Illumina Spatial Metadata Attributes

Fields that are collected for Illumina Spatial data, available at dataset.metadata.<attribute>  

* indicates a required field

Attribute Type Description Allowable Values
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 Visium HD 4i Illumina Spatial v0 LC-MS Thick section Multiphoton MxIF Light Sheet ATACseq Resolve HiFi-Slide COMET MPLEx 10X Multiome MALDI MACSima Raman Imaging Histology Cell DIVE FACS MS Lipidomics Visium (no probes) MUSIC RNAseq GeoMx (NGS) GeoMx (nCounter) RNAseq (with probes) Singular Genomics G4X Molecular Cartography CosMx Transcriptomics MERFISH Pixel-seqV2 2D Imaging Mass Cytometry Confocal seqFISH DART-FISH MIBI Olink Enhanced Stimulated Raman Spectroscopy (SRS) DESI Xenium iCLAP CyCIF SNARE-seq2 nanoSPLITS STARmap Stereo-seq Visium (with probes) SIMS Auto-fluorescence CyTOF CosMx Proteomics
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 um^2 mm^2
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  
permeabilization_time_value Permeabilization time used for this tissue section.  
permeabilization_time_unit The unit for the permeabilization time. minute
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  
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  
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 Thermo Fisher Scientific SunChrom Akoya Biosciences Leica Biosystems Ionpath Roche Diagnostics In-House Not applicable Hamamatsu HTX Technologies 10x Genomics
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 ST5020 Multistainer Visium CytAssist SunCollect Sprayer Chromium X Chromium iX EVOS M7000 NanoZoomer S210 NanoZoomer S60 NanoZoomer S360 Discovery Ultra Sublimator Not applicable TM-Sprayer M5 Sprayer M3+ Sprayer Chromium Controller Chromium Connect Custom
capture_area_width_value * The width of RNA capture area. Example: 10  
capture_area_width_unit The unit of measurement for the capture area width value. If the width value is not specified, this field may be left blank. Example: mm mm
capture_area_height_value The height of RNA capture area. Example: 10  
capture_area_height_unit The unit of measurement for the capture area height value. If the height value is not specified, this field may be left blank. Example: mm mm
spatial_discreatization_method The segmentation method used to divide the capture are into smaller, defined regions for analysis. Example: Cell segmentation Square binning Cell segmentation Hexagonal binning
bin_size The size (in µm) of each discrete spatial unit (“bin”) used to partition the capture area in bin-based spatial discretization. Example: 100  
analyte_class * The analyte class which is the target molecule that the assay is measuring. Example: DNA Nucleic acid + protein Lipid + metabolite Collagen RNA Fluorochrome DNA Metabolite DNA + RNA Saturated lipid Lipid Lipid + metabolite + protein RNA + protein Peptide Protein Unsaturated lipid Endogenous fluorophore Chromatin Polysaccharide
is_targeted Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes  
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 Complete Genomics Cytek Biosciences Thermo Fisher Scientific Sciex Vizgen Leica Microsystems Akoya Biosciences Keyence Andor Standard BioTools (Fluidigm) Leica Biosystems Zeiss Microscopy Ionpath Motic In-House Miltenyi Biotec Revvity Evident Scientific (Olympus) GE Healthcare Element Biosciences Hamamatsu Waters Bruker Illumina 3DHISTECH Singular Genomics Huron Digital Pathology Resolve Biosciences NanoString Cytiva 10x Genomics Microscopes International BGI Genomics
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 NovaSeq X NovaSeq X Plus Cytek Northern Lights Lightsheet 7 Resolve Biosciences Molecular Cartography timsTOF HT timsTOF Pro 2 timsTOF Pro timsTOF Ultra timsTOF Ultra 2 timsTOF SCP Axio Scan.Z1 MALDI timsTOF Flex Prototype LSM 710 Confocal Microscope CosMx Spatial Molecular Imager Unknown MERSCOPE Ultra Juno System timsTOF FleX Custom: Multiphoton CyTOF XT Helios EVOS M7000 Aperio AT2 Phenocycler-Fusion 2.0 Axio Observer 5 Axio Observer 7 Axio Observer 3 NanoZoomer-SQ NanoZoomer S210 NanoZoomer S60 NanoZoomer S360 DM6 B MoticEasyScan One In-House NextSeq 500 BZ-X710 MACSima System QTRAP 5500 DMi8 NextSeq 550 HiSeq 2500 HiSeq 4000 NovaSeq 6000 Opera Phenix Plus HCS SYNAPT G2-Si Q Exactive HF Orbitrap Fusion Tribrid Orbitrap Fusion Lumos Tribrid Q Exactive HF-X
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 hour month day minute 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 month day year