MIBI

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)

Attribute	Type	Description	Allowable Values	Required
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_value	Numeric	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.		True
source_storage_duration_unit	Allowable Value	The time duration unit of measurement	`hour` `month` `day` `minute` `year`	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
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
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
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
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
number_of_antibodies	Numeric	Number of antibodies		True
number_of_channels	Numeric	The number of distinct color channels in the image.		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.		True
roi_description	Textfield	A description of the anatomical structure being captured in the region of interest (ROI).		True
roi_id	Numeric	Multiple images are acquired from regions of interest (ROI1, ROI2, ROI3, etc) on a slide. The ROI ID is a number from 1 to N representing the ROI captured on a slide.		True
acquisition_id	Textfield	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.		True
area_normalized_ion_dose_value	Numeric	Number of primary ions delivered to the sample per unit area.		True
area_normalized_ion_dose_unit	Allowable Value	Area normalized ion dose unit.	`nA*hr/mm2`	True
data_precision_bytes	Numeric	Numerical data precision in bytes.		True
pixel_dwell_time_value	Numeric	Resident time of primary ion beam on each pixel to ionize it.		True
pixel_dwell_time_unit	Allowable Value	Pixel dwell time unit.	`ms`	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
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

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 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.		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 of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence.	[‘mass_spectrometry_imaging’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘MIBI’]	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 for detection/measurement by the assay.	[‘Yes’,’No’]	True
acquisition_instrument_vendor	Textfield	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.		True
acquisition_instrument_model	Textfield	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.		True
number_of_antibodies	Numeric	Number of antibodies		True
number_of_channels	Numeric	Number of fluorescent channels imaged during each cycle.		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
max_x_width_value	Numeric	Image width value of the ROI acquisition		True
max_x_width_unit	Allowable Value	Units of image width of the ROI acquisition	[‘um’]	False
max_y_height_value	Numeric	Image height value of the ROI acquisition		True
max_y_height_unit	Allowable Value	Units of image height of the ROI acquisition	[‘um’]	False
roi_description	Textfield	A description of the region of interest (ROI) captured in the image.		True
roi_id	Numeric	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.		True
acquisition_id	Textfield	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.		True
area_normalized_ion_dose_unit	Allowable Value	Area normalized ion dose unit	[‘nA*hr/mm2’]	False
area_normalized_ion_dose_value	Numeric	Number of primary ions delivered to the sample per unit area		True
data_precision_bytes	Numeric	Numerical data precision in bytes		True
dual_count_start	Numeric	Threshold for dual counting.		True
end_datetime	Datetime	Time stamp indicating end of ablation for ROI		True
pixel_dwell_time_value	Numeric	Resident time of primary ion beam on each pixel.		True
pixel_dwell_time_unit	Allowable Value	Pixel dwell time unit.	[‘ms’]	False
pixel_size_x_value	Numeric	Width value of the pixel or voxel measurement (distinct from the image resolution_x_value).		True
pixel_size_x_unit	Allowable Value	Width unit of the pixel or voxel measurement.	[‘nm’]	False
pixel_size_y_value	Numeric	Length value of the pixel or voxel measurement (distinct from the image resolution_y_value).		True
pixel_size_y_unit	Allowable Value	Length unit of the pixel or voxel measurement.	[‘nm’]	False
preparation_instrument_vendor	Allowable Value	The manufacturer of the instrument used to prepare the sample for the assay.	[‘Custom’, ‘Ionpath’]	True
preparation_instrument_model	Allowable Value	The model number/name of the instrument used to prepare the sample for the assay	[‘Custom’, ‘MIBIscope 1’, ‘MIBIscope 2’]	True
primary_ion	Allowable Value	Primary ion.	[‘Xe’]	True
primary_ion_current_value	Numeric	Primary ion current value.		True
primary_ion_current_unit	Allowable Value	Primary ion current unit, typically nA or pA	[‘nA’, ‘pA’]	False
reagent_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing reagents for the assay.		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.		True
segment_data_format	Allowable Value	This refers to the data type, which is a “float” for the IMC counts.	[‘float’, ‘integer’, ‘string’]	True
signal_type	Allowable Value	Type of signal measured per channel (usually dual counts)	[‘dual count’, ‘pulse count’, ‘intensity value’]	True
start_datetime	Datetime	Time stamp indicating start of ablation for ROI		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. Downstream processing will depend on filename extension conventions.		True