[N4BI AHM] Welcome to BioImage Town

All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Welcome to! BioImage Town! Josh Moore, Senior RDM Officer German BioImaging, e.V. / Open Microscopy Environment With the exception of logos and cited third-party content, the content of these slides is shared under the terms of the Creative Commons Attribution License (CC-BY 4.0) unless the content is marked otherwise. All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Special welcome 2 Honored Guests New Colleagues All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Value of bioimages 3 https://ome-model.readthedocs.io/ All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Value of bioimages 4 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Image Data Management isn’t always FAIR 5 "Clara shares" by Henning Falk, ©2022 NumFOCUS, is used under a CC BY 4.0 license. https://github.com/zarr-developers/zarr-illustrations-falk-2022#clara-shares Image: Simon Li https://twitter.com/penguinoops/status/643812318699225088 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 A brief history of making images go 6 2000 2024 JSON RFC (2006) “FAIR” Wilkinson (2016) 2005 2016 2018 "Bea computes" by Henning Falk, ©2022 NumFOCUS, is used under a CC BY 4.0 license. https://github.com/zarr-developers/zarrillustrations-falk-2022#bea-computes All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 7 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 8 https://doi.org/10.5281/zenodo.8019760 Moore et al., CC-BY 4.0 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 9 The OME Model is a specifica1on for storing data on biological imaging. The model includes image parameters, such as XYZ dimensions and pixels type, as well as extensive metadata on, for example, image acquisi1on, annota1on, and regions of interest (ROIs). This common specifica1on is essen1al for the exchange of image data between different soIware packages. “ 2000 Swedlow et al. (2003) Informatics and quantitative analysis in biological imaging. Science 300(5616), 100-2. Published 4 April 2003 DOI:!10.1126/science.1082602!" https://bit.ly/citing-ome https://en.wikipedia.org/wiki/Rapid_transit_track_gauge XML All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 16 16 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023  Apps using Bio-Formats were started >100,000 times per day in 2015 - 2022.  17 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 18 openmicroscopy.org/2016/01/06/format-support.html openmicroscopy.org/2019/06/25/formats.html openmicroscopy.org/2016/08/31/bf-partnerships.html 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 19 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 20 2005 https://omero-guides.readthedocs.io All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 21 Collaborate on data publication Annotate Rapidly edit figures https://lincs-omero.hms.harvard.edu http://ssbd.qbic.riken.jp/ https://www.mousephenotype.org 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 EMPIAR/EMDataBank / PDBe Ardan Patwardhan, Ingvar Lagerstadt & Gerard Kleywegt, EBI 22 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 HIRN Tissue Atlas: Pancreatlas.org Diane Saunders, Marcela Brissova, Alvin Powers, Vanderbilt University Medical Center 23 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 CHemoarchitectonic Atlas of the Mammalian Brain! Kouichi Nakamura & Peter Magill, Univ of Oxford 24 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 25 2005 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Tissue Data: Human Protein Atlas 32 https://www.proteinatlas.org 2016 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 In Situ Sequencing - Linking Multimodal Metadata 33 idr0101, Payne et al Science DOI:10.17867/10000169 2016 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 34 2016 idr0101, Payne et al Science DOI:10.17867/10000169 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 35 Jhu et al, 2022, Nature Methods https://vis.nucleome.org/static/apps/IDR_demo/ 2016 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Intermezzo 36 2016 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 37 Remote Storage Local Storage Centralized Storage Object Storage Complexity Cost 10e3 unique users per month 10e2 servers p.m. Extract metadata Extract pixels Collaborative annotation Remote viewing Curated metadata Scalable infrastructure Extensible metadata Chunked, cloud access 10e1 subs p.a. 2018 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Analysis clients & libraries Remote Local On-the-fly translation Proprietary File Formats (PFF) Imaging repositories Upload 38 2018 Download All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Analysis clients & libraries Remote Local On-the-fly translation Proprietary File Formats (PFF) Imaging repositories Upload 39 2018 Download ??? All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 40 Moore et al. (2021). OME-NGFF: a next-generation file format for expanding bioimaging data-access strategies. Nature methods (2021). Published: 29 November 2021 DOI:!10.1038/s41592-021-01326-w! # https://bit.ly/citing-ome 2018 Chunkable file format Monolithic file format SPLIT CONCATENAT NETWORK NETWORK Access via network External data storage Local computer All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 41 2018 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 48 Zarr CZI EOSS4 2021-2024 Languages: C/C++, Java, Javascript, Julia, Python, R, Rust SpatialData CZI Single Cell - Data Insights 2023-2025 Languages: Javascript, Python, R NGFF NFDI4BIOIMAGE 2023-2028 CZI EOSS5 2022-2024 Languages: Java, Javascript, Python Development WebAtlas HCA WSSS Extension through 2023 Napari CZI Core Funding BIA EBI Core Funding … IDR Wellcome into 2024 Formats Stack Consumers Today All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Intermezzo 49 Today All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 A brief history 50 "Bea computes" by Henning Falk, ©2022 NumFOCUS, is used under a CC BY 4.0 license. https://github.com/zarr-developers/zarrillustrations-falk-2022#bea-computes 2000 2024 2005 2016 2018 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 51 * XML * TIFF * Zarr * ImageJ Macros * Library * OME.Perl * OMERO3 * OMERO4 * OMERO5 All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 52 Convention Conversion Collaboration All-Hands Meeting · Josh Moore · Welcome to BioImage Town 16/10/2023 Acknowledgments Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under the National Research Data Infrasstructure – NFDI 46/1 – 501864659 The NFDI4BIOIMAGE consortium comprises legally independent partners and does not act autonomously towards third parties. The authors represent the contributions from their respective affiliated institutions and work together for the project. 53 openmicroscopy.org/about/#consortium