From 63a80e6483925c36d08f02c460ce2ef89d5ecac0 Mon Sep 17 00:00:00 2001 From: Birdmachine Date: Fri, 1 May 2026 10:59:41 -0400 Subject: [PATCH] Adds Illumina Spatial v0.0 page and row to Index --- docs/assays/metadata/Illumina-Spatial.md | 41 ++++++++++++++++++++++++ docs/assays/metadata/index.md | 1 + 2 files changed, 42 insertions(+) create mode 100644 docs/assays/metadata/Illumina-Spatial.md diff --git a/docs/assays/metadata/Illumina-Spatial.md b/docs/assays/metadata/Illumina-Spatial.md new file mode 100644 index 0000000..fd09fed --- /dev/null +++ b/docs/assays/metadata/Illumina-Spatial.md @@ -0,0 +1,41 @@ +--- +layout: page +--- +# Illumina Spatial + +
Version 0 (current) + +## Version 0 (current) + +| Attribute Name | Type | Description | Allowable Values | Required | +|---------------|------|-------------|------------------|----------| +| lab_id | Textfield | A locally assigned identifier provided by the data provider for the dataset. It is used to reference an external metadata record that may be maintained independently, enabling traceability and supporting provenance tracking. Example: Visium_9OLC_A4_S1 | | False | +| preparation_protocol_doi | Link | The DOI for the protocols.io page that details the assay or the procedures used for sample procurement and preparation. For example, in the case of an imaging assay, the protocol may start with tissue section staining and end with the generation of an OME-TIFF file. The documented protocol should also include any image processing steps involved in producing the final OME-TIFF. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 | | True | +| dataset_type | Assigned Value | The specific type of dataset being produced. Example: RNAseq | ```Visium HD```, ```4i```, ```Illumina Spatial v0```, ```LC-MS```, ```Thick section Multiphoton MxIF```, ```Light Sheet```, ```ATACseq```, ```Resolve```, ```HiFi-Slide```, ```COMET```, ```MPLEx```, ```10X Multiome```, ```MALDI```, ```MACSima```, ```Raman Imaging```, ```Histology```, ```Cell DIVE```, ```FACS```, ```MS Lipidomics```, ```Visium (no probes)```, ```MUSIC```, ```RNAseq```, ```GeoMx (NGS)```, ```GeoMx (nCounter)```, ```RNAseq (with probes)```, ```Singular Genomics G4X```, ```Molecular Cartography```, ```CosMx Transcriptomics```, ```MERFISH```, ```Pixel-seqV2```, ```2D Imaging Mass Cytometry```, ```Confocal```, ```seqFISH```, ```DART-FISH```, ```MIBI```, ```Olink```, ```Enhanced Stimulated Raman Spectroscopy (SRS)```, ```DESI```, ```Xenium```, ```iCLAP```, ```CyCIF```, ```SNARE-seq2```, ```nanoSPLITS```, ```STARmap```, ```Stereo-seq```, ```Visium (with probes)```, ```SIMS```, ```Auto-fluorescence```, ```CyTOF```, ```CosMx Proteomics``` | True | +| contributors_path | Textfield | The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv | | True | +| data_path | Textfield | The top-level directory containing the raw and/or processed data. For a single dataset upload, this might be represented as ".", whereas for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For example, if the data is within a directory named "TEST001-RK", use the syntax "./TEST001-RK" for this field. If there are multiple directory levels, use the format "./TEST001-RK/Run1/Pass2", where "Pass2" is the subdirectory where the single dataset's data is stored. This is an internal metadata field used solely for data ingestion. Example: ./TEST001-RK | | True | +| mapped_area_value | Numeric | The mapped area value, which refers to the specific area covered or captured in various assays. For Visium, it is the area of spots covered by tissue within the captured area, excluding the total possible captured area. For GeoMx, it refers to the area of the AOI being captured. In HiFi, it is the summed area of the ROIs in a single flowcell lane. For CosMx and Resolve, it indicates the area of the FOV (also known as ROI) region being captured. For Xenium, it is the total area of the FOV regions (also known as ROI) being captured. For Stereo-Seq, this value represents the number of beads. Example: 42.25 | | True | +| mapped_area_unit | Assigned Value | The unit of measurement for the mapped area value. If mapping area is not specified, this field may be left blank. Example: um^2 | ```um^2```, ```mm^2``` | True | +| capture_area_id | Radio | The capture area on the slide that was used during the process. For example, in the case for Visium, this would correspond to areas such as [A1, B1, C1, D1], while for HiFi, it would refer to the lane on the flowcell. Example: A1 | ```A1```, ```B1```, ```C1```, ```D1```, ```Lane 1```, ```Lane 2```, ```Lane 3```, ```Lane 4```, ```Lane 5```, ```Lane 6```, ```Lane 7```, ```Lane 8``` | False | +| permeabilization_time_value | Numeric | Permeabilization time used for this tissue section. | | False | +| permeabilization_time_unit | Assigned Value | The unit for the permeabilization time. | ```minute``` | False | +| metadata_schema_id | Textfield | The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 | | True | +| parent_sample_id | Textfield | The unique identifier from HuBMAP or SenNet for the sample (such as a