Spatial_Transcriptomics_Metadata

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1	Field Name	Data type	Definition	options: required, optional, n/a											Notes	CATEGORY FIELD VALUES
2	Field Name	Data type	Definition	Visium (no probes)	Visium (with probes)	GeoMx (NGS)	GeoMx (nCounter)	HiFi	hrsTP-seq (DBiTSeq)	Xenium	Resolve	CosMx	MERFISH	Stereo-Seq	Notes	mapping area unit	spot size unit	spot spacing unit	capture area id	permeabilization time unit	preparation instrument vendor	preparation instrument model	preparation instrument kit (manufacturer; model/name; product code)	probe hybridization time unit	oligo probe panel (manufacturer; model/name; product code)	target retrieval incubation time unit	proteinaseK incubation time unit	probe hybridization time unit	segmentation strategy

3	COMMON ASSAY FIELDS	varied	Either the single-assay or multi-assay fields from the "common assay fields" metadata schema should be included here.	required (multi- assay)	required (multi- assay)	required (single- assay)	required (single- assay)	required (single- assay)	required (single- assay)	required (single- assay)	required (single- assay)	required (single- assay)	required (single- assay)	required (multi- assay)		mm^2	um^2	um	A1	minute	10X Genomics	Visium CytAssist			GeoMx Immune Cell Profiling (Human Protein Core for nCounter)	minute	minute	minute	automated segmentation
4	mapped area value	float	For Visium, this is the area of spots that was covered by tissue within the captured area, not the total possible captured area which is fixed. For GeoMx this would be the area of the AOI being captured. For HiFi this is the summed area of the ROIs in a single flowcell lane. For CosMx, Xenium and Resolve, this is the area of the FOV (aka ROI) region being captured. For Stereo-Seq this is the number of beads.	required	required	required	required	required	required	required	optional	optional	optional	required	specific to a single AOI (GeoMx), FOV (CosMx), capture area (Visium), flowcell lane surface(HiFi)	um^2	mm^2		B1		Not applicable	Not applicable			GeoMx Neural Cell Profiling (Human Protein Core for nCounter)				manual segmentation
5	mapped area unit	category	The unit of measurement for the mapping area. For Visium and GeoMx this is typically um^2.	required	required	required	required	required	required	required	optional	optional	optional	required					C1						Custom
6	spot size value	float	For assays where spots are used to define discrete capture areas, this is the area of a spot.	required	required	n/a	n/a	required	required	n/a	n/a	n/a	n/a	required	Is this relevant to DBiTSeq?				D1						Not applicable
7	spot size unit	category	The unit for spot size value.	required	required	n/a	n/a	required	required	n/a	n/a	n/a	n/a	required	If this is required for Xenium, Resolve, CosMx, then spot_size_value should also be required. Is this supposed to be "n/a"?				Lane 1
8	number of spots	integer	Number of capture spots within the mapped area. For Visium this would be the number of spots covered by tissue, while it's the number of spots within ROIs for HiFi.	required	required	n/a	n/a	required	required	n/a	n/a	n/a	n/a	required					Lane 2
9	spot spacing value	float	Approximate center-to-center distance between capture spots. Synonyms: Inter-Spot distance, Spot resolution, Pit size	required	required	n/a	n/a	required	required	n/a	n/a	n/a	n/a	required					Lane 3
10	spot spacing unit	category	Units corresponding to inter-spot distance	required	required	n/a	n/a	required	required	n/a	n/a	n/a	n/a	required					Lane 4
11	capture area id	category	Which capture area on the slide was used. For Visium this would be [A1, B1, C1, D1]. For HiFi this would be the lane on the flowcell.	required	required	n/a	n/a	optional	optional	n/a	n/a	n/a	n/a	n/a					Lane 5
12	permeabilization time value	integer	Permeabilization time used for this tissue section.	optional	optional	n/a	n/a	required	required	n/a	n/a	n/a	optional	optional					Lane 6
13	permeabilization time unit	category	The unit for the permeabilization time.	optional	optional	n/a	n/a	required	required	n/a	n/a	n/a	optional	optional					Lane 7
