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Fix typos in names and add commenters to RFC pages (#450)
* Update typos in names Compared against https://github.com/German-BioImaging/ome-zarr-acknowledgments/blob/main/people.yaml * Add commenters, github handles and links * Fix typo on Nathalie Gaudreault's name * Standard GH handles + move comments to last * Add reviewers and rolet column to RFC 9
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rfc/1/index.md

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- Author ([PR](https://github.com/ome/ngff/pull/222))
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* - Reviewer
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- Davis Bennett, John Bogovic, Michael Innerberger, Mark Kittisopikul, Virginia Scarlett, Yurii Zubov
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- d-v-b, bogovicj, minnerbe, mkitti, virginiascarlett, yuriyzubov
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- [d-v-b](https://github.com/d-v-b), [bogovicj](https://github.com/bogovicj), [minnerbe](https://github.com/minnerbe), [mkitti](https://github.com/mkitti), [virginiascarlett](https://github.com/virginiascarlett), [yuriyzubov](https://github.com/yuriyzubov)
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- Janelia
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- 2024-02-26
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- [Review](./reviews/2/index)
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* - Reviewer
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- Kevin Yamauchi, Virginie Uhlmann
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- kevinyamauchi, vuhlmann
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- [kevinyamauchi](https://github.com/kevinyamauchi), [vuhlmann](https://github.com/vuhlmann)
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- ETH, BiovisionCenter
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- 2024-03-05
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- [Review](./reviews/1/index)
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* - Reviewer
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- Matthew Hartley
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- mrmh2
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- [mrmh2](https://github.com/mrmh2)
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- EMBL-EBI
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- 2024-03-05
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- [Review](./reviews/3/index)
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* - Commenter
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- Wouter-Michiel Vierdag, Luca Marconato
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- melonora, LucaMarconato
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- EMBL
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- 2024-01-13
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- [Comment](./comments/1/index)
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* - Commenter
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- Matt McCormick
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- thewtex
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- ITK
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- 2024-01-09
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- [Comment](./comments/2/index)
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* - Author
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- Josh Moore
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- joshmoore
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- [joshmoore](https://github.com/joshmoore)
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- German BioImaging
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- 2024-08-29
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- [Response](./responses/1/index)
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* - Endorser
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- Jean-Marie Burel
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- jburel
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- [jburel](https://github.com/jburel)
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- University of Dundee
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- 2024-09-09
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- [Endorse](https://github.com/ome/ngff/pull/258)
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* - Endorser
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- Will Moore
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- will-moore
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- [will-moore](https://github.com/will-moore)
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- University of Dundee
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- 2024-09-09
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- [Endorse](https://github.com/ome/ngff/pull/258)
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* - Endorser
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- Juan-Nuñez Iglesias
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- jni
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- Juan Nunez-Iglesias
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- [jni](https://github.com/jni)
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- Monash University
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- 2024-09-09
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- [Endorse](https://github.com/ome/ngff/pull/258)
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* - Endorser
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- Norman Rzepka
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- normanrz
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- [normanrz](https://github.com/normanrz)
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- scalable minds GmbH
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- 2024-09-09
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- [Endorse](https://github.com/ome/ngff/pull/258)
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* - Endorser
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- Jan Eglinger
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- imagejan
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- [imagejan](https://github.com/imagejan)
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- FMI Basel
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- 2024-09-09
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- [Endorse](https://github.com/ome/ngff/pull/258)
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* - Endorser
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- Joel Lüthi
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- jluethi
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- [jluethi](https://github.com/jluethi)
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- BioVisionCenter, University of Zurich
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- 2024-09-10
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- [Endorse](https://github.com/ome/ngff/pull/258)
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* - Reviewer
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- Kevin Yamauchi, Joel Lüthi, Virginie Uhlmann
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- kevinyamauchi, jluethi, vuhlmann
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- [kevinyamauchi](https://github.com/kevinyamauchi), [jluethi](https://github.com/jluethi), [vuhlmann](https://github.com/vuhlmann)
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- ETH, BiovisionCenter
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- 2024-10-03
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- [Accept](./reviews/1b/index)
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* - Reviewer
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- Matthew Hartley
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- mrmh2
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- [mrmh2](https://github.com/mrmh2)
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- EMBL-EBI
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- 2024-10-08
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- Accept (email)
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* - Reviewer
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- John Bogovic, Michael Innerberger, Virginia Scarlett
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- bogovicj, minnerbe, virginiascarlett
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- [bogovicj](https://github.com/bogovicj), [minnerbe](https://github.com/minnerbe), [virginiascarlett](https://github.com/virginiascarlett)
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- Janelia
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- 2024-10-11
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- [Accept](./reviews/2b/index)
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* - Commenter
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- Wouter-Michiel Vierdag, Luca Marconato
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- [melonora](https://github.com/melonora), [LucaMarconato](https://github.com/LucaMarconato)
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- EMBL
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- 2024-01-13
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- [Comment](./comments/1/index)
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* - Commenter
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- Matt McCormick
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- [thewtex](https://github.com/thewtex)
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- ITK
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- 2024-01-09
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- [Comment](./comments/2/index)
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```
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## Overview

