, Jay Mashl, Joshua McMichael, Jacqueline Mudd, Nataly Naser Al Deen, Stephen T. Oh, Gary J. Patti, Sidharth V. Puram, Kooresh I. Shoghi, Sheng Kwei Song, Deborah J. Veis, Richard Wahl, Michael C. Wendl, Matthew A. Wyczalkowski

Research output: Contribution to journal › Comment/debate

28 Scopus citations

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, Ademuyiwa, F. O., Aft, R., Bayguinov, P., Cao, S., Caravan, W., Chasnoff, S., Chatterjee, D., Chen, F., Chen, S., Chheda, M. G., Colditz, G. A., Zhou, D. C., Davies, S. R., Denardo, D., Ding, L., DiPersio, J., Eberlein, T. J., Fields, R. C., ... Wyczalkowski, M. A. (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{54d6335dec48451d9b57d3221f649950,

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

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 Changya Chen and Chen, {Chia hui} and Bob Chen and Feng Chen and Siqi Chen and Chheda, {Milan G.} and Koei Chin and Hyeyoung Cho and Jaeyoung Chun and Luis Cisneros and Coffey, {Robert J.} and Ofir Cohen and Colditz, {Graham A.} and Cole, {Kristina A.} and Natalie Collins and Daniel Cotter and Coussens, {Lisa M.} and Shannon Coy and Creason, {Allison L.} and Yi Cui and Zhou, {Daniel Cui} and Christina Curtis and Davies, {Sherri R.} and Inode Bruijn and Delorey, {Toni M.} and Emek Demir and David Denardo and Dinh Diep and Li Ding and John DiPersio and Dubinett, {Steven M.} and Eberlein, {Timothy J.} and Eddy, {James A.} and Esplin, {Edward D.} and Factor, {Rachel E.} and Kayvon Fatahalian and Feiler, {Heidi S.} and Jose Fernandez and Andrew Fields and Fields, {Ryan C.} and James Fitzpatrick and Ford, {James M.} and Jeff Franklin and Bob Fulton and Giorgio Gaglia and Luciano Galdieri and Karuna Ganesh and Jianjiong Gao and Gaudio, {Benjamin L.} and Gad Getz and Gibbs, {David L.} and Gillanders, {William E.} and Jeremy Goecks and Daniel Goodwin and Gray, {Joe W.} and William Greenleaf and Grimm, {Lars J.} and Qiang Gu and Guerriero, {Jennifer L.} and Tuhin Guha and Guimaraes, {Alexander R.} and Belen Gutierrez and Nir Hacohen and Hanson, {Casey Ryan} and Harris, {Coleman R.} and Hawkins, {William G.} and Heiser, {Cody N.} and John Hoffer and Hollmann, {Travis J.} and Hsieh, {James J.} and Jeffrey Huang and Hunger, {Stephen P.} and Hwang, {Eun Sil} and Christine Iacobuzio-Donahue and Iglesia, {Michael D.} and Mohammad Islam and Benjamin Izar and Jacobson, {Connor A.} and Samuel Janes and Jayasinghe, {Reyka G.} and Tiarah Jeudi and Johnson, {Bruce E.} and Johnson, {Brett E.} and Tao Ju and Humam Kadara and Karnoub, {Elias Ramzey} and Alla Karpova and Aziz Khan and Warren Kibbe and Kim, {Albert H.} and King, {Lorraine M.} and Elyse Kozlowski and Praveen Krishnamoorthy and Robert Krueger and Anshul Kundaje and Uri Ladabaum and Rozelle Laquindanum and Clarisse Lau and Lau, {Ken Siu Kwong} and LeBoeuf, {Nicole R.} and Hayan Lee and Marc Lenburg and Ignaty Leshchiner and Rochelle Levy and Yize Li and Lian, {Christine G.} and Liang, {Wen Wen} and Lim, {Kian Huat} and Yiyun Lin and David Liu and Qi Liu and Ruiyang Liu and Joseph Lo and Pierrette Lo and Longabaugh, {William J.} and Teri Longacre and Katie Luckett and Cynthia Ma and Chris Maher and Allison Maier and Danika Makowski and Carlo Maley and Zoltan Maliga and Parvathy Manoj and Maris, {John M.} and Nick Markham and Marks, {Jeffrey R.} and Daniel Martinez and Jay Mashl and Ignas Masilionis and Joan Massague and Mazurowski, {Marciej A.} and McKinley, {Eliot T.} and Joshua McMichael and Matthew Meyerson and Mills, {Gordon B.} and Mitri, {Zahi I.} and Andrew Moorman and Jacqueline Mudd and Murphy, {George F.} and Deen, {Nataly Naser Al} and Navin, {Nicholas E.} and Oh, {Stephen T.} and Patti, {Gary J.} and Puram, {Sidharth V.} and Shoghi, {Kooresh I.} and Song, {Sheng Kwei} and Veis, {Deborah J.} and Richard Wahl and Wendl, {Michael C.} and Wyczalkowski, {Matthew A.}",

