# Deconvolute spatial transcriptomics (visium) with unannotated single-cell (10x)

**URL:** <https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694>\
**Category:** Visium\
**Tags:** scvi\
**Created:** [June 24, 2025, 6:56am UTC](https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694 "2025-06-24T06:56:22Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![cell\_kc](https://avatars.discourse-cdn.com/v4/letter/c/46a35a/32.png) [@cell\_kc](https://discourse.scverse.org/u/cell_kc)\
**Post date:** [June 24, 2025, 6:56am UTC](https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694/1 "2025-06-24T06:56:22Z")

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I have a spatial transcriptomics dataset (10x visium) of a tumour microarray and some of the samples have matched single-cell RNA-seq data (10x). I would like to annotate my spatial data with the single-cell data. However the single-cell data is not annotated. Can this be done with any scverse tool?

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**Author:** ![ori-kron-wis](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/ori-kron-wis/32/1099_2.png) [@ori-kron-wis](https://discourse.scverse.org/u/ori-kron-wis)\
**Post date:** [July 9, 2025, 12:57pm UTC](https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694/2 "2025-07-09T12:57:24Z")

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Not sure I followed.  
Do you have **any** annotations at all? whether on the spatial data or the single cell data?

Basically you can use scvi-tools for annotate your data as a query data but only given you have some suitable reference data which is annotated (scvi/scanvi).  
Following that you can use other tools to also try to annotate that overlapping part of your spatial data.  
But you can perhaps auto-annotate your spatial data using tools like cell2location.

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**Author:** ![cell\_kc](https://avatars.discourse-cdn.com/v4/letter/c/46a35a/32.png) [@cell\_kc](https://discourse.scverse.org/u/cell_kc)\
**Post date:** [July 10, 2025, 1:45am UTC](https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694/3 "2025-07-10T01:45:01Z")

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Hi @ori-kron-wis  
The matched single-cell data does not have any annotations and is just processed to GEX count matrices. I understand that this needs to be annotated first in order to transfer labels?

Does cell2location annotate spatial data based on a single-cell reference?

Thanks

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<div class="post-metadata">

**Author:** ![ori-kron-wis](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/ori-kron-wis/32/1099_2.png) [@ori-kron-wis](https://discourse.scverse.org/u/ori-kron-wis)\
**Post date:** [July 10, 2025, 8:10am UTC](https://discourse.scverse.org/t/deconvolute-spatial-transcriptomics-visium-with-unannotated-single-cell-10x/3694/4 "2025-07-10T08:10:36Z")

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> [@cell\_kc](#):
>
> The matched single-cell data does not have any annotations and is just processed to GEX count matrices. I understand that this needs to be annotated first in order to transfer labels?

Yes. I suggested that it will be annotated using a model like scanvi (if you have similar annotated data as references) or cellassign (if you know whether or not each given gene is a marker of different cell types you think you have).

> [@cell\_kc](#):
>
> Does cell2location annotate spatial data based on a single-cell reference?

Yes. that will be the 2nd part , if your RNA-seq data will be annotated you will be able to use it and estimate the annotation of the spatial part with cell2location based on location of cells.  
I guess there are other tools for that.