Visium-(no-probes)

NOTE: Several versions of this metadata schema have been created over time. The (Latest) version contains most attributes, but there may be some deprecated attributes in the older versions for which data has been collected. HuBMAP is in the process of creating a reference which combines all of these versions into a single view. That reference will be available here once completed.

Version3 (current)

Version 3

Attribute	Type	Description	Allowable Values	Required
preparation_protocol_doi	Textfield	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		True
dataset_type	Allowable Value	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	True
contributors_path	Textfield	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.		True
data_path	Textfield	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.		True
mapped_area_value	Numeric	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.		True
mapped_area_unit	Allowable Value	The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2.	um^2 mm^2	True
spot_size_value	Numeric	For assays where spots are used to define discrete capture areas, this is the area of a spot.		True
spot_size_unit	Allowable Value	The unit for spot size value.	um^2 mm^2	True
number_of_spots	Numeric	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.		True
spot_spacing_value	Numeric	Approximate center-to-center distance between capture spots. Synonyms: Inter-Spot distance, Spot resolution, Pit size		True
spot_spacing_unit	Allowable Value	Units corresponding to inter-spot distance	um	True
capture_area_id	Allowable Value	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	True
permeabilization_time_value	Numeric	Permeabilization time used for this tissue section.		False
permeabilization_time_unit	Allowable Value	The unit for the permeabilization time.	minute	False
metadata_schema_id	Textfield	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		True
parent_sample_id	Textfield	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		True
preparation_instrument_vendor	Allowable Value	The manufacturer of the instrument used to prepare (staining/processing) the sample for the assay. If an automatic slide staining method was indicated this field should list the manufacturer of the instrument.	10x Genomics Hamamatsu HTX Technologies In-House Leica Biosystems Not applicable Roche Diagnostics SunChrom Thermo Fisher Scientific	False
preparation_instrument_model	Allowable Value	Manufacturers of a staining system instrument may offer various versions (models) of that instrument with different features. Differences in features or sensitivities may be relevant to processing or interpretation of the data.	AutoStainer XL Chromium Connect Chromium Controller Chromium iX Chromium X 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	False

Version 2

Version 2

Attribute	Type	Description	Allowable Value	Required
preparation_protocol_doi	Textfield	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		True
dataset_type	Textfield	The specific type of dataset being produced.		True
contributors_path	Textfield	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.		True
data_path	Textfield	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.		True
mapped_area_value	Numeric	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.		True
mapped_area_unit	Textfield	The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2.		True
spot_size_value	Numeric	For assays where spots are used to define discrete capture areas, this is the area of a spot.		True
spot_size_unit	Textfield	The unit for spot size value.		True
number_of_spots	Numeric	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.		True
spot_spacing_value	Numeric	Approximate center-to-center distance between capture spots. Synonyms: Inter-Spot distance, Spot resolution, Pit size		True
spot_spacing_unit	Textfield	Units corresponding to inter-spot distance		True
capture_area_id	Allowable Value	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]	True
permeabilization_time_value	Numeric	Permeabilization time used for this tissue section.		False
permeabilization_time_unit	Textfield	The unit for the permeabilization time.		False
metadata_schema_id	Textfield	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		True
parent_sample_id	Textfield	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		True