Microscopy Metadata Captured to date… (as of 11-06-2023)
4DN-BINA-OME Microscopy Metadata Specifications adopted by HuBMAP.
- Download from GitHub the latest version of the Micro-Meta App.
- Get more details about the Micro-Meta App here.
- See how the Micro-Meta App has been embedded in the 4D Nucleome Data Portal.
- Read the paper about the Micro-Meta App in Nature.
Note: The table below is a much smaller subset of the HuBMAP Microscope Hardware Collection Roll Call sheet.
See that linked sheet for more detailed information about each instrument and other related details.
| Group | Instrument | Assay Category | JSON File? |
|---|---|---|---|
| TMC-JHU | Hamamatsu NanoZoomer S210 slide scanner | Stained Microscopy |
JSON Placeholder |
| TMC-WUSTL | Akoya - Phenocycler-Fusion 1.0 (v1.0.5 software) | CODEX | JSON |
| ▼ | Akoya - Phenocycler-Fusion 1.0 (v1.0.8 software) | ▼ | JSON |
| ▼ | Akoya - Phenocycler-Fusion 1.0 (v2beta software) | ▼ | JSON |
| ▼ | Akoya - Phenocycler-Fusion 1.0 (v2.1.0 software) | ▼ | JSON |
| ▼ | Keyence BZ-X800 microscope | VISIUM (workflow 1 + 2) |
JSON Incomplete |
| ▼ | 10x Genomics Visium CytAssist | VISIUM (workflow 2) |
JSON Placeholder |
| ▼ | Zeiss Light Sheet 7 | Lightsheet | Not Required |
| TMC-UCSD (Pregnant female reproductive) |
Akoya - Phenocycler-Fusion 1.0 | CODEX | JSON |
| ▼ | Hamamatsu NanoZoomer 2.0-HT slide scanner | Stained Microscopy |
JSON Placeholder |
| ▼ | Hamamatsu NanoZoomer-SQ slide scanner | VISIUM & Stained Microscopy |
JSON Placeholder |
| ▼ | Motic EasyScan One | ▼ | JSON Incomplete |
| ▼ | Leica DM6-B microscope | ▼ | JSON Incomplete |
| ▼ | 10x Genomics Visium CytAssist | VISIUM | JSON Placeholder |
| ▼ | nanoString GeoMx Digital Spatial Profiler | GeoMx (NGS) | |
| TMC-UPenn | Zeiss Axio Observer 7 microscope | VISIUM & Stained Microscopy |
JSON |
| ▼ | Akoya - Phenocycler-Fusion 2.0 | CODEX | JSON |
| TMC-BIDMC | Akoya - Phenocycler-Fusion 1.0 (v2.0.0 software) | ▼ | JSON |
| ▼ | ▼ | ▼ | JSON |
| TMC-CHOP (Heart) | Akoya - Phenocycler-Fusion 1.0 | ▼ | JSON |
| RTI-GEscd | GE Healthcare IN Cell Analyzer 2200 | MxIF | JSON Incomplete |
| TMC-URMC | Akoya - Phenocycler-Fusion 1.0 | CODEX | JSON |
| HIVE-TC-CMU | No Instrument - Example Image Metadata only | NA | Example Only |
| NA | Akoya CODEX 1st Generation (Keyence BZ-800) | CODEX | Template |
| ▼ | Akoya CODEX 1st Generation (Zeiss Axio Observer 7) | ▼ | Template |
| TMC-DUSM (SenNet) | Zeiss_Axio-Scan.Z1 microscope | VISIUM & Stained Microscopy |
JSON |
| ▼ | 10x Genomics Visium CytAssist | VISIUM | JSON Placeholder |
| TMC-PNNL | nanoString GeoMx Digital Spatial Profiler | GeoMx (NGS) | JSON Placeholder |
| TMC-Vanderbilt (Kidney) | ▼ | ▼ | JSON Placeholder |
| ▼ | Zeiss_Axio-Scan.Z1 microscope | Autofluorescence Microscopy (AF) |
JSON |
| TMC-Stanford (Intestine) | CODEX 1st Generation (Keyence BZ-X700) | Histology + CODEX | JSON |
| ▼ | Akoya - Phenocycler-Fusion 2.0 | CODEX | JSON |
| ▼ | 10x Genomics Xenium Analyzer | XENIUM | JSON Placeholder |
( ▼ - Indicates that the item in the cell immediately above is repeated in the current cell. )
How to Use this Table (above…)
- Find an instrument in the table similar (closest) to what you are using
- Download the JSON file from the table above for that instrument
- JSON files that are placeholders or incomplete are noted. JSON files without a notation can be considered complete.
- Use the downloaded JSON as a template, filling out the specifics for your instrument
- Upload the updated JSON file to HuBMAP along with your other Metadata
Some Helpful Links related to Microscopy Metadata
- Read the paper describing the specifications developed by 4DNucleome and BioImaging North America to expand the OME-Data Model 4DN-BINA-OME (NBO) Microscopy Metadata Specifications.
- Get more details about NBO Microscopy Metadata Specifications on GitHub.
- FAIRsharing record for 4DN-BINA-OME (NBO) Microscopy Metadata Specifications.
Acknowledgements
- This work could not have been achieved without the essential cooperation of Akoya Biosciences and the Micro-Meta App Rigano et al. 2021.
- The associated microscope hardware metadata JSON files comply with Tier 2 of the NBO-Q Microscope Metadata specifications Hammer et al. 2021.
- These specifications were developed by the NIH 4D Nucleome (4DN) consortium and BioImaging North America (BINA).
- These specifications have been endorsed by QUAREP-LiMi Boehm et al. 2021 to extend the Open Microscopy Environment (OME) data-model Goldberg et al. 2005.