PhenoCycler

Version 2 (current)

Version 2 (current)

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.   True
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 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
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
nuclear_marker_or_stain Allowable Value For markers, an antibody-targetted molecule present in or around the cell nucleus, the protein or gene symbol that identifies the antibody target that is used as the nuclear marker. This symbol must match the antibody target that is either generated from the panel used or entered with custom panels. Preferably, if using a custom antibody marker, this symbol should be the HGNC symbol (https://www.genenames.org/). For non-protein targets this is the stain name (e.g., DAPI) and, when appropriate, associated staining kit and vendor. For the PhenoCycler, this symbol must match the value found in the XPD output file. DAPI Not applicable True
cell_boundary_marker_or_stain Allowable Value If a marker or stain was used to identify all cell boundaries in the tissue, then the name of the marker or stain should be included here. The name of the antibody-targeted molecule marker or non-antibody targeted molecule stain included here must be identical to what is found in the imaging data. For example, with the PhenoCycler, this name must match the value found in the XPD output file. If multiple marker or stains are used to identify all cell boundaries, then a comma separated list should be used here. NAKATPASE CD298 Not applicable True
non_global_files Textfield A semicolon separated list of non-shared files to be included in the dataset. The path assumes the files are located in the “TOP/non-global/” directory. For example, for the file is TOP/non-global/lab_processed/images/1-tissue-boundary.geojson the value of this field would be “./lab_processed/images/1-tissue-boundary.geojson”. After ingest, these files will be copied to the appropriate locations within the respective dataset directory tree. This field is used for internal SenNet processing. Examples for GeoMx and PhenoCycler are provided in the File Locations documentation: https://docs.google.com/document/d/1n2McSs9geA9Eli4QWQaB3c9R3wo5d5U1Xd57DWQfN5Q/edit#heading=h.1u82i4axggee   False