HiFi-Slide Metadata Attributes

Fields that are collected for HiFi-Slide data, available at dataset.metadata.<attribute>  

* indicates a required field

Attribute Type Description Allowable Values
dataset_type * The specific type of dataset being produced. 10X Multiome 2D Imaging Mass Cytometry ATACseq Auto-fluorescence Cell DIVE CODEX Confocal CosMx CyCIF DBiT DESI Enhanced Stimulated Raman Spectroscopy (SRS) GeoMx (nCounter) GeoMx (NGS) HiFi-Slide Histology LC-MS Light Sheet MALDI MERFISH MIBI Molecular Cartography MUSIC nanoSPLITS PhenoCycler Resolve RNAseq RNAseq (with probes) Second Harmonic Generation (SHG) SIMS SNARE-seq2 Stereo-seq Thick section Multiphoton MxIF Visium (no probes) Visium (with probes) Xenium
analyte_class Analytes are the target molecules being measured with the assay. Chromatin DNA DNA + RNA Endogenous fluorophores Fluorochrome Lipid Metabolite Nucleic acid and protein Peptide Polysaccharide Protein RNA
acquisition_instrument_vendor An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. Akoya Biosciences Andor BGI Genomics Bruker Cytiva Evident Scientific (Olympus) GE Healthcare Hamamatsu Huron Digital Pathology Illumina In-House Ionpath Keyence Leica Biosystems Leica Microsystems Motic NanoString Resolve Biosciences Sciex Standard BioTools (Fluidigm) Thermo Fisher Scientific Zeiss Microscopy
acquisition_instrument_model Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. Aperio AT2 Aperio CS2 Axio Observer 3 Axio Observer 5 Axio Observer 7 Axio Scan.Z1 BZ-X710 BZ-X800 BZ-X810 CosMx Spatial Molecular Imager Custom: Multiphoton Digital Spatial Profiler DM6 B DNBSEQ-T7 EVOS M7000 HiSeq 2500 HiSeq 4000 Hyperion Imaging System IN Cell Analyzer 2200 Lightsheet 7 MALDI timsTOF Flex Prototype MIBIscope MoticEasyScan One NanoZoomer 2.0-HT NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 NanoZoomer-SQ NextSeq 2000 NextSeq 500 NextSeq 550 NovaSeq 6000 NovaSeq X NovaSeq X Plus Orbitrap Eclipse Tribrid Orbitrap Fusion Lumos Tribrid Phenocycler-Fusion 1.0 Phenocycler-Fusion 2.0 PhenoImager Fusion Q Exactive Q Exactive HF Q Exactive UHMR QTRAP 5500 Resolve Biosciences Molecular Cartography SCN400 STELLARIS 5 TissueScope LE Slide Scanner Unknown VS200 Slide Scanner Xenium Analyzer Zyla 4.2 sCMOS
source_storage_duration_value How long was the source material stored, prior to this sample being processed? For assays applied to tissue sections, this would be how long the tissue section (e.g., slide) was stored, prior to the assay beginning (e.g., imaging). For assays applied to suspensions such as sequencing, this would be how long the suspension was stored before library construction began.  
source_storage_duration_unit The time duration unit of measurement hour month day minute year
time_since_acquisition_instrument_calibration_value The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture.  
time_since_acquisition_instrument_calibration_unit The time unit of measurement Column-by-column Not applicable Row-by-row Snake-by-columns Snake-by-rows
preparation_protocol_doi * DOI for the protocols.io page that describes the assay or sample procurment and preparation. For example for an imaging assay, the protocol might include staining of a section through the creation of an OME-TIFF file. In this case the protocol would include any image processing steps required to create the OME-TIFF file. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1  
is_targeted Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay (“Yes” or “No”). The CODEX analyte is protein. Yes No
contributors_path The path to the file with the ORCID IDs for all contributors of this dataset (e.g., “./extras/contributors.tsv” or “./contributors.tsv”). This is an internal metadata field that is just used for ingest.  
data_path The top level directory containing the raw and/or processed data. For a single dataset upload this might be “.” where as for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For instance, if the data is within a directory called “TEST001-RK” use syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2” in which “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field that is just used for ingest.  
parent_sample_id Unique HuBMAP or SenNet identifier of the sample (i.e., block, section or suspension) used to perform this assay. For example, for a RNAseq assay, the parent would be the suspension, whereas, for one of the imaging assays, the parent would be the tissue section. If an assay comes from multiple parent samples then this should be a comma separated list. Example: HBM386.ZGKG.235, HBM672.MKPK.442 or SNT232.UBHJ.322, SNT329.ALSK.102  
mapped_area_value For Visium, this is the area of spots that was covered by tissue within the captured area, not the total possible captured area which is fixed. For GeoMx this would be the area of the AOI being captured. For HiFi this is the summed area of the ROIs in a single flowcell lane. For CosMx, Xenium and Resolve, this is the area of the FOV (aka ROI) region being captured.  
mapped_area_unit The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2. um^2 mm^2
spot_size_value FModified progressive staining, Not applicable, Progressive staining, Regressive stainingor 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. um^2 mm^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
capture_area_id Which capture area on the slide was used. For Visium this would be A1, B1, C1, D1. For HiFi this would be the lane on the flowcell. 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
slide_id A unique ID denoting the slide used. This allows users the ability 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 values overlapping across centers.  
target_retrieval_incubation_temperature Will normally be 100 degrees Celsius for RNA assays, and 80 degrees Celsius for protein assays.  
target_retrieval_incubation_time_value The duration for which a sample is exposed to a target retrieval solution.  
target_retrieval_incubation_time_unit The units for target retrieval incubation time value. minute
proteinasek_concentration The amount or concentration of the enzyme Proteinase K within a sample (in ug/ml).  
proteinasek_incubation_time_value The duration for which a sample is exposed to Proteinase K.  
proteinasek_incubation_time_unit The units for proteinaseK incubation time value. minute
anatomical_structure_label The overarching anatomical structure.  
anatomical_structure_id The ontology ID for the parent structure. Typically this would be an UBERON ID.  
metadata_schema_id * The string that serves as the definitive identifier for the metadata schema version and is readily interpretable by computers for data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9  
roi_label A label for the region of interest (ROI). For Xenium, Resolve and CosMx, this is the field of view (FOV) label. For GeoMx this can be found in the “Initial Dataset” spreadsheet (download from within Data Analysis Suite).