Hi spatialdata team,
It seems that the parser function for cosmx data appends path to the file name two times: first, when checking whether the file exists, and second, when reading the file:
counts_file = path / f"{dataset_id}_{CosmxKeys.COUNTS_SUFFIX}"
...
counts = pd.read_csv(path / counts_file, header=0, index_col=CosmxKeys.INSTANCE_KEY)
This leads to the error when reading:
FileNotFoundError: [Errno 2] No such file or directory: '../cosmx_data/12345/../cosmx_data/12345/12345_exprMat_file.csv'
Best regards,
Vasily