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import SpatialDE
import numpy as np
import anndata
import scanpy as sc
import cv2
from sklearn.metrics import silhouette_score
from sklearn import metrics
import scanpy as sc
import pandas as pd
from decimal import Decimal
from decimal import Decimal,ROUND_HALF_UP
mousebrain_after_normalization_path='/home/user/imputation_test_data/MouseBrain_D1_normalization.h5ad'
adata_before = anndata.read_h5ad(mousebrain_after_normalization_path)
counts_before = pd.DataFrame(adata_before.X, columns=adata_before.var_names, index=adata_before.obs_names)
coord_before = pd.DataFrame(adata_before.obsm['spatial'], columns=['x', 'y'], index=adata_before.obs_names)
result_before = SpatialDE.run(coord_before, counts_before)
adata_before.obsm['spatialDE_result'] = result_before
I tried to use SpatialDE to evaluate my anndata on the computer server, I have transferred anndata.X to counts_before(which is a dataframe) and adata.obsm['spatial'] to be coord_before. and using SpatialDE.run to finish them. But no result.