rfc/2/index.md

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- 2024-02-16
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- [Endorse](https://github.com/ome/ngff/pull/227#issuecomment-1947942934)
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* - Endorser
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- John Bogivic
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- John Bogovic
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- [bogovicj](https://github.com/bogovicj)
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- HHMI Janelia Research Campus
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- 2024-02-16
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- [Endorse](https://github.com/ome/ngff/pull/227#issuecomment-1998594492)
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* - Reviewer
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- Melissa Linkert, Sébastien Besson, Chris Allan, Jason Swedlow
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- glencoesoftware
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- [glencoesoftware](https://github.com/glencoesoftware)
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- Glencoe Software
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- 2024-05-23
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- [Review](./reviews/1/index)
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* - Reviewer
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- Yaroslav O. Halchenko
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- yarikoptic
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- [yarikoptic](https://github.com/yarikoptic)
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- Dartmouth College, DANDI Project
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- 2024-06-10
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- [Review](./reviews/2/index)
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* - Reviewer
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- Jeremy Maitin-Shepard
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- jbms
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- [jbms](https://github.com/jbms)
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- Google
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- 2024-04-30
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- [Review](./reviews/3/index)
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* - Reviewer
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- Melissa Linkert, Sébastien Besson, Chris Allan, Jason Swedlow
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- glencoesoftware
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- [glencoesoftware](https://github.com/glencoesoftware)
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- Glencoe Software
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- 2024-08-05
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- [Accept](./reviews/1b/index)
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* - Reviewer
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- Jeremy Maitin-Shepard
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- jbms
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- [jbms](https://github.com/jbms)
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- Google
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- 2024-09-11
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- [Accept](./reviews/3b/index)
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* - Reviewer
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- Yaroslav O. Halchenko
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- yarikoptic
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- [yarikoptic](https://github.com/yarikoptic)
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- Dartmouth College, DANDI Project
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- 2024-09-11
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- [Accept](./reviews/2b/index)

rfc/3/index.md

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- Carl Zeiss Microscopy GmbH
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- 2024-06-05
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- [Endorse](https://github.com/ome/ngff/pull/239#issue-2308436425)
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* - Commenter
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- Benedikt Best
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- [btbest](https://github.com/btbest)
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-
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- 2026-02-02
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- [Comment](./comments/1/index)
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* - Commenter
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- Chris Barnes
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- [clbarnes](https://github.com/clbarnes)
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- German BioImaging
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- 2026-02-05
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- [Comment](./comments/2/index)
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```
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## Overview

rfc/4/index.md

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- EMBL
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- 2025-07-16
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-
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* - Commenter
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- David Stansby
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- [dstansby](https://github.com/dstansby)
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-
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- 2025-04-02
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- [Comment](./comments/1/index)
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* - Commenter
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- Chris Barnes
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- [clbarnes](https://github.com/clbarnes)
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- German BioImaging
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- 2026-02-05
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- [Comment](./comments/2/index)
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```
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## Overview

