[FAIR Facilities and Instruments] Persistent Hardware Descriptors: persistent identification of instrument instances and hardware configurations

1 Persistent Hardware Descriptors: persistent identification of instrument instances and hardware configurations Caterina Strambio-De-Castillia 2025-9-22 FAIR Facilities and Instrument Workshop 3 David Grunwald James Chambers Judith Lacoste Adrian Zai Josh Moore Anita Bandrowsky Nate Herzog Most of the world’s bioimaging data lacks a clear path to being FAIR and potentially shared Most of the world’s bioimage data is not FAIR and is not ready to be shared … hidden treasure Available FAIR bioimage data… •Lost/Misplaced/Fragmented •Poorly annotated •Insufficient metadata •Poorly managed Moore and Kunis, 2024; https://doi.org/10.5281/zenodo.11235513 Bioimages: complex data and metadata Moore and Kunis, 2024; https://doi.org/10.5281/zenodo.11235513 Microscopy Core Facilities ImageJ, Nikon Elements®️, Imaris®️, Amira®️, Hyugens®️, custom software, CellProfiler, QuPath, Python based tools, etc. •Digital pathology (brightfield and fluorescence slide scans) •Spatial omics •Multiplexed FISH/RNA Scope •Widefield microscopy •Confocal microscopy •Super-resolution microscopy •Live-cell imaging Full-service core-facilities Researchers using microscopes at core-facilities and in individual labs •Multiple production sites •Diverse samples + experimental conditions •Thousands of diverse microscopes with multiple parts •Multiple modalities •>150 file formats •TB, PB, …. •Multiple analysis software •Need to integrate with other data-types All information that is needed to interpret, evaluate the quality reproduce and share microscopy images Nature Methods FOCUS issue on Reporting and Reproducibility in Microscopy: https://www.nature.com/collections/djiciihhjh BioImage Metadata © Thao Do (Allen Institute, Seattle, WA, USA) •Sample preparation •Image Acquisition •Hardware configuration •Acquisition setting •Quality Control •Image data processing and analysis ●Notebooks (Paper or ELN) ●Excel sheets ●Word docs etc. ●Log files ●Proprietary Image files ●OME-TIFF (via BioFormats) ●Microscope hardware descriptions ●Personal notes during acquisition ●Log files ●Personal notes ●Script/Workflow/Pipe line code ●Often not reported Experimental and Sample Metadata Microscopy Metadata Analysis and Visualization Metadata Fragmentation is the enemy Where is bioimage metadata? PIDs can help maintain links between different essential information Persistent Hardware Descriptors help making data FAIR Linked PIDs for •Instrument instance •Instrument model •Hardware configuration Labs and Core Facilities have different overlapping needs for the Instrument Data Management ? QUAREP - Metadata for cameras –we did not start from scratch Community standards: Microscopy Metadata Specifications to expand the OME-data model 16 Hammer et al. (2021) Nat Methods; https://doi.org/10.1038/s41592-021-01327-9 Image Acquisition 4DN-BINA-OMEQUAREP (NBO-Q) Hardware, Acquisition Settings and QC 1717 QUAREP - Metadata for cameras –we did not start from scratch Community tools: Micro-Meta App can be used to capture NBO-Q Image Acquisition metadata Image Acquisition NBO-Q QUAREP - Metadata for cameras –we did not start from scratch Community standards: Microscopy Metadata Specifications to expand the OME-data model 18 QUAREP - Metadata for cameras –we did not start from scratch Community standards: Microscopy Metadata Specifications to expand the OME-data model 19 Now the official host and responsible party! 