2D Imaging Mass Cytometry Metadata Attributes
Fields that are collected for 2D Imaging Mass Cytometry 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 | ||
| total_run_time_value | How long the tissue was on the acquisition instrument. | ||
| total_run_time_unit | The units for the total run time unit field. | Hour Minute |
|
| number_of_antibodies | Number of antibodies | ||
| number_of_channels | The number of distinct color channels in the image. | ||
| 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. | ||
| data_precision_bytes | Numerical data precision in bytes. | ||
| ablation_frequency_value | Frequency value of laser ablation | ||
| ablation_frequency_unit | Frequency unit of laser ablation | Hz |
|
| 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”. | ||
| 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
* indicates a field that was previously required
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| version | Version of the schema to use when validating this metadata. | '1' |
|
| description | Free-text description of this assay. | ||
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| tissue_id | HuBMAP Display ID 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. | ||
| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| 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. | 'mass_spectrometry_imaging' |
|
| assay_type | The specific type of assay being executed. | 'Imaging Mass Cytometry' |
|
| analyte_class | Analytes are the target molecules being measured with the assay. | 'protein' |
|
| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | 'Yes' 'No' |
|
| 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. | ||
| 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. | ||
| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | ||
| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay | ||
| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | ||
| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | ||
| number_of_channels | Number of mass channels measured | ||
| ablation_distance_between_shots_x_value | x resolution. Distance between laser ablation shots in the X-dimension. | ||
| ablation_distance_between_shots_x_units | Units of x resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_distance_between_shots_y_value | y resolution. Distance between laser ablation shots in the Y-dimension. | ||
| ablation_distance_between_shots_y_units | Units of y resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_frequency_value | Frequency value of laser ablation (in Hz) | ||
| ablation_frequency_unit | Frequency unit of laser ablation | 'Hz' |
|
| roi_description | A description of the region of interest (ROI) captured in the image. | ||
| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. | ||
| acquisition_id | The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image. | ||
| dual_count_start | Threshold for dual counting. | ||
| max_x_width_value | Image width value of the ROI acquisition | ||
| max_x_width_unit | Units of image width of the ROI acquisition | 'um' |
|
| max_y_height_value | Image height value of the ROI acquisition | ||
| max_y_height_unit | Units of image height of the ROI acquisition | 'um' |
|
| segment_data_format | This refers to the data type, which is a “float” for the IMC counts. | 'float' 'integer' 'string' |
|
| signal_type | Type of signal measured per channel (usually dual counts) | 'dual count' 'pulse count' 'intensity value' |
|
| data_precision_bytes | Numerical data precision in bytes | ||
| antibodies_path | Relative path to file with antibody information for this dataset. | ||
| 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. | ||
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| tissue_id | HuBMAP Display ID 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. | ||
| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| 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. | 'mass_spectrometry_imaging' |
|
| assay_type | The specific type of assay being executed. | 'Imaging Mass Cytometry' |
|
| analyte_class | Analytes are the target molecules being measured with the assay. | 'protein' |
|
| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | 'Yes' 'No' |
|
| 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. | ||
| 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. | ||
| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | ||
| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay | ||
| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | ||
| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | ||
| number_of_channels | Number of mass channels measured | ||
| ablation_distance_between_shots_x_value | x resolution. Distance between laser ablation shots in the X-dimension. | ||
| ablation_distance_between_shots_x_units | Units of x resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_distance_between_shots_y_value | y resolution. Distance between laser ablation shots in the Y-dimension. | ||
| ablation_distance_between_shots_y_units | Units of y resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_frequency_value | Frequency value of laser ablation (in Hz) | ||
| ablation_frequency_unit | Frequency unit of laser ablation | 'Hz' |
|
| roi_description | A description of the region of interest (ROI) captured in the image. | ||
| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. | ||
| acquisition_id | The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image. | ||
| dual_count_start | Threshold for dual counting. | ||
| end_datetime | Time stamp indicating end of ablation for ROI | ||
| max_x_width_value | Image width value of the ROI acquisition | ||
| max_x_width_unit | Units of image width of the ROI acquisition | 'um' |
|
| max_y_height_value | Image height value of the ROI acquisition | ||
| max_y_height_unit | Units of image height of the ROI acquisition | 'um' |
|
| segment_data_format | This refers to the data type, which is a “float” for the IMC counts. | 'float' 'integer' 'string' |