rfc/5/index.md

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| **Role** | Name | GitHub Handle | Institution | Date | Status |
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|----------|------|---------------|-------------|------|--------|
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| **Author** | John Bogovic | @bogovicj | HHMI Janelia | 2024-07-30 | (Corresponding Author) Implemented |
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| **Author** | Davis Bennett | @d-v-b | | 2024-07-30 | Implemented validation |
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| **Author** | Luca Marconato | @LucaMarconato | EMBL | 2024-07-30 | Implemented |
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| **Author** | Matt McCormick | @thewtex | ITK | 2024-07-30 | Implemented |
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| **Author** | Stephan Saalfeld | @axtimwalde | HHMI Janelia | 2024-07-30 | Implemented (with JB) |
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| **Author** | Johannes Soltwedel | @jo-mueller | German Bioimaging e.V. | 2025-10-07 | (Corresponding Author) Implemented |
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| **Endorser** | Will Moore | @will-moore | University of Dundee | 2025-10-23 | Implemented |
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| **Endorser** | David Stansby | @dstansby | University College London | 2025-10-23 | Implemented |
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| **Endorser** | Norman Rzepka | @normanrz | Scalable Minds | 2024-08-22 | |
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| **Reviewer** | Dan Toloudis, David Feng, Forrest Collman, Nathalie GAudreault, Gideon Dunster | toloudis, dyf, fcollman | Allen Institutes | 2024-11-28 | [Review](rfcs:rfc5:review1) |
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| **Reviewer** | Will Moore, Jean-Marie Burel, Jason Swedlow | will-moore, jburel, jrswedlow | University of Dundee | 2025-01-22 | [Review](rfcs:rfc5:review2)|
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| **Author** | John Bogovic | [bogovicj](https://github.com/bogovicj) | HHMI Janelia | 2024-07-30 | (Corresponding Author) Implemented |
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| **Author** | Davis Bennett | [d-v-b](https://github.com/d-v-b) | | 2024-07-30 | Implemented validation |
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| **Author** | Luca Marconato | [LucaMarconato](https://github.com/LucaMarconato) | EMBL | 2024-07-30 | Implemented |
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| **Author** | Matt McCormick | [thewtex](https://github.com/thewtex) | ITK | 2024-07-30 | Implemented |
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| **Author** | Stephan Saalfeld | [axtimwalde](https://github.com/axtimwalde) | HHMI Janelia | 2024-07-30 | Implemented (with JB) |
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| **Author** | Johannes Soltwedel | [jo-mueller](https://github.com/jo-mueller) | German Bioimaging e.V. | 2025-10-07 | (Corresponding Author) Implemented |
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| **Endorser** | Will Moore | [will-moore](https://github.com/will-moore) | University of Dundee | 2025-10-23 | Implemented |
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| **Endorser** | David Stansby | [dstansby](https://github.com/dstansby) | University College London | 2025-10-23 | Implemented |
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| **Endorser** | Norman Rzepka | [normanrz](https://github.com/normanrz) | Scalable Minds | 2024-08-22 | |
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| **Reviewer** | Dan Toloudis, David Feng, Forrest Collman, Nathalie Gaudreault, Gideon Dunster | [toloudis](https://github.com/toloudis), [dyf](https://github.com/dyf), [fcollman](https://github.com/fcollman) | Allen Institutes | 2024-11-28 | [Review](rfcs:rfc5:review1) |
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| **Reviewer** | Will Moore, Jean-Marie Burel, Jason Swedlow | [will-moore](https://github.com/will-moore), [jburel](https://github.com/jburel), [jrswedlow](https://github.com/jrswedlow) | University of Dundee | 2025-01-22 | [Review](rfcs:rfc5:review2)|
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| **Commenter** | Ilan Gold | [ilan-gold](https://github.com/ilan-gold) | | 2025-02-20 | [Comment](./comments/1/index) |
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| **Commenter** | Jeremy Maitin-Shephard | [jbms](https://github.com/jbms) | | 2025-02-20 | [Comment](./comments/2/index) |
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| **Commenter** | David Stansby | [dstansby](https://github.com/dstansby) | | 2025-10-10 | [Comment](./comments/3/index) |
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## Overview
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rfc/5/versions/1/index.md