14	slide ID	text	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. For GeoMx this is found in the "Initial Dataset" spreadsheet (download from within Data Analysis Suite); can also use "scan name". For HiFi-Slide, this is the ID of used illumina flow cell. HiFi-Slide lay a piece of tissue on a used illumina flow cell and then RNA released from the tissue could be captured by spots on that flow cell.	n/a	n/a	required	required	required	optional	required	required	required	required	n/a	For Visium this is captured in the histology assay.				Lane 8
15	preparation instrument vendor	categorical	The manufacturer of the instrument used to prepare the sample for the assay.	optional	required	n/a	n/a	n/a		n/a	n/a	n/a	n/a	optional
16	preparation instrument model	categorical	The model number/name of the instrument used to prepare the sample for the assay.	optional	required	n/a	n/a	n/a		n/a	n/a	n/a	n/a	optional
17	preparation instrument kit	categorical	The reagent kit used with the preparation instrument.	n/a	n/a	n/a	n/a	n/a		n/a	n/a	n/a	n/a	n/a
18	Histology Assay	varied	The histology assay metadata should be additional completed, per dataset, if required by the assay. This histology metadata should be uploaded in a separate TSV or Excel file. For example, Visium would include three TSV/Excel metadata files (Visium, RNAseq, and histology).	required	required	n/a	n/a	required		n/a	n/a	n/a	n/a	required
19	Sequencing Assay	varied	The appropriate sequencing assay metadata should be additional completed, per dataset, as required by the assay. This sequencing metadata should be uploaded in a separate TSV or Excel file. For example, Visium would include three TSV/Excel metadata files (Visium, RNAseq, and histology).	required RNAseq	required RNAseq (with probes)	required RNAseq (with probes)	n/a	required RNAseq	required DBiT (RNA)	n/a	n/a	n/a	n/a	required RNAseq	This would potentially be "RNAseq with probes" for GeoMx assays that use ngs as the readout method.
20	number of channels	integer	The number of distinct color channels in the image.	n/a	n/a	required	required	n/a	required	n/a	n/a	n/a	n/a	n/a
21	target retrieval incubation temperature	integer	The temperature in Celsius. This will normally be 100 degrees Celsius for RNA assays, and 80 degrees Celsius for protein assays.	n/a	n/a	required	required	required		optional	optional	optional	optional	n/a
22	target retrieval incubation time value	float	The duration for which a sample is exposed to a target retrieval solution.	n/a	n/a	required	required	required		optional	optional	optional	optional	n/a
23	target retrieval incubation time unit	category	The units for target retrieval incubation time value.	n/a	n/a	required	required	required		optional	optional	optional	optional	n/a
24	proteinaseK concentration	float	The amount or concentration of the enzyme Proteinase K within a sample (in ug/ml).	n/a	n/a	optional	optional	required		optional	optional	optional	optional	n/a
25	proteinaseK incubation time value	float	The duration for which a sample is exposed to Proteinase K.	n/a	n/a	optional	optional	required		optional	optional	optional	optional	n/a
26	proteinaseK incubation time unit	category	The units for proteinaseK incubation time value.	n/a	n/a	optional	optional	required		optional	optional	optional	optional	n/a
27	probe hybridization time value	float	How many hours were the oligo-conjugated RNA or oligo-conjugated antibody probes hybridized with the sample?	n/a	n/a	captured in the RNAseq metadata	required	n/a		optional	optional	optional	optional	n/a
28	probe hybridization time unit	category	The units for probe hybridization time value.	n/a	n/a		required	n/a		optional	optional	optional	optional	n/a
31	oligo probe panel	category	This is the probe panel used to target genes and/or proteins. In cases where there is a core panel and add-on modules, the core panel should be selected here. If additional panels are used, then they must be included in the "additional_panels_used.csv" file that's uploaded with the dataset.	n/a	n/a		required	n/a	optional	required	required	required	required	n/a
32	is custom probes used	boolean	State ("Yes" or "No") whether custom RNA or antibody probes were used. If custom probes were used, they must be listed in the "custom_probe_set.csv" file.	n/a	n/a		required	n/a		required	required	required	required	n/a	Any spike ins used should be included in the probe panel file. We need to define the file structure.
