Metadata Reporting Standards

Spatial Enhanced Resolution Omics Sequencing (Stereo-seq)

Stereo-seq is a spatial transcriptomics platform that captures RNA expression across tissue sections at single-cell to subcellular resolution over a wide field of view. RNA molecules are captured in situ on a patterned chip containing spatially indexed DNA nanoballs (DNBs)—each assigned a unique Coordinate ID (CID)—enabling precise spatial mapping of transcripts from fresh-frozen tissue. The resulting data supports multi-scale analysis of tissue biology, from tissue-level organization to single-cell gene expression and subcellular transcript localization.

DOI: https://doi.org/10.35079/HBM577.XHHB.694

Published: September 3, 2026

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MD5 hash: 5f39ed6fff95b011c24dc613e75bcf14

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Schema

Legend: Text field Allowable value Radio Numeric

* Required

Attribute Type Description Allowable Values
Parent sample ID * The unique identifier from HuBMAP or SenNet for the sample (such as a block, section, or suspension) used to perform the assay. For instance, in an RNAseq assay, the parent sample would be the suspension, while in imaging assays, it would be the tissue section. If the assay is derived from multiple parent samples, this field should contain a comma-separated list of identifiers. Example: HBM386.ZGKG.235, HBM672.MKPK.442  
Lab ID A locally assigned identifier provided by the data provider for the dataset. It is used to reference an external metadata record that may be maintained independently, enabling traceability and supporting provenance tracking. Example: Visium_9OLC_A4_S1  
Preparation protocol DOI * The DOI for the protocols.io page that details the assay or the procedures used for sample procurement and preparation. For example, in the case of an imaging assay, the protocol may start with tissue section staining and end with the generation of an OME-TIFF file. The documented protocol should also include any image processing steps involved in producing the final OME-TIFF. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1  
Dataset type * The specific type of dataset being produced. Example: RNAseq HiFi-Slide SNARE-seq2 COMET Visium (no probes) DESI Confocal Stereo-seq Visium (with probes) Molecular Cartography DBiT-seq Seq-Scope CosMx Transcriptomics CyCIF Light Sheet seqFISH ATACseq CosMx Proteomics Singular Genomics G4X Visium HD MERFISH 10X Multiome 4i PhenoCycler Second Harmonic Generation (SHG) Thick section Multiphoton MxIF CyTOF Olink MIBI Auto-fluorescence FACS Xenium SIMS Cell DIVE CODEX GeoMx (NGS) MUSIC Pixel-seqV2 MALDI 2D Imaging Mass Cytometry Histology Enhanced Stimulated Raman Spectroscopy (SRS) DART-FISH Resolve RNAseq LC-MS nanoSPLITS GeoMx (nCounter) RNAseq (with probes) MS Lipidomics MPLEx
Contributors path * The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv  
Data path * The top-level directory containing the raw and/or processed data. For a single dataset upload, this might be represented as “.”, whereas for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For example, if the data is within a directory named “TEST001-RK”, use the syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2”, where “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field used solely for data ingestion. Example: ./TEST001-RK  
