# Imaging data from seurat to scanpy

**URL:** <https://discourse.scverse.org/t/imaging-data-from-seurat-to-scanpy/1428>\
**Category:** Visium\
**Created:** [May 15, 2023, 12:29pm UTC](https://discourse.scverse.org/t/imaging-data-from-seurat-to-scanpy/1428 "2023-05-15T12:29:45Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![archanabhardwaj](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/archanabhardwaj/32/658_2.png) [@archanabhardwaj](https://discourse.scverse.org/u/archanabhardwaj)\
**Post date:** [May 15, 2023, 12:29pm UTC](https://discourse.scverse.org/t/imaging-data-from-seurat-to-scanpy/1428/1 "2023-05-15T12:29:45Z")

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I am working on spatial transcriptome data. I performed all standard analyses in R, including QC filtration, normalization and data clustering. I want to use the normalized data from given Seurat object and read in python for further analysis. I used the following steps for the conversion :

SaveH5Seurat(test\_object, overwrite = TRUE, filename = “A1”)

Convert(“A1.h5seurat”, dest = “h5ad”, overwrite = TRUE)

#Next, imported h5ad format file into scanpy :

adata1 = sc.read\_h5ad(“A1.h5ad”)

**But it does not contain any spatial and image information.**

obs: ‘orig.ident’, ‘nCount\_Spatial’, ‘nFeature\_Spatial’, ‘cell.ids’, ‘nCount\_SCT’, ‘nFeature\_SCT’, ‘seurat\_clusters’, var: ‘features’, ‘SCT\_features’, ‘genename’ obsm: ‘X\_pca’, ‘X\_umap’ varm: ‘PCs’ layers: ‘SCT’

**raise KeyError( KeyError: “Could not find entry in `obsm` for ‘spatial’.\nAvailable keys are: [‘X\_pca’, ‘X\_umap’].”**

How can I add image and coordinate information in ‘obsm’ for spatial information ?

I would appreciate all the suggestion .

Thanks in advance

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<div class="post-metadata">

**Author:** ![howtofindme](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/howtofindme/32/819_2.png) [@howtofindme](https://discourse.scverse.org/u/howtofindme)\
**Post date:** [October 4, 2023, 7:49am UTC](https://discourse.scverse.org/t/imaging-data-from-seurat-to-scanpy/1428/2 "2023-10-04T07:49:23Z")

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have you solved it ? i meet the same problem