block, section, or suspension) used to perform the assay. For instance, in an RNAseq assay, the parent sample would be the suspension, while in imaging assays, it would be the tissue section. If the assay is derived from multiple parent samples, this field should contain a comma-separated list of identifiers. Example: HBM386.ZGKG.235, HBM672.MKPK.442 | | True | +| preparation_instrument_vendor | Assigned Value | The company that manufactures the instrument used to prepare the sample (e.g., for staining or other processing steps) prior to the assay. If the instrument was custom-built or developed internally, enter "In-House". If no sample preparation occurred, enter "Not applicable". Example: 10X Genomics | ```Thermo Fisher Scientific```, ```SunChrom```, ```Akoya Biosciences```, ```Leica Biosystems```, ```Ionpath```, ```Roche Diagnostics```, ```In-House```, ```Not applicable```, ```Hamamatsu```, ```HTX Technologies```, ```10x Genomics``` | False | +| preparation_instrument_model | Assigned Value | The specific model of the instrument used for sample preparation, such as staining. Manufacturers may offer multiple models with varying features or sensitivities, which can influence how the sample is processed and how the resulting data is interpreted. If no sample preparation occurred, enter "Not applicable". Example: Chromium X | ```AutoStainer XL```, ```ST5020 Multistainer```, ```Visium CytAssist```, ```SunCollect Sprayer```, ```Chromium X```, ```Chromium iX```, ```EVOS M7000```, ```NanoZoomer S210```, ```NanoZoomer S60```, ```NanoZoomer S360```, ```Discovery Ultra```, ```Sublimator```, ```Not applicable```, ```TM-Sprayer```, ```M5 Sprayer```, ```M3+ Sprayer```, ```Chromium Controller```, ```Chromium Connect```, ```Custom``` | False | +| capture_area_width_value | Numeric | The width of RNA capture area. Example: 10 | | True | +| capture_area_width_unit | Assigned Value | The unit of measurement for the capture area width value. If the width value is not specified, this field may be left blank. Example: mm | ```mm``` | True | +| capture_area_height_value | Numeric | The height of RNA capture area. Example: 10 | | True | +| capture_area_height_unit | Assigned Value | The unit of measurement for the capture area height value. If the height value is not specified, this field may be left blank. Example: mm | ```mm``` | True | +| spatial_discreatization_method | Assigned Value | The segmentation method used to divide the capture are into smaller, defined regions for analysis. Example: Cell segmentation | ```Square binning```, ```Cell segmentation```, ```Hexagonal binning``` | True | +| bin_size | Textfield | The size (in µm) of each discrete spatial unit ("bin") used to partition the capture area in bin-based spatial discretization. Example: 100 | | False | +| analyte_class | Assigned Value | The analyte class which is the target molecule that the assay is measuring. Example: DNA | ```Nucleic acid + protein```, ```Lipid + metabolite```, ```Collagen```, ```RNA```, ```Fluorochrome```, ```DNA```, ```Metabolite```, ```DNA + RNA```, ```Saturated lipid```, ```Lipid```, ```Lipid + metabolite + protein```, ```RNA + protein```, ```Peptide```, ```Protein```, ```Unsaturated lipid```, ```Endogenous fluorophore```, ```Chromatin```, ```Polysaccharide``` | True | +| is_targeted | Radio | Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes | ```Yes```, ```No``` | True | +| acquisition_instrument_vendor | Assigned Value | The company that manufactures or supplies the acquisition instrument. An acquisition instrument is a device equipped with signal detection hardware and signal processing software. It captures signals produced by assays, such as variations in light intensity or color, or signals corresponding to molecular mass. If the instrument was custom-built or developed internally, enter "In-House". Example: Illumina | ```Complete Genomics```, ```Cytek Biosciences```, ```Thermo Fisher Scientific```, ```Sciex```, ```Vizgen```, ```Leica Microsystems```, ```Akoya Biosciences```, ```Keyence```, ```Andor```, ```Standard BioTools (Fluidigm)```, ```Leica Biosystems```, ```Zeiss Microscopy```, ```Ionpath```, ```Motic```, ```In-House```, ```Miltenyi Biotec```, ```Revvity```, ```Evident Scientific (Olympus)```, ```GE Healthcare```, ```Element Biosciences```, ```Hamamatsu```, ```Waters```, ```Bruker```, ```Illumina```, ```3DHISTECH```, ```Singular Genomics```, ```Huron Digital Pathology```, ```Resolve Biosciences```, ```NanoString```, ```Cytiva```, ```10x Genomics```, ```Microscopes International```, ```BGI Genomics``` | True | +| acquisition_instrument_model | Assigned Value | The specific model of the acquisition instrument, as manufacturers often offer various versions with differing features or sensitivities. These differences may be relevant to the processing or interpretation of the data. If the instrument was custom-built or developed internally, enter "In-House". If the model is unknown, enter "Unknown". Example: HiSeq 4000 | ```NovaSeq X```, ```NovaSeq X Plus```, ```Cytek Northern Lights```, ```Lightsheet 7```, ```Resolve