Mapped area value * The mapped area value, which refers to the specific area covered or captured in various assays. For Visium, it is the area of spots covered by tissue within the captured area, excluding the total possible captured area. For GeoMx, it refers to the area of the AOI being captured. In HiFi, it is the summed area of the ROIs in a single flowcell lane. For CosMx and Resolve, it indicates the area of the FOV (also known as ROI) region being captured. For Xenium, it is the total area of the FOV regions (also known as ROI) being captured. For Stereo-Seq, this value represents the number of beads. Example: 42.25  
Mapped area unit * The unit of measurement for the mapped area value. If mapping area is not specified, this field may be left blank. Example: um^2 mm^2 um^2
Spot size value * For assays where spots are used to define discrete capture areas, this is the area of a spot.  
Spot size unit * The unit for spot size value. mm^2 um^2
Number of spots * Number of capture spots within the mapped area. For Visium this would be the number of spots covered by tissue, while it’s the number of spots within ROIs for HiFi.  
Spot spacing value * Approximate center-to-center distance between capture spots. Synonyms: Inter-Spot distance, Spot resolution, Pit size  
Spot spacing unit * Units corresponding to inter-spot distance um
Permeabilization time value Permeabilization time used for this tissue section.  
Permeabilization time unit The unit for the permeabilization time. minute
Preparation instrument vendor The company that manufactures the instrument used to prepare the sample (e.g., for staining or other processing steps) prior to the assay. If the instrument was custom-built or developed internally, enter “In-House”. If no sample preparation occurred, enter “Not applicable”. Example: 10X Genomics In-House Leica Biosystems Not applicable Thermo Fisher Scientific Roche Diagnostics HTX Technologies 10x Genomics Hamamatsu SunChrom
Preparation instrument model The specific model of the instrument used for sample preparation, such as staining. Manufacturers may offer multiple models with varying features or sensitivities, which can influence how the sample is processed and how the resulting data is interpreted. If no sample preparation occurred, enter “Not applicable”. Example: Chromium X NanoZoomer S210 Not applicable Sublimator EVOS M7000 Chromium Controller NanoZoomer S360 NanoZoomer S60 Chromium X AutoStainer XL Visium CytAssist SunCollect Sprayer M3+ Sprayer Discovery Ultra ST5020 Multistainer Chromium iX Chromium Connect M5 Sprayer TM-Sprayer
Non global files Specifies a semicolon-separated list of non-global files that are to be included in the dataset. The file paths assume that the files are located in the “TOP/non-global/” directory. For instance, if the file is located at TOP/non-global/lab_processed/images/1-tissue-boundary.geojson, the value for this field would be “./lab_processed/images/1-tissue-boundary.geojson”. Once ingested, these files will be copied to their appropriate locations within the respective dataset directory tree. This field is intended for internal HuBMAP processing. Examples for GeoMx and PhenoCycler are provided in the File Locations documentation: https://docs.google.com/document/d/1n2McSs9geA9Eli4QWQaB3c9R3wo5d5U1Xd57DWQfN5Q/edit#heading=h.1u82i4axggee Example: ./lab_processed/images/1-tissue-boundary.geojson  
Metadata schema ID * The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9  
CEDAR OpenView Documentation CEDAR Validator

