| 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 |
False |
| is_batch_staining_done |
Allowable Value |
Are the slides stained using a linear batch method or individually? |
Yes No |
True |
| is_staining_automated |
Allowable Value |
Is the slide staining automated with an instrument? |
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 |
| 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 |
| 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 |
| stain_name |
Allowable Value |
The name of the chemical stains (dyes) applied to histology samples to highlight important features of the tissue as well as to enhance the tissue contrast. |
AB-PAS H&E H-DAB LFB PAS Trichrome |
True |
| stain_technique |
Allowable Value |
There are typically three types of stains: progressive, modified progressive, and regressive. Progressive staining occurs when the hematoxylin is added to the tissue without being followed by a differentiator to remove excess dye. With regressive and modified progressive staining, a differentiator is used. |
Modified progressive staining Not applicable Progressive staining Regressive staining |
False |
| 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 |
False |
| 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 |
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 |
| 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 |
| 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 |
| 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 |
