CODEX Metadata Attributes

Fields that are collected for CODEX data, available at dataset.metadata.<attribute>

* indicates a required field

Attribute	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 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 *	Relative path to file with antibody information for this dataset.
preparation_instrument_vendor *	The manufacturer of the instrument used to prepare the sample for the assay.	`10x Genomics` `Hamamatsu` `HTX Technologies` `In-House` `Leica Biosystems` `Not applicable` `Roche Diagnostics` `SunChrom` `Thermo Fisher Scientific`
preparation_instrument_model *	The model number/name of the instrument used to prepare the sample for the assay	`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`
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 *	Number of fluorescent channels imaged during each cycle.
number_of_biomarker_imaging_rounds *	Number of imaging rounds to capture the tagged biomarkers. For CODEX a biomarker imaging round consists of 1. oligo application, 2. fluor application, 3. washes. For Cell DIVE a biomarker imaging round consists of 1. staining of a biomarker via secondary detection or direct conjugate and 2. dye inactivation.
number_of_total_imaging_rounds *	The total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal (e.g., histology).
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.
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	Description	Allowable Values
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`
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.
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.
resolution_x_unit	The unit of measurement of width of a pixel.(nm)	`mm` `um` `nm`
resolution_x_value	The width of a pixel. (Akoya pixel is 377nm square)
resolution_y_unit	The unit of measurement of height of a pixel. (nm)	`mm` `um` `nm`
resolution_y_value	The height of a pixel. (Akoya pixel is 377nm square)
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 (for Akoya, z-pitch=1.5um) ie. the microscope stage is moved up or down in increments of 1.5um to capture images of several focal planes. The best one will be used & the rest discarded. The thickness of the sample itself is sample metadata.