HuBMAP Datasets

The HuBMAP Data Portal is an open platform to discover, visualize, and download standardized healthy single-cell and spatial tissue data.


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Citation

Fisher SA, Hardi J, Morgan R, Nordgren E, Kant PM, Honick B, Rosario J, O'Connor MJ, Turner ML, DCWG Members, Gehlenborg N, Blood PD, Silverstein JC, Musen MA. 2026. The HuBMAP Framework for Advancing Data FAIRness. submitted. https://doi.org/10.64898/2026.06.01.728946


Reuse

This standard may be reused, expanded, or referenced by external repositories. It represents version 2.0 of the metadata schema and version 2.0 of the file directory structure. If you are uploading data, the latest versions of both are available at the "Latest Versions" link below. If you are querying or using HuBMAP or SenNet metadata, a harmonized view of the metadata specification is available at the "Harmonized Version" link below.


Latest Versions    Harmonized Version

Contributors

Below is the information for the individuals who contributed to the HuBMAP and SenNet metadata reporting standards.

For questions about this standard, email HuBMAP Helpdesk. You can alternatively reach out to the individuals listed below, either via the email address listed in the table or via contact information provided on their ORCID profile page.

Name Affiliation Contact ORCID
Stephen A Fisher University of Pennsylvania, Philadelphia PA, USA safisher@upenn.edu 0000-0001-8034-7685
Josef Hardi Stanford University, Stanford, CA, USA johardi@stanford.edu 0000-0002-2533-6681
Richard Morgan University of Pittsburgh, Pittsburgh, PA, USA rsm66@pitt.edu 0009-0003-1800-8545
Mark A Musen Stanford University, Stanford, CA, USA musen@stanford.edu 0000-0003-3325-793X
Jonathan C Silverstein University of Pittsburgh, Pittsburgh, PA, USA j.c.s@pitt.edu 0000-0002-9252-6039
Erik Nordgren University of Pennsylvania, Philadelphia PA, USA   0000-0002-5024-0278
Peter M Kant University of Pittsburgh, Pittsburgh, PA, USA; Currently - Otsuka Precision Health, Princeton, NJ, USA   0009-0002-6510-5041
Brendan John Honick Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA   0000-0001-6128-9854
Martin J O’Connor Stanford University, Stanford, CA, USA   0000-0002-2256-2421
Jean G Rosario University of Pennsylvania, Philadelphia PA, USA   0000-0002-6116-5058
Nils Gehlenborg Harvard Medical School, Boston, MA, USA   0000-0003-0327-8297
Philip D Blood Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, USA   0000-0002-9129-1223
Kyung Jin Ahn Children’s Hospital of Philadelphia, Philadelphia, PA, USA   0000-0002-4184-482X
Christopher R Anderton Pacific Northwest National Laboratory, Richland, WA, USA   0000-0002-6170-1033
Shovik Bandyopadhyay Children’s Hospital of Philadelphia, Philadelphia, PA, USA; Brigham and Women’s Hospital, Boston, MA, USA   0000-0003-3919-3914
Kenneth C Bedi University of Pennsylvania, Philadelphia PA, USA   0000-0003-3588-9324
Maigan Brusko University of Florida, Gainesville, FL, USA   0000-0002-4331-2202
Martha Campbell-Thompson University of Florida, Gainesville, FL, USA   0000-0001-6878-1235
James Carson The University of Texas at Austin, Austin, TX, USA   0000-0001-9009-5645
Chase M Carver Mayo Clinic, Rochester, MN, USA   0000-0003-4002-2418
Jing Chen University of Florida, Gainesville, FL, USA   0000-0001-8008-8062
Anthony M Corbett University of Rochester Medical Center, Rochester, NY, USA   0000-0001-9545-0853
Alexandra E Cuaycal University of Florida, Gainesville, FL, USA   0000-0002-9060-6326
Penny Cuda Carnegie Mellon University, Pittsburgh, PA, USA   0009-0002-6547-2650
Dinh Diep University of California, San Diego, CA, USA; Currently - Altos Labs, San Diego, CA, USA   0000-0001-6057-4119
Sergii Domanskyi The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA   0000-0002-6847-6019
Sean Donahue Carnegie Mellon University, Pittsburgh, PA, USA   0000-0002-4072-2046
Michael P Duffy University of Pennsylvania, Philadelphia PA, USA   0000-0001-5325-3683
Michael T Eadon Indiana University School of Medicine, Indianapolis, IN, USA   0000-0003-3066-2876
Jean Fan Johns Hopkins University, Baltimore, MD, USA   0000-0002-0212-5451
Melissa A Farrow Vanderbilt University, Nashville, TN, USA   0000-0002-1602-2082
Kathleen M Fisch University of California San Diego, La Jolla, CA, USA   0000-0002-0117-7444
William F Flynn The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA   0000-0001-6533-0340