20 QUAREP - Metadata for cameras –we did not start from scratch NBO-Q Light Microscopy Metadata Model ●Hosted and maintained by QUAREP-LiMi ●Covers hardware configuration, image acquisition settings and quality control metadata ●Revision process codified by Best Practices document ●Large community of imaging scientists, microscopy experts, manufacturers and standards organizations stakeholders https://quarep.org/working-groups/wg-7-metadata/ ⮚January – August 2022: 10+ focused feedback sessions to build consensus ⮚Completed first parsing of camera hardware specifications and image acquisition settings! ⮚Due soon:Revision of 4DN-BINA-OMEQUAREP Camera Metadata model + vocabulary Governance gives QUAREP a path forward towards NBO-Q v3.0 in partnership with key stakeholders •Evaluate fields •Inspect structure •Open discussion Consensus •Listen to recording •Debrief •Extract decision Proposal for Change •Evaluate fields •Inspect structure •Open discussion Consensus WG2 & WG7 joint endeavor Focus groups to review model elements and attributes WG2 & WG7 joint endeavor Outcome NBO-Q 2025 version Core Marketplace + RRID: supporting the persistent identification of core-facilities Core Marketplace + RRID: supporting the persistent identification of core-facilities Rigor, Reproducibility, Ruse Use-Case in Light Microscopy Identification of Instrument Instances + Standardized Hardware, Settings and Quality Control Description Light Microscopy metadata 2 4 3 1 Light Microscopy metadata 2 4 3 1 PID concatenation Core Facility RRID: SRC_XYZQ Model RRID:SRC_XYZW Instance PIDINST:10.1000/XYZ - Hardware Descriptor 🡪 PHDID: 10.1000/XYZ FAIR Facilities and Instruments: PID recommendations 1. Flexible PID recommendations: based on the requirements of different use cases and different scientific domains 2. Capability of assigning PID in different tiers. For example: 1. Core Facilities 2. Instrument Model/Type 3. Instrument Instance 4. Descriptor (Hardware Configuration / Settings / Parameters) 3. PID concatenation 4. PID connection FAIR Facilities and Instruments: PID recommendations 1. Facility PID 2. Model PID 3. Instance PID 4. Descriptor PID 1. Flexible PID recommendations: based on the requirements of different use cases and different scientific domains 2. Capability of assigning PID in different tiers. For example: 1. Core Facilities 2. Instrument Model/Type 3. Instrument Instance 4. Descriptor (Hardware Configuration / Settings / Parameters) 3. PID concatenation 4. PID connection FAIR Facilities and Instruments: PID recommendations 1. Flexible PID recommendations: based on the requirements of different use cases and different scientific domains 2. Capability of assigning PID in different tiers to: 1. Facilities 2. Instrument Model/Type 3. Instrument Instance 4. Descriptor (Hardware Configuration / Settings / Parameters) 3. PID concatenation 4. PID connection https://africapidalliance.org/ 37 BINA+QUAREP-LiMi •Alison North, The Rockefeller University •Roland Nitschke, Uni Freiburg •Britta Schroth-Diez, Max Plank, Dresden •Damir Sudar, Uni Oregon, QIS •Caroline Miller •Nikki Bilay + Vanessa Orr, BINA •BINA Quality Control and Data Management WG •QUAREP-LiMi WG7 –Metadata THANK YOU! UMass Med + Canada Bioimaging Grunwald lab –UMMS-RTI •David Grunwald •Mathias Hammer •Max Huisman •Farzin Farzam OME community •Jason Swedlow, OME •Josh Moore, OME •Shuichi Onami, RIKEN Imaging Scientists Community •Lisa Cameron, Duke •Michelle Itano, CZI, UNC •Paula Montero-Llopis, HMS •Jennifer Waters, CZI, HMS 4DN Community •4DN IWG: Sarah Aufmkolk, Lacra Bintu, Alistair Boettingerr, Steve Wang, Ting Wu •DCIC: Burak Alver, Andrea Cosolo, •Shannon Ehmsen, Koray Kirli, Rahi Navelkar, Peter Park, Andrew Schroder, Serkan Utku Ozturk Alice Kang Judith Lacoste Thomas Stroh Pina Colarusso Gabriel Pelletier Stephen Ogg Joel Ryan Alex Rigano Claire Brown Alex Kiepas Alex Kiepas HuBMAP Community and Pittsburgh Supercomputing Center (PSC) •Katy Borner, Phil Blood, Chris Csonka, Stephen Fisher, Brendan Honick, Ajay Pillai Alex Ropelewski