KeyError:"Spatial key 'spatial' not found in `adata.uns`." about tangram HOT 1 CLOSED

Hi,

Yes, this is a function from the squidpy library which requires the spatial data ('adata_st') to be arranged in some required structure. There are two keys needed in this function: adata_st.obsm['spatial'] and adata_st.uns['spatial']. The adata_st.obsm['spatial'] defines the location of measured spots, which is always required in order to have the features calculated at the right locations of the image.

In the error popped up in your code, it is due to the lacking keys adata_st.uns['spatial']. The function is trying to extract the diameter of the measured spots from this key. Such information is stored at:
adata_st.uns['spatial']['V1_Adult_Mouse_Brain_Coronal_Section_2']['scalefactors']['spot_diameter_fullres']

If you know the diameter of your measured spot, you can either store this information in your spatial data (make the data structure the same as the one used in tutorial, it should be easier to do compare to changing the source code), or you can also hack into the squidpy package you installed and change the source code to directly input the spot diameter. The code requires this key is at .../squidpy/im/_container.py, 'generate_spot_crops' function at line 713~826, replace those lines with 'Key.uns.library_id' or 'Key.uns.spot_diameter' and you should be able to run the image segmentation code.

Best,
Hejin

from tangram.