James M Fulcher Pacific Northwest National Laboratory, Richland, WA, USA   0000-0001-9033-3623
Soumya Ghose GE HealthCare, Niskayuna, NY, USA   0000-0002-2730-1482
Fiona Ginty GE HealthCare, Niskayuna, NY, USA   0000-0001-6638-683X
Joana P Gonçalves Delft University of Technology, Delft, The Netherlands   0000-0001-6072-9627
Yongqun He University of Michigan, Ann Arbor, MI, USA   0000-0001-9189-9661
Po Hu Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA   0000-0003-2422-1652
Sanjay Jain Washington University School of Medicine, St. Louis, MO, USA   0000-0003-2804-127X
Thomas V Karathanos Stanford University, Stanford, CA, USA   0000-0003-1754-3872
Madhurima Kaushal Washington University School of Medicine   0000-0003-2760-0586
Angela RS Kruse Vanderbilt University, Nashville, TN, USA; Currently - The Ohio State University, Columbus, OH, USA   0000-0001-8776-2769
Yumi Kwon Pacific Northwest National Laboratory, Richland, WA, USA   0000-0003-0523-6197
Blue B Lake University of California San Diego, La Jolla, CA, USA; Currently - Altos Labs, San Diego, CA, USA   0000-0002-8637-9044
Roy Lardenoije Delft University of Technology, Delft, The Netherlands   0000-0002-9026-7870
Shin Lin Emory University, Atlanta, GA, USA   0000-0003-0118-0413
Yiing Lin Washington University, St. Louis, MO, USA   0000-0002-0317-7608
Scott A Lindsay University of California, San Diego, CA, USA   0000-0002-2929-7755
Peiran Lu Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA   0009-0001-5096-3046
Clayton Mathews University of Florida, Gainesville, FL, USA   0000-0002-8817-6355
Elizabeth McDonough GE HealthCare, Niskayuna, NY, USA   0000-0001-7524-8260
Ricardo Melo Ferreira Indiana University School of Medicine, Indianapolis, IN, USA   0000-0003-2063-9744
Emma M Monte Stanford University, Stanford, CA, USA   0000-0003-2566-1967
Kathleen O’Neill University of Pennsylvania, Philadelphia PA, USA   0000-0003-1980-6840
Minxing Pang University of Pennsylvania, Philadelphia PA, USA   0000-0001-5208-5972
Mana Parast University of California San Diego, La Jolla, CA, USA   0000-0001-5963-2246
Liming Pei Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA   0000-0002-1924-0333
Samuel Peters University of Minnesota, Minneapolis, MN, USA   0000-0003-1479-8087
Ajay Pillai National Institute of Health, Bethesda, MD, USA   0000-0002-9789-7189
Gloria Pryhuber University of Rochester Medical Center, Rochester, NY, USA   0000-0002-9185-3994
Ling Qin University of Pennsylvania, Philadelphia PA, USA   0000-0002-2582-0078
Presha Rajbhandari Columbia University, NYC, NY, USA   0000-0003-2184-7238
Matthew M Ruffalo Carnegie Mellon University, Pittsburgh, PA, USA   0000-0003-2222-6169
Pinaki Sarder University of Florida, Gainesville, FL, USA   0000-0003-2450-5233
Diane C Saunders Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, USA; Northwestern University, Chicago, IL, USA   0000-0002-8849-6746
Kevin Schneider Buck Institute, Novato, CA, USA   0009-0001-8046-0167
Lingyan Shi University of California San Diego, La Jolla, CA, USA   0000-0003-1373-3206
Santhosh Sivajothi The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA   0000-0002-8854-4517
David Smith Children’s Hospital of Philadelphia, Philadelphia, PA, USA   0000-0001-7858-3785
Jeff M Spraggins Vanderbilt University, Nashville, TN, USA   0000-0001-9198-5498
Valentina Stanley University of California, San Diego, CA, USA   0000-0002-2212-7796
Kai Tan Children’s Hospital of Philadelphia, Philadelphia, PA, USA; University of Pennsylvania, Philadelphia, PA, USA   0000-0002-9104-5567
Anusha Thadi Children’s Hospital of Philadelphia, Philadelphia, PA, USA   0000-0002-1271-0398
Hua Tian Columbia University Medical Center, NYC, NY, USA   0000-0002-3598-0219
Morgan L Turner Harvard Medical School, Boston, MA, USA   0000-0002-1512-9742
Ioannis S Vlachos Beth Israel Deaconess Medical Center, Boston, MA, USA; Harvard Cancer Center, Boston, MA, USA; Broad Institute of MIT and Harvard, Boston, MA, USA   0000-0002-8849-808X
Seth Winfree University of Nebraska Medical Center, Omaha, NE, USA; Currently - QCDx Inc, Farmington, CT, USA    
Pei-Hsun Wu Johns Hopkins University, Baltimore, MD, USA   0000-0002-7371-2960
Kevin J Zemaitis Pacific Northwest National Laboratory, Richland, WA, USA   0000-0002-3524-9776
Mowei Zhou Pacific Northwest National Laboratory, Richland, WA, USA; Currently - Zhejiang University, Hangzhou, Zhejiang 310058, China   0000-0003-3575-3224
Chenchen Zhu Department of Genetics, Stanford University, Stanford, CA, USA   0000-0003-2165-9456