33	number of panel targets	integer	How many genes, RNA isoforms or RNA regions are targeted by probes.	n/a	n/a	n/a	n/a	n/a		required	required	required	required	n/a
34	roi_label	text	A label for the region of interest. For Resolve and CosMx, this is the field of view (FOV) label. For GeoMx this can be found in the "Initial Dataset" spreadsheet (download from within Data Analysis Suite).	n/a	n/a	required	required	optional		required	optional	optional	optional	n/a
35	is overlay used	boolean	State ("Yes" or "No") whether an ROI overlay was used to guide ROI selection. If an overlay is used, then the overlay details will be provided in the preparation protocols.io protocol.	n/a	n/a	n/a	n/a	n/a	optional	n/a	n/a	n/a	n/a	n/a	If used, this needs to be uploaded. It is not included in the OME TIFF.
36	is roi segmentation performed	boolean	Was the image segmented. For GeoMx this refers to whether segmentation was used to split ROIs (regions of interest) into AOIs (areas of interest).	n/a	n/a	required	required	n/a		n/a	n/a	n/a	n/a	n/a
37	roi segmentation strategy	category	The method of segmentation that was applied in a GeoMx assay. If an overlay was used the overlay image needs to be included in the dataset upload.	n/a	n/a	optional	optional	n/a	n/a	n/a	n/a	n/a	n/a	n/a	is required if "segmentation performed" is true. If value = "overlay" then an overlay file needs to be uploaded.
38	anatomical structure label	text	The overarching anatomical structure.	n/a	n/a	optional	optional	optional	n/a	optional	optional	optional	optional	n/a
39	anatomical structure ID	ontology ID	The ontology ID for the parent structure. Typically this would be an UBERON ID.	n/a	n/a	optional	optional	optional	n/a	optional	optional	optional	optional	n/a
40	targeted entity label	text	State what cell type(s) or functional tissue unit was targeted in this ROI/AOI.	n/a	n/a	required	required	n/a	n/a	n/a	n/a	n/a	n/a	n/a
41	targeted entity ID	ontology ID	The ontology ID for the targeted entity.	n/a	n/a	optional	optional	n/a	n/a	n/a	n/a	n/a	n/a	n/a	is required if "segmentation performed" is true.
42	segment ID	text	This is the ID for the area of interest (AOI) in a GeoMx dataset. From "Initial Dataset" spreadsheet (download from within Data Analysis Suite), e.g. 9a828e39-43d8-4051-9bcc-581a520a85d4.	n/a	n/a	required	required	n/a		n/a	n/a	n/a	n/a	n/a
43	is technical replicate	boolean	Is the sequencing reaction run in replicate, "Yes" or "No". If "Yes", FASTQ files in dataset need to be merged.	n/a	n/a	required	required	n/a	n/a	n/a	n/a	n/a	n/a	n/a
44	HybCode pack lot number	text	Enter the lot number noted within the LabWorksheet.txt file (and used in downstream nCounter processing).	n/a	n/a	n/a	required	n/a	n/a	n/a	n/a	n/a	n/a	n/a
45	non global files	text	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 HuBMAP processing. Examples for GeoMx and PhenoCycler are provided in the File Locations documentation: https://docs.google.com/document/d/1n2McSs9geA9Eli4QWQaB3c9R3wo5d5U1Xd57DWQfN5Q/edit#heading=h.1u82i4axggee	n/a	n/a	required	required	n/a	n/a	optional	optional	optional	optional	optional
46	number of additional stains	integer	this would be minimally 2 (always include DAPI and polyT) and can include 6 more.	n/a	n/a	n/a	n/a	n/a		n/a	n/a	n/a	required	n/a
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