note = "Funding Information: This work is supported by the HTAN Consortium and the Cancer Systems Biology Consortium (CSBC). A list of all current HTAN Consortium members can be found at https://humantumoratlas.org/ . 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. Funding Information: P.K.S. is a member of the Scientific Advisory Board (SAB) or Board of Directors of Applied Biomath, RareCyte Inc. and Glencoe Software, which distributes a commercial version of the OMERO data management platform; P.K.S. is also a member of the NanoString SAB and a consultant to Merck and Montai Health. In the past five years, the Sorger laboratory has received research funding from Novartis and Merck. P.K.S. declares that none of these relationships have influenced the content of this manuscript. S.S. is a consultant for RareCyte Inc. N.G. is a co-founder and equity owner of Datavisyn. D. Schapiro is a consultant for Roche Glycart AG. J.R.S. is founder and CEO of Glencoe Software, which distributes a commercial version of the OMERO data management platform. S.J.R. receives research funding from Bristol Myers Squibb, Merck, Affimed and Kite/Gilead and is on the SAB of Immunitas Therapeutics. D. Sudar is employed by Quantitative Imaging Systems LLC. E.A.B. is an employee of Indica Labs. ",

year = "2022",

month = mar,

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

language = "English",

volume = "19",

pages = "262--267",

journal = "Nature Methods",

issn = "1548-7091",

number = "3",

}

Human Tumor Atlas Network, Ademuyiwa, FO , Aft, R , Bayguinov, P , Cao, S, Caravan, W, Chasnoff, S, Chatterjee, D, Chen, F, Chen, S , Chheda, MG , Colditz, GA, Zhou, DC, Davies, SR, Denardo, D , Ding, L , DiPersio, J , Eberlein, TJ , Fields, RC, Fitzpatrick, J, Fulton, B , Gillanders, WE, Hawkins, WG, Hsieh, JJ, Iglesia, MD , Jayasinghe, RG , Ju, T , Kim, AH, Krishnamoorthy, P, Li, Y, Liang, WW, Lim, KH, Liu, R, Ma, C , Maher, C, Mashl, J, McMichael, J, Mudd, J, Deen, NNA, Oh, ST , Patti, GJ , Puram, SV , Shoghi, KI , Song, SK , Veis, DJ , Wahl, R , Wendl, MC & Wyczalkowski, MA 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 - Chen, Changya

AU - Chen, Chia hui

AU - Chen, Bob

AU - Chen, Feng

AU - Chen, Siqi

AU - Chheda, Milan G.

AU - Chin, Koei

AU - Cho, Hyeyoung

AU - Chun, Jaeyoung

AU - Cisneros, Luis

AU - Coffey, Robert J.

AU - Cohen, Ofir

AU - Colditz, Graham A.

AU - Cole, Kristina A.

AU - Collins, Natalie

AU - Cotter, Daniel

AU - Coussens, Lisa M.

AU - Coy, Shannon

AU - Creason, Allison L.

AU - Cui, Yi

AU - Zhou, Daniel Cui

AU - Curtis, Christina

AU - Davies, Sherri R.

AU - Bruijn, Inode

AU - Delorey, Toni M.

AU - Demir, Emek

AU - Denardo, David

AU - Diep, Dinh

AU - Ding, Li

AU - DiPersio, John

AU - Dubinett, Steven M.

AU - Eberlein, Timothy J.

AU - Eddy, James A.

AU - Esplin, Edward D.

AU - Factor, Rachel E.

AU - Fatahalian, Kayvon

AU - Feiler, Heidi S.

AU - Fernandez, Jose

AU - Fields, Andrew

AU - Fields, Ryan C.

AU - Fitzpatrick, James

AU - Ford, James M.

AU - Franklin, Jeff

AU - Fulton, Bob

AU - Gaglia, Giorgio

AU - Galdieri, Luciano

AU - Ganesh, Karuna

AU - Gao, Jianjiong

AU - Gaudio, Benjamin L.

AU - Getz, Gad

AU - Gibbs, David L.

AU - Gillanders, William E.

AU - Goecks, Jeremy

AU - Goodwin, Daniel

AU - Gray, Joe W.

