Spatial studies
Published spatial omics studies show where molecular programmes and cell states sit within a tumour and how they relate to its morphology. They usually come from patients other than those in TCGA, so they add tissue context to the reference but no measurements for TCGA patients.
At a glance
By cancer type
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Image levels
A resource with matched spatial data is shown at one of two image levels. Both have measured expression whose barcodes or cell labels were matched to their tissue coordinates; they differ in the H&E image that was found.
| Level | Image located | Supports | Does not support |
|---|---|---|---|
Original H&E located | The original H&E scan of the assayed tissue, with measured expression and coordinates | Molecular spatial maps; whole-slide and tile models, morphology and distance measurements once registration and scanner calibration are checked | Any use that assumes registration, calibration or tissue QC are complete |
Matched data with preview image | A reduced preview released with the data (for example a Space Ranger image); the original scan was not located | Molecular spatial visualisation and analyses of expression in tissue coordinates | Whole-slide or tile modelling, cell morphology, physical-distance comparisons or registration sign-off |
A resource counts once, at its best level; when only some of its sections have an original scan, that subset is stated and the other sections are shown at the preview level. Section counts are records of each study, one per tissue section or capture area. They are not globally unique physical sections: several specimens can share one array area, and reused or mirrored data are linked to their original study rather than counted again. Patients are counted only where the source gives a study-local patient ID, and no eligible-patient total is established.
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Verification and access
- Original H&E located
- The original H&E image, measured expression and spatial coordinates were found for individual tissue sections, which are listed one by one in the data explorer. Image registration, scanner calibration and tissue QC are still to be completed.
- Matched data with preview image
- Measured expression and spatial coordinates were found and match each other, with a preview image released alongside them; the original H&E scan was not located. The sections are listed one by one in the data explorer.
- Verification pending
- A catalogued study that may provide matched data but has an open check, such as original scans not located, an unconfirmed section relationship, an unresolved donor count or a pending histology review. Its eligible patients are not established.
- Access-dependent
- Data that are controlled, available on request, not yet released or without an established release route. Listing them does not mean that access has been requested or granted.
Each resource's details record how H&E and measurements are linked (same section, released together, serial section or unverified), the assay type, the tissue it comes from (primary, metastatic, adjacent-normal, normal or precursor) and treatment before sampling. Linkage levels · How resources are reviewed.
Package review
Candidates that had not yet been checked file by file were reviewed against their public records and packages. Each result states how far the check went, what was found for the images and for the expression and coordinates, and the next step. Sections were listed only where the source supports them, and unsupported resources stay candidates with their dependencies. No author was contacted and no access was requested.
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Follow-up review
A follow-up pass checked the reviewed resources again from public sources: original scans for the preview-level resources, image headers and coordinate frames for the original-level ones, patient and clinical details for listed sections, and the remaining public packages and releases. It found original scans for one resource, qualified two more at the preview level and listed the sections that had been counted only for their study. Pixel sizes read from image headers and frame checks are recorded on the sections; they do not sign off registration or calibration accuracy.
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Open dependencies
The public routes of the reviewed resources were followed to a retrieved result, a registration or controlled-access boundary, a missing release or a reproducible download failure. Each resource's open dependencies are kept apart below: a failed download is a technical gap, not a permission requirement.
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Related leads, not counted
These releases add no resources or patients to the figures on this page: their patients cannot yet be assigned to a cancer type, they concern precursor lesions, or they reuse data catalogued elsewhere.
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Browse and export
The resource list in the data explorer shows every spatial study, with filters for assay type, H&E linkage, tissue, treatment and access. The spatial transcriptomics view lists every tissue section record with located data, with its image level, histology, tissue site, treatment before sampling, donor mapping and access, including a filter for untreated primary tumours. Both export the current selection as CSV or JSON.