Roman Perik-Zavodskii
Roman Perik-Zavodskii
I fixed the cell, it now works: ``` #Read original 10x_h5 data and save it to h5ad from scanpy import read_10x_h5 adata = read_10x_h5("path/filtered_feature_bc_matrix.h5") spatial=pd.read_csv("path/spatial/tissue_positions_list.csv", sep=",",header=None,na_filter=False,index_col=0) adata.obs["Sample"]=spatial[1] adata.obs["array_x"]=spatial[2] adata.obs["array_y"]=spatial[3] adata.obs["pixel_x"]=spatial[4]...
Also if using cv2 (method 1), this line of code: `spots=counts.obs.loc[:, ['pixel_x', 'pixel_y', "array_x", "array_y"]]` must also be executed