AU - Greenleaf, William

AU - Grimm, Lars J.

AU - Gu, Qiang

AU - Guerriero, Jennifer L.

AU - Guha, Tuhin

AU - Guimaraes, Alexander R.

AU - Gutierrez, Belen

AU - Hacohen, Nir

AU - Hanson, Casey Ryan

AU - Harris, Coleman R.

AU - Hawkins, William G.

AU - Heiser, Cody N.

AU - Hoffer, John

AU - Hollmann, Travis J.

AU - Hsieh, James J.

AU - Huang, Jeffrey

AU - Hunger, Stephen P.

AU - Hwang, Eun Sil

AU - Iacobuzio-Donahue, Christine

AU - Iglesia, Michael D.

AU - Islam, Mohammad

AU - Izar, Benjamin

AU - Jacobson, Connor A.

AU - Janes, Samuel

AU - Jayasinghe, Reyka G.

AU - Jeudi, Tiarah

AU - Johnson, Bruce E.

AU - Johnson, Brett E.

AU - Ju, Tao

AU - Kadara, Humam

AU - Karnoub, Elias Ramzey

AU - Karpova, Alla

AU - Khan, Aziz

AU - Kibbe, Warren

AU - Kim, Albert H.

AU - King, Lorraine M.

AU - Kozlowski, Elyse

AU - Krishnamoorthy, Praveen

AU - Krueger, Robert

AU - Kundaje, Anshul

AU - Ladabaum, Uri

AU - Laquindanum, Rozelle

AU - Lau, Clarisse

AU - Lau, Ken Siu Kwong

AU - LeBoeuf, Nicole R.

AU - Lee, Hayan

AU - Lenburg, Marc

AU - Leshchiner, Ignaty

AU - Levy, Rochelle

AU - Li, Yize

AU - Lian, Christine G.

AU - Liang, Wen Wen

AU - Lim, Kian Huat

AU - Lin, Yiyun

AU - Liu, David

AU - Liu, Qi

AU - Liu, Ruiyang

AU - Lo, Joseph

AU - Lo, Pierrette

AU - Longabaugh, William J.

AU - Longacre, Teri

AU - Luckett, Katie

AU - Ma, Cynthia

AU - Maher, Chris

AU - Maier, Allison

AU - Makowski, Danika

AU - Maley, Carlo

AU - Maliga, Zoltan

AU - Manoj, Parvathy

AU - Maris, John M.

AU - Markham, Nick

AU - Marks, Jeffrey R.

AU - Martinez, Daniel

AU - Mashl, Jay

AU - Masilionis, Ignas

AU - Massague, Joan

AU - Mazurowski, Marciej A.

AU - McKinley, Eliot T.

AU - McMichael, Joshua

AU - Meyerson, Matthew

AU - Mills, Gordon B.

AU - Mitri, Zahi I.

AU - Moorman, Andrew

AU - Mudd, Jacqueline

AU - Murphy, George F.

AU - Deen, Nataly Naser Al

AU - Navin, Nicholas E.

AU - Oh, Stephen T.

AU - Patti, Gary J.

AU - Puram, Sidharth V.

AU - Shoghi, Kooresh I.

AU - Song, Sheng Kwei

AU - Veis, Deborah J.

AU - Wahl, Richard

AU - Wendl, Michael C.

AU - Wyczalkowski, Matthew A.

N1 - Funding Information: This work is supported by the HTAN Consortium and the Cancer Systems Biology Consortium (CSBC). A list of all current HTAN Consortium members can be found at https://humantumoratlas.org/ . 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. Funding Information: P.K.S. is a member of the Scientific Advisory Board (SAB) or Board of Directors of Applied Biomath, RareCyte Inc. and Glencoe Software, which distributes a commercial version of the OMERO data management platform; P.K.S. is also a member of the NanoString SAB and a consultant to Merck and Montai Health. In the past five years, the Sorger laboratory has received research funding from Novartis and Merck. P.K.S. declares that none of these relationships have influenced the content of this manuscript. S.S. is a consultant for RareCyte Inc. N.G. is a co-founder and equity owner of Datavisyn. D. Schapiro is a consultant for Roche Glycart AG. J.R.S. is founder and CEO of Glencoe Software, which distributes a commercial version of the OMERO data management platform. S.J.R. receives research funding from Bristol Myers Squibb, Merck, Affimed and Kite/Gilead and is on the SAB of Immunitas Therapeutics. D. Sudar is employed by Quantitative Imaging Systems LLC. E.A.B. is an employee of Indica Labs.

PY - 2022/3

Y1 - 2022/3

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

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