API

API functions

load_bin(gem_file, bin_size, library_id, image_file=None)

Read BGI data and image file, and return an AnnData object.

Parameters:

• gem_file – The path of the BGI data file

• bin_size – The size of the bin

• library_id – The library id

• image_file – The path of the image file (optional)

Returns:

AnnData object with the following keys:

• anndata.AnnData.obsm ['spatial'] - spatial spot coordinates

• anndata.AnnData.uns ['spatial']['{library_id}']['images'] - hires images

• anndata.AnnData.uns ['spatial']['{library_id}']['scalefactors'] - scale factors for the spots