|
| signal_type | Type of signal measured per channel (usually dual counts) | 'dual count' 'pulse count' 'intensity value' |
|
| start_datetime | Time stamp indicating start of ablation for ROI | ||
| data_precision_bytes | Numerical data precision in bytes | ||
| 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. | ||
| version | Version of the schema to use when validating this metadata. | '1' |
|
| description | Free-text description of this assay. | ||
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| tissue_id | HuBMAP Display ID 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. | ||
| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| 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. | 'mass_spectrometry_imaging' |
|
| assay_type | The specific type of assay being executed. | '3D Imaging Mass Cytometry' |
|
| analyte_class | Analytes are the target molecules being measured with the assay. | 'protein' |
|
| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | 'Yes' 'No' |
|
| 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. | ||
| 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. | ||
| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | ||
| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay | ||
| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | ||
| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | ||
| number_of_channels | Number of mass channels measured | ||
| number_of_sections | Number of sections | ||
| ablation_distance_between_shots_x_value | x resolution. Distance between laser ablation shots in the X-dimension. | ||
| ablation_distance_between_shots_x_units | Units of x resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_distance_between_shots_y_value | y resolution. Distance between laser ablation shots in the Y-dimension. | ||
| ablation_distance_between_shots_y_units | Units of y resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_frequency_value | Frequency value of laser ablation (in Hz) | ||
| ablation_frequency_unit | Frequency unit of laser ablation | 'Hz' |
|
| roi_description | A description of the region of interest (ROI) captured in the image. | ||
| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. | ||
| acquisition_id | The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image. | ||
| max_x_width_value | Image width value of the ROI acquisition | ||
| max_x_width_unit | Units of image width of the ROI acquisition | 'um' |
|
| max_y_height_value | Image height value of the ROI acquisition | ||
| max_y_height_unit | Units of image height of the ROI acquisition | 'um' |
|
| segment_data_format | This refers to the data type, which is a “float” for the IMC counts. | 'float' 'integer' 'string' |
|
| signal_type | Type of signal measured per channel (usually dual counts) | 'dual count' 'pulse count' 'intensity value' |
|
| antibodies_path | Relative path to file with antibody information for this dataset. | ||
| 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. | ||
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| tissue_id | HuBMAP Display ID 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. | ||
| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| 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. | 'mass_spectrometry_imaging' |
|
| assay_type | The specific type of assay being executed. | '3D Imaging Mass Cytometry' |
|
| analyte_class | Analytes are the target molecules being measured with the assay. | 'protein' |
|
| is_targeted | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | 'Yes' 'No' |
|
| 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. | ||
| 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. | ||
| preparation_instrument_vendor | The manufacturer of the instrument used to prepare the sample for the assay. | ||
| preparation_instrument_model | The model number/name of the instrument used to prepare the sample for the assay | ||
| section_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing tissue sections for the assay. | ||
| reagent_prep_protocols_io_doi | DOI for protocols.io referring to the protocol for preparing reagents for the assay. | ||
| number_of_channels | Number of mass channels measured | ||
| number_of_sections | Number of sections | ||
| ablation_distance_between_shots_x_value | x resolution. Distance between laser ablation shots in the X-dimension. | ||
| ablation_distance_between_shots_x_units | Units of x resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_distance_between_shots_y_value | y resolution. Distance between laser ablation shots in the Y-dimension. | ||
| ablation_distance_between_shots_y_units | Units of y resolution distance between laser ablation shots. | 'um' 'nm' |
|
| ablation_frequency_value | Frequency value of laser ablation (in Hz) | ||
| ablation_frequency_unit | Frequency unit of laser ablation | 'Hz' |
|
| roi_description | A description of the region of interest (ROI) captured in the image. | ||
| roi_id | Multiple images (1-n) are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The roi_id is a number from 1-n representing the ROI captured on a slide. | ||
| acquisition_id | The acquisition_id refers to the directory containing the ROI images for a slide. Together, the acquisition_id and the roi_id indicate the slide-ROI represented in the image. | ||
| max_x_width_value | Image width value of the ROI acquisition | ||
| max_x_width_unit | Units of image width of the ROI acquisition | 'um' |
|
| max_y_height_value | Image height value of the ROI acquisition | ||
| max_y_height_unit | Units of image height of the ROI acquisition | 'um' |
|
| segment_data_format | This refers to the data type, which is a “float” for the IMC counts. | 'float' 'integer' 'string' |
|
| signal_type | Type of signal measured per channel (usually dual counts) | 'dual count' 'pulse count' 'intensity value' |
|
| antibodies_path | Relative path to file with antibody information for this dataset. | ||
| 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. |