I get the following error when I want to implement this :
(older_path = '/Users/Desktop/MonkeyBread
adata = mb.util.load_merscope(folder_path)
... reading from cache file cache/Users-pedram-Desktop-MonkeyBread-cell_by_gene.h5ad)
KeyError Traceback (most recent call last) Input In [16], in <cell line: 2>() 1 folder_path = '/Users/pedram/Desktop/MonkeyBread' ----> 2 adata = mb.util.load_merscope(folder_path)
File ~/opt/anaconda3/lib/python3.9/site-packages/monkeybread/util/_load_merscope.py:74, in load_merscope(folder, use_cache, cell_bounds, transcript_locations, paths) 72 coordinates = pd.read_csv(f"{folder}/{paths['coordinates']}") 73 coordinates = coordinates.rename({"Unnamed: 0": "cell_id"}, axis=1) ---> 74 data = counts[coordinates.cell_id] # Slice data by coordinate index 75 data.obsm["X_spatial"] = coordinates[["center_x", "center_y"]].to_numpy() 76 data.obs["width"] = coordinates["max_x"].to_numpy() - coordinates["min_x"].to_numpy()
File ~/opt/anaconda3/lib/python3.9/site-packages/anndata/_core/anndata.py:1113, in AnnData.__getitem__(self, index) 1111 def __getitem__(self, index: Index) -> "AnnData": 1112 """Returns a sliced view of the object.""" -> 1113 oidx, vidx = self._normalize_indices(index) 1114 return AnnData(self, oidx=oidx, vidx=vidx, asview=True)
File ~/opt/anaconda3/lib/python3.9/site-packages/anndata/_core/anndata.py:1094, in AnnData._normalize_indices(self, index) 1093 def _normalize_indices(self, index: Optional[Index]) -> Tuple[slice, slice]: -> 1094 return _normalize_indices(index, self.obs_names, self.var_names)
File ~/opt/anaconda3/lib/python3.9/site-packages/anndata/_core/index.py:35, in _normalize_indices(index, names0, names1) 33 index = index[0].values, index[1] 34 ax0, ax1 = unpack_index(index) ---> 35 ax0 = _normalize_index(ax0, names0) 36 ax1 = _normalize_index(ax1, names1) 37 return ax0, ax1
File ~/opt/anaconda3/lib/python3.9/site-packages/anndata/_core/index.py:101, in _normalize_index(indexer, index) 99 if np.any(positions < 0): 100 not_found = indexer[positions < 0] --> 101 raise KeyError( 102 f"Values {list(not_found)}, from {list(indexer)}, " 103 "are not valid obs/ var names or indices." 104 ) 105 return positions # np.ndarray[int] 106 else:
KeyError: "Values ['AAACAAGTATCTCCCA.1', 'AAACAATCTACTAGCA.1', 'AAACACCAATAACTGC.1', 'AAACAGAGCGACTCCT.1', 'AAACAGGGTCTATATT.1', 'AAACAGTGTTCCTGGG.1', 'AAACATTTCCCGGATT.1', 'AAACCGGGTAGGTACC.1', 'AAACCGTTCGTCCAGG.1', 'AAACCTAAGCAGCCGG.1', 'AAACCTCATGAAGTTG.1', 'AAACGAAGAACATACC.1', 'AAACGAGACGGTTGAT.1', 'AAACGGGCGTACGGGT.1', 'AAACGGTTGCGAACTG.1', 'AAACGTGTTCGCCCTA.1', 'AAACT
