CODEX

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. SenNet 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.

Version 2 (Latest)

Version 2

Attribute	Type	Description	Allowable Values	Required
source_storage_duration_value	Numeric	How long was the source material (parent) stored, prior to this sample being processed.		True
time_since_acquisition_instrument_calibration_value	Numeric	The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture.		False
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
number_of_antibodies	Numeric	Number of antibodies		True
number_of_channels	Numeric	Number of fluorescent channels imaged during each cycle.		True
number_of_biomarker_imaging_rounds	Numeric	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.		True
number_of_total_imaging_rounds	Numeric	The total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal (e.g., histology).		True
slide_id	Textfield	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.		False
total_run_time_value	Numeric	How long the tissue was on the acquisition instrument.		False
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
analyte_class	Allowable Value	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`	True
acquisition_instrument_vendor	Allowable Value	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`	True
acquisition_instrument_model	Allowable Value	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`	True
source_storage_duration_unit	Allowable Value	The time duration unit of measurement	`hour` `month` `day` `minute` `year`	True
time_since_acquisition_instrument_calibration_unit	Allowable Value	The time unit of measurement	`Column-by-column` `Not applicable` `Row-by-row` `Snake-by-columns` `Snake-by-rows`	False
total_run_time_unit	Allowable Value	The units for the total run time unit field.	`Hour` `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
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
is_targeted	Allowable Value	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`	True
antibodies_path	Textfield	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”.		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`	True
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`	True
parent_sample_id	Textfield	Unique SenNet 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

Version 1

Attribute	Type	Description	Allowable Values	Required
version	Allowable Value	Version of the schema to use when validating this metadata.	[‘1’]	True
description	Textfield	Free-text description of this assay.		True
source_id	Textfield	SenNet Display ID of the source of the assayed tissue.		True
tissue_id	Textfield	SenNet Display ID of the assayed tissue.		True
execution_datetime	Datetime	Start date and time of assay, typically a date-time stamped foldergenerated 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 thehour with leading zeros, mm are the minutes with leading zeros.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence.	[‘imaging’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘CODEX’, ‘CODEX2’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘protein’]	True
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay.	[‘Yes’, ‘No’]	True
acquisition_instrument_vendor	Allowable Value	An acquisition_instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing molecular mass.	[‘Keyence’, ‘Zeiss’]	True
acquisition_instrument_model	Allowable Value	Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.	[‘BZ-X800’, ‘BZ-X710’, ‘Axio Observer Z1’]	True
resolution_x_value	Numeric	The width of a pixel. (Akoya pixel is 377nm square)		True
resolution_x_unit	Allowable Value	The unit of measurement of width of a pixel.(nm)	[‘mm’, ‘um’, ‘nm’]	False
resolution_y_value	Numeric	The height of a pixel. (Akoya pixel is 377nm square)		True
resolution_y_unit	Allowable Value	The unit of measurement of height of a pixel. (nm)	[‘mm’, ‘um’, ‘nm’]	False
resolution_z_value	Numeric	Optional if assay does not have multiple z-levels. Note that thisis resolution within a given sample: z-pitch (resolution_z_value) is the incrementdistance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stageis moved up or down in increments of 1.5um to capture images of several focalplanes. The best one will be used & the rest discarded. The thickness of the sampleitself is sample metadata.		False
resolution_z_unit	Allowable Value	The unit of incremental distance between image slices.	[‘mm’, ‘um’, ‘nm’]	False
preparation_instrument_vendor	Allowable Value	The manufacturer of the instrument used to prepare the sample for theassay.	[‘CODEX’]	True
preparation_instrument_model	Allowable Value	The model number/name of the instrument used to prepare the samplefor the assay	[‘version 1 robot’, ‘prototype robot - Stanford/Nolan Lab’]	True
number_of_antibodies	Numeric	Number of antibodies		True
number_of_channels	Numeric	Number of fluorescent channels imaged during each cycle.		True
number_of_cycles	Numeric	Number of cycles of 1. oligo application, 2. fluor application, 3.washes		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissuesections for the assay.		True
reagent_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing reagentsfor the assay.		True
antibodies_path	Textfield	Relative path to file with antibody information for this dataset.		True
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions.		True

Version 0

Attribute	Type	Description	Allowable Values	Required
source_id	Textfield	SenNet Display ID of the source of the assayed tissue.		True
tissue_id	Textfield	SenNet Display ID of the assayed tissue.		True
execution_datetime	Datetime	Start date and time of assay, typically a date-time stamped foldergenerated 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 thehour with leading zeros, mm are the minutes with leading zeros.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence.	[‘imaging’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘CODEX’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘protein’]	True
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay.	[‘Yes’, ‘No’]	True
acquisition_instrument_vendor	Allowable Value	An acquisition_instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing molecular mass.	[‘Keyence’, ‘Zeiss’]	True
acquisition_instrument_model	Allowable Value	Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.	[‘BZ-X800’, ‘BZ-X710’, ‘Axio Observer Z1’]	True
resolution_x_value	Numeric	The width of a pixel. (Akoya pixel is 377nm square)		True
resolution_x_unit	Allowable Value	The unit of measurement of width of a pixel.(nm)	[‘mm’, ‘um’, ‘nm’]	False
resolution_y_value	Numeric	The height of a pixel. (Akoya pixel is 377nm square)		True
resolution_y_unit	Allowable Value	The unit of measurement of height of a pixel. (nm)	[‘mm’, ‘um’, ‘nm’]	False
resolution_z_value	Numeric	Optional if assay does not have multiple z-levels. Note that thisis resolution within a given sample: z-pitch (resolution_z_value) is the incrementdistance between image slices (for Akoya, z-pitch=1.5um) ie. the microscope stageis moved up or down in increments of 1.5um to capture images of several focalplanes. The best one will be used & the rest discarded. The thickness of the sampleitself is sample metadata.		False
resolution_z_unit	Allowable Value	The unit of incremental distance between image slices.	[‘mm’, ‘um’, ‘nm’]	False
	Textfield
preparation_instrument_vendor	Allowable Value	The manufacturer of the instrument used to prepare the sample for theassay.	[‘CODEX’]	True
preparation_instrument_model	Allowable Value	The model number/name of the instrument used to prepare the samplefor the assay	[‘version 1 robot’, ‘prototype robot - Stanford/Nolan Lab’]	True
number_of_antibodies	Numeric	Number of antibodies		True
number_of_channels	Numeric	Number of fluorescent channels imaged during each cycle.		True
number_of_cycles	Numeric	Number of cycles of 1. oligo application, 2. fluor application, 3.washes		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissuesections for the assay.		True
reagent_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing reagentsfor the assay.		True
antibodies_path	Textfield	Relative path to file with antibody information for this dataset.		True
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions.		True