Spatial Imaging File Annotation Template

A data contributor template outlining metadata to be collected as file annotations for imaging-based data files.

Attribute	Description	Required	Valid Values
Component	A high-level attribute for grouping attributes into templates.	True
resourceType	High-level classification of the file content	TRUE	experimental data, metadata
fileFormat	Standard file format name or file extension	True	bai, bam, bed, bim, csv, czi, docx, dose, erate, fam, fastq, fcs, geojson, h5, h5ad, info, mcd, mtx, parquet, pdf, rds, rec, svs, tbi, tgz, tsv, txt, vcf, xls, xlsx, zip
assay	The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'.		Xenium, CosMX, GenePS SeqFISH, imaging mass cytometry, Visium, H&E, serial IHC
specimenModality	Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens	True	multispecimen, single specimen
processedDataType	A label used for file annotations to provide a brief description of the processed data file.	False	barcode counts, differential expression results, epigenomic peaks, gene counts
metadataType	A label further classifying the content of metadata resource.	TRUE	single-cell metadata, cell coordinates, target panel, tissue multiarray map, other
RObjectClass	Rds files store R objects, one per file. This label details the class of the R object saved to the Rds file or other similar file types.	False	ROCR prediction.object, Seurat object, SummarizedExperiment, Symphony reference, data.frame, list, matrix, sparse matrix, vector
slideID	A library label or name, unique within an experiment, used to distinguish imaging slides.	True
individualID	Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list.	True
biospecimenID	A unique identifier assigned to specimens collected from study participants. For multi-specimen data files provide all IDs in a comma-separated list.	True