Light-Sheet

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 3 (latest)

Version 3 (latest)

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
is_image_preprocessing_required Allowable Value Depending on if the acquisition instrument was a microscope, slide scanner, etc. will indicate whether or not any level of preprocessing was required to assemble the image (e.g., fusing image tiles) . Yes No 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
tiled_image_columns Numeric This is how many columns used in stitching. This is sometimes referred to as the grid size x.   False
tiled_image_count Numeric This is the total number of raw (tiled) images captured, that are to be stitched together.   False
intended_tile_overlap_percentage Numeric The amount of overlap between tiled images. This is the set point, where as during image acquisition there will be slight variations due to stage registration.   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
tile_configuration Allowable Value This is how the tiles are configured for stitching. Column-by-column Not applicable Row-by-row Snake-by-columns Snake-by-rows False
scan_direction Allowable Value This is the direction of imaging, which is required for stitching. Left-and-down Left-and-up Not applicable Right-and-down Right-and-up 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
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 2

Version 2

Attribute Type Description Allowable Values Required
version Allowable Value Version of the schema to use when validating this metadata. [‘2’] 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. [‘Light Sheet’] 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 Textfield 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 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. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.   True
resolution_x_value Numeric The width of a pixel.   True
resolution_x_unit Allowable Value The unit of measurement of the width of a pixel. [‘nm’, ‘um’] False
resolution_y_value Numeric The height of a pixel   True
resolution_y_unit Allowable Value The unit of measurement of the height of a pixel. [‘nm’, ‘um’] False
range_z_value Numeric The total range of the z axis.   True
range_z_unit Allowable Value The unit of range_z_value. [‘nm’, ‘um’] False
step_z_value Numeric The number of optical sections in z axis range.   True
increment_z_value Numeric The distance between sequential optical sections.   True
increment_z_unit Allowable Value The units of increment z value. [‘nm’, ‘um’] False
number_of_antibodies Numeric Number of antibodies   True
number_of_channels Numeric Number of fluorescent channels imaged during each cycle.   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 1

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. [‘Light Sheet’] 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 Textfield 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 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. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.   True
resolution_x_value Numeric The width of a pixel.   True
resolution_x_unit Allowable Value The unit of measurement of the width of a pixel. [‘nm’, ‘um’] False
resolution_y_value Numeric The height of a pixel   True
resolution_y_unit Allowable Value The unit of measurement of the height of a pixel. [‘nm’, ‘um’] False
resolution_z_value Numeric The distance at which two objects along the detection z-axis can bedistinguished (resolved as 2 objects).   True
resolution_z_unit Allowable Value The unit of distance at which two objects along the detection z-axiscan be distinguished (resolved as 2 objects). [‘mm’, ‘um’, ‘nm’] False
number_of_antibodies Numeric Number of antibodies   True
number_of_channels Numeric Number of fluorescent channels imaged during each cycle.   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

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. [‘Light Sheet’] 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 Textfield 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 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. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.   True
resolution_x_value Numeric The width of a pixel.   True
resolution_x_unit Allowable Value The unit of measurement of the width of a pixel. [‘nm’, ‘um’] False
resolution_y_value Numeric The height of a pixel   True
resolution_y_unit Allowable Value The unit of measurement of the height of a pixel. [‘nm’, ‘um’] False
resolution_z_value Numeric The distance at which two objects along the detection z-axis can bedistinguished (resolved as 2 objects).   True
resolution_z_unit Allowable Value The unit of distance at which two objects along the detection z-axiscan be distinguished (resolved as 2 objects). [‘mm’, ‘um’, ‘nm’] False
number_of_antibodies Numeric Number of antibodies   True
number_of_channels Numeric Number of fluorescent channels imaged during each cycle.   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