Xenium Metadata Attributes

These metadata fields have been collected for Xenium data.
These fields are available from the HuBMAP Search and Entity APIs at Dataset.metadata.<attribute>.
See the latest version of the Xenium Ingest Metadata Specifications for the schema and directory structure needed when uploading data.  

* indicates a required field

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 An identifier assigned by the data provider to reference an external metadata record for the dataset. The external record may be maintained independently and can support dataset traceability and provenance tracking. Leave this field empty if no such identifier exists.  
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 10X Multiome 2D Imaging Mass Cytometry 4i ATACseq Auto-fluorescence Cell DIVE CODEX COMET Confocal CosMx Proteomics CosMx Transcriptomics CyCIF CyTOF DART-FISH DBiT-seq DESI DNA Methylation Enhanced Stimulated Raman Spectroscopy (SRS) FACS GeoMx (nCounter) GeoMx (NGS) HiFi-Slide Histology iCLAP Illumina Spatial ver0 LC-MS Light Sheet MACSima MALDI MERFISH MIBI Molecular Cartography MPLEx MS Lipidomics MUSIC nanoSPLITS Olink PhenoCycler Pixel-seqV2 Raman Imaging Resolve RNAseq RNAseq (with probes) Second Harmonic Generation (SHG) Seq-Scope seqFISH SIMS Singular Genomics G4X SNARE-seq2 STARmap Stereo-seq Thick section Multiphoton MxIF Virtual Histology Visium (no probes) Visium (with probes) Visium HD Xenium
analyte_class * The analyte class which is the target molecule that the assay is measuring. Example: DNA Chromatin Collagen DNA DNA + RNA Endogenous fluorophore Fluorochrome Lipid Lipid + metabolite Lipid + metabolite + protein Metabolite Nucleic acid + protein Peptide Polysaccharide Protein RNA RNA + protein Saturated lipid Unsaturated lipid
is_targeted * Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes Yes No
acquisition_instrument_vendor * The company that manufactures or supplies the acquisition instrument. An acquisition instrument is a device equipped with signal detection hardware and signal processing software. It captures signals produced by assays, such as variations in light intensity or color, or signals corresponding to molecular mass. If the instrument was custom-built or developed internally, enter “In-House”. Example: Illumina 10x Genomics 3DHISTECH Akoya Biosciences Andor BGI Genomics Bruker Complete Genomics Cytek Biosciences Cytiva Element Biosciences Evident Scientific (Olympus) GE Healthcare Hamamatsu Huron Digital Pathology Illumina In-House Ionpath Keyence Leica Biosystems Leica Microsystems Microscopes International Miltenyi Biotec Motic NanoString Resolve Biosciences Revvity Sciex Singular Genomics Standard BioTools (Fluidigm) Thermo Fisher Scientific Vizgen Waters Zeiss Microscopy
acquisition_instrument_model * The specific model of the acquisition instrument, as manufacturers often offer various versions with differing features or sensitivities. These differences may be relevant to the processing or interpretation of the data. If the instrument was custom-built or developed internally, enter “In-House”. If the model is unknown, enter “Unknown”. Example: HiSeq 4000 Aperio AT2 Aperio CS2 AVITI Axio Observer 3 Axio Observer 5 Axio Observer 7 Axio Scan.Z1 Axio Zoom.V16 Biomark HD BZ-X710 BZ-X800 BZ-X810 Cell DIVE CosMx Spatial Molecular Imager Custom: Multiphoton Cytek Northern Lights CyTOF 2 CyTOF XT Digital Spatial Profiler DM6 B DMi8 DNBSEQ-T7 EVOS M7000 G4X Spatial Sequencer Helios HiSeq 2500 HiSeq 4000 Hyperion Imaging System IN Cell Analyzer 2200 In-House Juno System Lightsheet 7 LSM 710 Confocal Microscope MACSima System MALDI timsTOF Flex Prototype MERSCOPE MERSCOPE Ultra MIBIscope MoticEasyScan One NanoZoomer 2.0-HT NanoZoomer 2.0-RS NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 NanoZoomer-SQ NextSeq 2000 NextSeq 500 NextSeq 550 Not applicable NovaSeq 6000 NovaSeq X NovaSeq X Plus Opera Phenix HCS Opera Phenix Plus HCS Orbitrap Eclipse Tribrid Orbitrap Fusion Lumos Tribrid Orbitrap Fusion Tribrid Pannoramic MIDI II Digital Scanner Panoramic 150 Digital Scanner Phenocycler-Fusion 1.0 Phenocycler-Fusion 2.0 PhenoImager Fusion Q Exactive Q Exactive HF Q Exactive HF-X Q Exactive UHMR QTRAP 5500 Resolve Biosciences Molecular Cartography SCN400 solariX STELLARIS 5 SYNAPT G2-Si timsTOF FleX timsTOF FleX MALDI-2 timsTOF HT timsTOF Pro timsTOF Pro 2 timsTOF SCP timsTOF Ultra timsTOF Ultra 2 TissueScope LE Slide Scanner Unknown uScopeHXII-20 VS200 Slide Scanner Xenium Analyzer Zeiss LightSheet Z.1 Zyla 4.2 sCMOS
source_storage_duration_value * The length of time the sample was stored prior to processing it. For assays performed on tissue sections, this refers to how long the tissue section (e.g., slide) was stored before the assay began (e.g., imaging). For assays performed on suspensions, such as sequencing, it refers to how long the suspension was stored before library construction started. Example: 12  
source_storage_duration_unit * The unit of measurement used to specify the source storage duration value. Example: hour day hour minute month year
time_since_acquisition_instrument_calibration_value The length of time since the acquisition instrument was last serviced or calibrated. This provides a metric for assessing drift in data capture. Example: 10  
time_since_acquisition_instrument_calibration_unit The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month day month year
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
