How to concatenate spatial AnnData objects

Help squidpy
1

What’s the recommended way of merging multiple visium samples into a single AnnData object?

Let’s assume I have a dict with the individual samples:

adatas_vis = {
  "sample1": sq.read.visium(path, library_id="sample1",
  "sample2": sq.read.visium(path, library_id="sample2",
}

When using

adata_vis_all = anndata.concat(adatas_vis, index_unique="_", merge="same", uns_merge="same")

uns doesn’t get merged and the images are lost.

I am now using

def concat_spatial(adatas):
    spatial_dict = {}
    for ad in adatas:
        spatial_dict.update(ad.uns["spatial"])
    return spatial_dict

adata_vis_all.uns["spatial"] = concat_spatial(adatas_vis.values())

to re-add them, but I feel there must be a better way?

1 Like
2

Have you considered integration after merging? I know that this is an important step to reduce batch effects. scvi does this and might have included methods on merging too

3

super late on this but if you just set uns_merge='unique' should do the job to handle the concatenation of unique library ids, rest is standard anndata. HTH

4

Awesome @giovp, this works. The different merge strategies are still getting me confused :see_no_evil:

5

Hi,

I am trying to merge multiple CosMX nanostring samples in a single AnnData object using this approach with uns_merge = “unique”.
adata_cosmx_all = anndata.concat(adata_cosmx, index_unique = "_", merge="same", uns_merge = "unique")

However, I get an error message ‘ValueError: Must pass 2-d input. shape=(4480, 4480, 3)’. Eliminating the uns_merge parameter results in the concatenated cell x gene matrix.

I am trying to use the z-stacked image containers, which is also failing.
Each nanostring sample has different number of FOVs, how should consider setting the ‘library_id’ parameter in this case. Ref - [Use z-stacks with ImageContainer — squidpy documentation]

I would highly appreciate any guidance on ways to merge multiple nanostring cosmx objects.
Thanks!