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- 2024-08-22
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-
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* - Reviewer
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- Dan Toloudis, David Feng, Forrest Collman, Nathalie GAudreault, Gideon Dunster
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- Dan Toloudis, David Feng, Forrest Collman, Nathalie Gaudreault, Gideon Dunster
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- toloudis, dyf, fcollman
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- Allen Institutes
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reverse transformations as needed for different analysis purposes. This flexibility is critical for tasks such as
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longitudinal studies, multi-modal imaging, and comparative analysis across different subjects or experimental conditions.
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Toward these goals, this RFC expands the set of transformations in the OME-Zarr spec covering many of the use cases
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Toward these goals, this RFC expands the set of transformations in the OME-Zarr spec covering many of the use cases
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requested in [this github issue](https://github.com/ome/ngff/issues/84). It also adds "coordinate systems" - named
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sets of "axes." Related the relationship of discrete arrays to physical coordinates and the interpretation and motivation for
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axis types.
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name `"dim_i"` is the ith element of the `"axes"` list. The axes and their order align with the `shape`
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attribute in the zarr array attributes (in `.zarray`), and whose data depends on the byte order used to store
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chunks. As described in the [zarr array metadata](https://zarr.readthedocs.io/en/stable/spec/v2.html#arrays),
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the last dimension of an array in "C" order are stored contiguously on disk or in-memory when directly loaded.
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the last dimension of an array in "C" order are stored contiguously on disk or in-memory when directly loaded.
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The name and axes names MAY be customized by including a `arrayCoordinateSystem` field in
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the user-defined attributes of the array whose value is a coordinate system object. The length of
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`axes` MUST be equal to the dimensionality. The value of `"type"` for each object in the
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`axes` MUST be equal to the dimensionality. The value of `"type"` for each object in the
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axes array MUST equal `"array"`.
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"coordinateTransformations" describe the mapping between two coordinate systems (defined by "axes").
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For example, to map an array's discrete coordinate system to its corresponding physical coordinates.
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Coordinate transforms are in the "forward" direction. They represent functions from *points* in the
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input space to *points* in the output space.
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input space to *points* in the output space.
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- MUST contain the field "type".
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<table>
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<tr><th><code>identity</code>
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<td>
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<td>
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<td>The identity transformation is the default transformation and is typically not explicitly defined.
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<tr><th><code>mapAxis</code>
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<td><code>"mapAxis":Dict[String:String]</code>
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#### <a name="mapAxis">mapAxis</a>
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`mapAxis` transformations describe axis permutations as a mapping of axis names. Transformations MUST include a `mapAxis` field
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whose value is an object, all of whose values are strings. If the object contains `"x":"i"`, then the transform sets the value
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whose value is an object, all of whose values are strings. If the object contains `"x":"i"`, then the transform sets the value
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of the output coordinate for axis "x" to the value of the coordinate of input axis "i" (think `x = i`). For every axis in its output coordinate
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system, the `mapAxis` MUST have a corresponding field. For every value of the object there MUST be an axis of the input
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coordinate system with that name. Note that the order of the keys could be reversed.
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#### <a name="translation">translation</a>
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`translation` transformations are special cases of affine transformations. When possible, a
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`translation` transformations are special cases of affine transformations. When possible, a
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translation transformation should be preferred to its equivalent affine. Input and output dimensionality MUST be
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identical and MUST equal the the length of the "translation" array (N). `translation` transformations are
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invertible.
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The transformations included in the `transformations` array may omit their `input` and `output` fields under the conditions
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outlined below:
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- The `input` and `output` fields MAY be omitted for the following transformation types:
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- The `input` and `output` fields MAY be omitted for the following transformation types:
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- `identity`, `scale`, `translation`, `rotation`, `affine`, `displacements`, `coordinates`
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- The `input` and `output` fields MAY be omitted for `inverseOf` transformations if those fields may be omitted for the
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transformation it wraps
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- The `input` and `output` fields MAY be omitted for `bijection` transformations if the fields may be omitted for
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- The `input` and `output` fields MAY be omitted for `bijection` transformations if the fields may be omitted for
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both its `forward` and `inverse` transformations
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- The `input` and `output` fields MAY be omitted for `sequence` transformations if the fields may be omitted for
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all transformations in the sequence after flattening the nested sequence lists.
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of the `i`th output axis. See the example below.
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`coordinates` and `displacements` transformations are not invertible in general, but implementations MAY approximate their
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inverses. Metadata for these coordinate transforms have the following field:
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inverses. Metadata for these coordinate transforms have the following field:
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<dl>
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<dt><strong>path</strong></dt>
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<dl>
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<dt><strong>transformations</strong></dt>
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<dd> A list of transformations, each of which applies to a (non-strict) subset of input and output dimensions (axes).
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<dd> A list of transformations, each of which applies to a (non-strict) subset of input and output dimensions (axes).
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The values of <code>input</code> and <code>output</code> fields MUST be an array of strings.
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Every axis name in <code>input</code> MUST correspond to a name of some axis in this parent object's <code>input</code> coordinate system.
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Every axis name in the parent byDimension's <code>output</code> MUST appear in exactly one of its child transformations' <code>output</code>.
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Many RFCs have an "implementation" section which details how the implementation
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will work. This section should explain the rough specification changes. The
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goal is to give an idea to reviewers about the subsystems that require change
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and the surface area of those changes.
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and the surface area of those changes.
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This knowledge can result in recommendations for alternate approaches that
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perhaps are idiomatic to the project or result in less packages touched. Or, it
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transformations of arbitrary dimension and axis type, where there is not a strong convention we are aware of.
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An early consideration was to use axis names to indicate correspondence across different coordinate systems (i.e. if two
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coordinate systems both have the "x" axis, then it is "the same" axis. We abandoned this for several reasons. It was
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coordinate systems both have the "x" axis, then it is "the same" axis. We abandoned this for several reasons. It was
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restrictive - it is useful to have many coordinate systems with an "x" axis without requiring that they be "identical." Under our
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early idea, every set of spatial axes would need unique names ("x1", "x2", ...), and this seemed burdensome. As well, this
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approach would have also made transformations less explicit and likely would have required more complicated implementations.
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* thin-plate spline
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* b-spline
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* velocity fields
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* by-coordinate
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## Performance
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