Biosciences Molecular Cartography```, ```timsTOF HT```, ```timsTOF Pro 2```, ```timsTOF Pro```, ```timsTOF Ultra```, ```timsTOF Ultra 2```, ```timsTOF SCP```, ```Axio Scan.Z1```, ```MALDI timsTOF Flex Prototype```, ```LSM 710 Confocal Microscope```, ```CosMx Spatial Molecular Imager```, ```Unknown```, ```MERSCOPE Ultra```, ```Juno System```, ```timsTOF FleX```, ```Custom: Multiphoton```, ```CyTOF XT```, ```Helios```, ```EVOS M7000```, ```Aperio AT2```, ```Phenocycler-Fusion 2.0```, ```Axio Observer 5```, ```Axio Observer 7```, ```Axio Observer 3```, ```NanoZoomer-SQ```, ```NanoZoomer S210```, ```NanoZoomer S60```, ```NanoZoomer S360```, ```DM6 B```, ```MoticEasyScan One```, ```In-House```, ```NextSeq 500```, ```BZ-X710```, ```MACSima System```, ```QTRAP 5500```, ```DMi8```, ```NextSeq 550```, ```HiSeq 2500```, ```HiSeq 4000```, ```NovaSeq 6000```, ```Opera Phenix Plus HCS```, ```SYNAPT G2-Si```, ```Q Exactive HF```, ```Orbitrap Fusion Tribrid```, ```Orbitrap Fusion Lumos Tribrid```, ```Q Exactive HF-X``` | True | +| source_storage_duration_value | Numeric | The length of time the sample was stored prior to processing it. For assays performed on tissue sections, this refers to how long the tissue section (e.g., slide) was stored before the assay began (e.g., imaging). For assays performed on suspensions, such as sequencing, it refers to how long the suspension was stored before library construction started. Example: 12 | | True | +| source_storage_duration_unit | Assigned Value | The unit of measurement used to specify the source storage duration value. Example: hour | ```hour```, ```month```, ```day```, ```minute```, ```year``` | True | +| time_since_acquisition_instrument_calibration_value | Numeric | The length of time since the acquisition instrument was last serviced or calibrated. This provides a metric for assessing drift in data capture. Example: 10 | | False | +| time_since_acquisition_instrument_calibration_unit | Assigned Value | The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month | ```month```, ```day```, ```year``` | False | + +
\ No newline at end of file diff --git a/docs/assays/metadata/index.md b/docs/assays/metadata/index.md index db8c27f..ba28b26 100644 --- a/docs/assays/metadata/index.md +++ b/docs/assays/metadata/index.md @@ -20,6 +20,7 @@ A list of available dataset types (data types from multiple supported assays), w | [HiFi](https://www.researchgate.net/publication/370676672_HiFi-Slide_spatial_RNA-Sequencing_v2) [](HiFi "Attribute description")| High-Fidelity Spatial Transcriptomic Slide (HiFi-Slide) sequencing, a super-resolution spatial transcriptomics sequencing technology, captures and spatially resolves genome-wide RNA expression in a submicron resolution for fresh-frozen tissue. Link to [HiFi directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/hifi-slide/current/). | | [Histology](https://en.wikipedia.org/wiki/Histology) [](Histology "Attribute description")| The microscopic study of tissue composition and structure, often referred to as microscopic anatomy. It involves examining tissue samples, typically after they've been sectioned, stained, and placed under a microscope. Link to [Histology directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/histology/current/). | | iCLAP [](iCLAP "Attribute description") | iCLAP (individual-nucleotide resolution UV-crosslinking and affinity purification) is a specialized, high-stringency technique designed to map the specific RNA binding sites of RNA-binding proteins (RBPs) at the single-nucleotide level. | +| Illumina Spatial [](Illumina-Spatial "Attribute description") | Illumina Spatial v0 is a high-resolution, sequencing-based spatial transcriptomics solution that maps gene expression within intact tissue samples, preserving spatial context. It combines broad, unbiased whole-transcriptome profiling with cellular-level resolution (1-µm features) over large areas () using standard Illumina NextSeq and NovaSeq. | | [IMC](https://docs.hubmapconsortium.org/assays/imc) [](IMC "Attribute description")| Combines standard immunohistochemistry with CyTOF mass cytometry to resolve the cellular localization of up to 40 proteins in a tissue sample. Link to [IMC directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/imc-2d/current/). | | [LC-MS](https://docs.hubmapconsortium.org/assays/lcms) [](LC-MS "Attribute description")| Coupling of liquid chromatography (LC) to mass spectrometry (MS). Link to [LC-MS directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/lcms/current/). | | [Light Sheet](https://en.wikipedia.org/wiki/Light_sheet_fluorescence_microscopy) [](LightSheet "Attribute description")| A fluorescence imaging technique that uses a thin sheet of laser light to illuminate a sample, allowing for high-resolution, 3D imaging with reduced photobleaching and phototoxicity; particularly useful for imaging large, thick, or delicate biological samples, like developing embryos or organoids. Link to [Light Sheet directory schema](https://hubmapconsortium.github.io/ingest-validation-tools/lightsheet/current/). |