Auto-fluorescence Metadata Attributes

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

* indicates a required field

Attribute Type Description Allowable Values
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  
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 * 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  
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
is_targeted * Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.  
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
contributors_path * Relative path to file with ORCID IDs for contributors for this dataset.  
data_path * Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.  
antibodies_path * This is the location of the antibodies.tsv file relative to the root of the top level of the upload directory structure. This path should begin with “.” and would likely be something like “./extras/antibodies.tsv”.  
is_image_preprocessing_required Indicates whether image preprocessing is necessary based on the type of acquisition instrument used, such as a microscope or slide scanner. This may involve steps like fusing image tiles to assemble the complete image. Example: Yes  
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.  
tile_configuration The configuration of tiles used for stitching in the assay process. If no tile configuration is applicable, enter “Not applicable”. Example: Row-by-row Column-by-column Not applicable Snake-by-columns Row-by-row Snake-by-rows
scan_direction The direction of imaging, which is necessary for the stitching process. Example: Left-and-down Left-and-down Right-and-down Not applicable Right-and-up Left-and-up
tiled_image_columns The number of columns used in the stitching process of a tiled image, often referred to as the grid size in the x-dimension. Example: 5  
tiled_image_count The total number of raw tiled images captured, which are intended to be stitched together. Example: 75  
intended_tile_overlap_percentage The intended percentage of overlap between tiled images. This value serves as the set point, although slight variations may occur during image acquisition due to stage registration. Example: 5  
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  

 

Deprecated Attributes

These attributes were supported by older metadata version specifications. They are no longer collected but there may be some older datasets that contain data for these attributes.

Attribute Type Description Allowable Values
resolution_x_unit The unit of measurement of the width of a pixel. mm um nm
resolution_x_value The width of a pixel.  
resolution_y_unit The unit of measurement of the height of a pixel. mm um nm
resolution_y_value The height of a pixel  
resolution_z_unit The unit of incremental distance between image slices. mm um nm
resolution_z_value Optional if assay does not have multiple z-levels. Note that this is resolution within a given sample: z-pitch (resolution_z_value) is the increment distance between image slices, ie. the microscope stage is moved up or down in increments to capture images of several focal planes.  
assay_category Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. sequence
description Free-text description of this assay.  
donor_id HuBMAP Display ID of the donor of the assayed tissue.  
execution_datetime Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros.  
number_of_channels Number of channels capturing the emission spectrum from natural fluorophores in the sample.  
operator Name of the person responsible for executing the assay.  
operator_email Email address for the operator.  
overall_protocols_io_doi DOI for protocols.io referring to the overall protocol for the assay.  
principal_investigator The full name of the principal investigator who is responsible for the data.  
pi_email Email address for the principal investigator.  
version Version of the schema to use when validating this metadata. 1