Visium HD Metadata Attributes
These metadata fields have been collected for Visium HD data.
These fields are available from the HuBMAP Search and Entity APIs at Dataset.metadata.<attribute>.
See the latest version of the Visium HD 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 |
|
| 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 * | The area of a spot used in assays where spots define discrete capture areas. Example: 2375.9 | ||
| spot_size_unit * | The unit of measurement for the spot size value. If no spot size value is specified, this field may be left blank. Example: um^2 | 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 * | The approximate center-to-center distance between capture spots, also known as inter-spot distance, spot resolution, or pit size. Example: 100 | ||
| spot_spacing_unit * | Units corresponding to inter-spot distance | um |
|
| capture_area_id * | The capture area on the slide that was used during the process. For example, in the case for Visium, this would correspond to areas such as [A1, B1, C1, D1], while for HiFi, it would refer to the lane on the flowcell. Example: A1 | A1 B1 C1 D1 Lane 1 Lane 2 Lane 3 Lane 4 Lane 5 Lane 6 Lane 7 Lane 8 |
|
| 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 | 10x Genomics Akoya Biosciences Hamamatsu HTX Technologies In-House Ionpath Leica Biosystems Not applicable Roche Diagnostics SunChrom Thermo Fisher Scientific |
|
| 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 | AutoStainer XL Chromium Connect Chromium Controller Chromium iX Chromium X Custom Discovery Ultra EVOS M7000 M3+ Sprayer M5 Sprayer NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 Not applicable ST5020 Multistainer Sublimator SunCollect Sprayer TM-Sprayer Visium CytAssist |
|
| 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 |