| lab_id |
Textfield |
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 |
|
False |
| source_storage_duration_value |
Numeric |
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 |
|
True |
| time_since_acquisition_instrument_calibration_value |
Numeric |
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 |
|
False |
| contributors_path |
Textfield |
The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv |
|
True |
| data_path |
Textfield |
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 |
|
True |
| is_image_preprocessing_required |
Radio |
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 |
Yes, No |
False |
| slide_id |
Textfield |
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 |
|
False |
| tiled_image_columns |
Numeric |
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 |
|
False |
| tiled_image_count |
Numeric |
The total number of raw tiled images captured, which are intended to be stitched together. Example: 75 |
|
False |
| intended_tile_overlap_percentage |
Numeric |
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 |
|
False |
| dataset_type |
Assigned Value |
The specific type of dataset being produced. Example: RNAseq |
Visium HD, 4i, LC-MS, Thick section Multiphoton MxIF, Light Sheet, ATACseq, Resolve, HiFi-Slide, COMET, MPLEx, 10X Multiome, MALDI, 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, CyCIF, SNARE-seq2, nanoSPLITS, STARmap, Stereo-seq, Visium (with probes), SIMS, Auto-fluorescence, CyTOF, CosMx Proteomics, Virtual Histology, DBiT-seq, PhenoCycler |
True |
| analyte_class |
Assigned Value |
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, RNA + protein, Peptide, Protein, Unsaturated lipid, Endogenous fluorophore, Chromatin, Polysaccharide |
True |
| acquisition_instrument_vendor |
Assigned Value |
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, 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 |
True |
| acquisition_instrument_model |
Assigned Value |
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, 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, 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, VS200 Slide Scanner, Not applicable |
True |
| source_storage_duration_unit |
Assigned Value |
The unit of measurement used to specify the source storage duration value. Example: hour |
hour, month, day, minute, year |
True |
| time_since_acquisition_instrument_calibration_unit |
Assigned Value |
The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month |
month, day, year |
False |
| tile_configuration |
Assigned Value |
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 |
False |
| scan_direction |
Assigned Value |
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 |
False |
| metadata_schema_id |
Textfield |
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 |
|
True |
| preparation_protocol_doi |
Link |
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 |
|
True |
| is_targeted |
Radio |
Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes |
Yes, No |
True |
| parent_sample_id |
Textfield |
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 |
|
True |
| number_of_pixels |
Numeric |
The total number of spatial sampling points in an image; for example, in a Raman image, each pixel corresponds to one recorded Raman spectrum. Example: 40000 |
|
True |
| pixel_physical_size_height_value |
Numeric |
The physical height of a single pixel in the image. Example: 1000 |
|
True |
| pixel_physical_size_height_unit |
Assigned Value |
The unit of measurement for the pixel physical size height value. If the pixel height is not specified, this field may be left blank. Example: um |
um, mm, nm |
True |
| pixel_physical_size_width_value |
Numeric |
The physical width of a single pixel in the image. Example: 1000 |
|
True |
| pixel_physical_size_width_unit |
Assigned Value |
The unit of measurement for the pixel physical size width value. If the pixel width value is not specified, this field may be left blank. Example: um |
um, mm, nm |
True |
| pixel_physical_size_depth_value |
Numeric |
The physical depth of a single pixel in the image. Example: 10 |
|
True |
| pixel_physical_size_depth_unit |
Assigned Value |
The unit of measurement for the pixel physical size depth value. If the pixel depth value is not specified, this field may be left blank. Example: um |
um, mm, nm |
True |
| objective_numerical_aperture |
Numeric |
Numerical aperture of the microscope objective used to focus the excitation laser on the sample and collect the resulting scattered signal, such as Raman-scattered light. Example: 0.5 |
|
True |
| laser_power |
Numeric |
Power of the excitation laser at the sample’s focal plane, measured after the objective and reported in milliwatts (mW). Example: 10 |
|
True |
| raman_shift_range |
Textfield |
Range of Raman shifts acquired in the measurement, expressed in wavenumbers (cm⁻¹). Example: 400-3200 |
|
True |