slide_id * The unique identifier assigned to each slide, enabling users to determine which tissue sections were processed together on the same slide. It is recommended that data providers prefix the ID with the center name to prevent overlapping values across different centers. Example: VAN0071-PA-1-1_AF  
target_retrieval_incubation_temperature The incubation temperature required for target retrieval, which is typically 100 degrees Celsius for RNA assays and 80 degrees Celsius for protein assays. Example: 100  
target_retrieval_incubation_time_value The duration for which a sample is exposed to a target retrieval solution. Example: 15  
target_retrieval_incubation_time_unit The unit of measurement for the target retrieval incubation time value. If no incubation time is specified, this field may be left blank. Example: minute minute
proteinasek_concentration The concentration of the enzyme Proteinase K within a sample, measured in micrograms per milliliter (ug/ml). Example: 10  
proteinasek_incubation_time_value The duration for which a sample is incubated with Proteinase K. Example: 15  
proteinasek_incubation_time_unit The unit of measurement for the proteinaseK incubation time value. If no incubation time is specified, this field may be left blank. Example: minute minute
probe_hybridization_time_value The duration for which the oligo-conjugated RNA or oligo-conjugated antibody probes were hybridized with the sample. Example: 30  
probe_hybridization_time_unit The unit of measurement for the probe hybridization time value. If the hybridization time is not specified, this field may be left blank. Example: minute hour minute
oligo_probe_panel * The oligo probe panel used to target genes and/or proteins. If there is a core panel along with add-on modules, the core panel should be selected in this field. Any additional panels utilized should be documented in the “additional_panels_used.csv” file, which must be uploaded alongside the dataset. Example: 10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 16 rxns x 16 BC; PN 1000547 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome 4 rxns x 4 BC; PN 1000475 10x Genomics; Chromium Fixed RNA Kit, Human Transcriptome, 4 rxns x 1 BC; PN 1000474 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 16 rxns; PN 1000420 10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 64 rxns; PN 1000456 10x Genomics; Chromium Next GEM Single Cell Fixed RNA Mouse Transcriptome Probe Kit, 64 rxns; PN 1000492 10x Genomics; GEM-X Flex Human Transcriptome Probe Kit, 16 samples; PN 1000785 10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466 10x Genomics; Visium Human Transcriptome Probe Kit-Large; PN 1000364 10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363 10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365 10x Genomics; Visium Mouse Transcriptome Probe Kit v2.0 - Small; PN 1000667 10x Genomics; Xenium Custom Gene Expression Panel (51-100 genes); PN 1000561 10x Genomics; Xenium Custom Gene Expression Panel (up to 50 genes); PN 1000464 10x Genomics; Xenium Human Colon Gene Expression Panel; PN 1000642 10x Genomics; Xenium Human Lung Gene Expression Panel; PN 1000601 10x Genomics; Xenium Human Multi-Tissue and Cancer Panel v1; PN 1000626 10x Genomics; Xenium Human Skin Gene Expression Panel; PN 1000643 10x Genomics; Xenium Mouse Multi-Tissue Atlassing Panel; PN 1000627 10x Genomics; Xenium Prime 5K Human Pan Tissue & Pathways Panel; PN 1000724 Custom NanoString Technologies; CosMx Hs Univ Cell (RNA, 1000 Plex); PN 121500002 NanoString Technologies; CosMx Hs WTX RNA Panel Kit, 2 slides: PN 121500047 NanoString Technologies; CosMx Human 6K Discovery Panel (RNA, 6175 Plex); PN 121500041 NanoString Technologies; CosMx Human Immuno-Oncology Panel (Protein, 64 Plex); PN CMX-H-IOP-64P-P NanoString Technologies; CosMx Human Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-H-USCP-1KP-R NanoString Technologies; CosMx Mouse Neuroscience Panel (Protein, 64 Plex); PN CMX-M-Neuro-64P-P NanoString Technologies; CosMx Mouse Neuroscience Panel (RNA, 1000 Plex); PN CMX-M-NEUP-R NanoString Technologies; CosMx Mouse Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-M-USCP-1KP-R NanoString Technologies; GeoMx Human IO Proteome Atlas, 4 slides; PN 121300160 NanoString Technologies; GeoMx Human Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-HuWTA-4 NanoString Technologies; GeoMx Mouse Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-MsWTA-4
is_custom_probes_used * Indicates whether custom RNA or antibody probes were utilized in the assay. If custom probes were employed, they should be documented in the “custom_probe_set.csv” file. Example: No Yes No
number_of_panel_targets * The number of panel targets, which refers to the total count of genes, RNA isoforms, or RNA regions that are targeted by probes. Example: 1000  
roi_label * The label for the region of interest (ROI). For Resolve and CosMx, this corresponds to the field of view (FOV) label. In the case of Xenium, it refers to the ID of the region containing the analysis. For GeoMx, this information can be located in the “Initial Dataset” spreadsheet, which can be downloaded from within the Data Analysis Suite. Example: Decidua  
anatomical_structure_label The label for the overarching anatomical structure. If the anatomical structure is not applicable or not specified, this field may be left blank. Example: Kidney  
anatomical_structure_id The ontology ID associated with the anatomical structure, typically represented by an UBERON ID. Example: UBERON:0002113  
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