IndexError in bidcell/processing/cell_gene_matrix.py

[diala-ar]

Hi,

Thanks for the nice tool. I am trying to perform cell segmentation for Xenium data. I used the default parameters you shared for Xenium. When I run your pipeline, I get some errors during the processing step (please see below). The errors are the same, but generated for different processes (from Process-217 to Process-240). These errors do not stop the pipeline from performing the training and prediction and from generating all the expected outputs. How can I change the parameters in the yaml file in order to prevent this error? Or can I just ignore those errors?

Reading DAPI image
/cluster/projects/mcgahalab/SEQUENCES/2024/20240209__214539__Brooks_Matthew_240207/output-XETG00082__0018494__INS_D_008_C2T__20240209__214556/morphology_mip.ome.tif
DAPI shape h: 20461 w: 42632
Segmenting DAPI patches h: 20461 w: 32000
Nuclei image h: 4348 w: 9059
...

Transforming x_location
Transforming y_location
0 12609 10180 14999
Extracting cell-gene matrix chunks
50%|█████ | 3/6 [03:58<03:13, 64.46s/it]/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
return bound(*args, **kwds)
Combining cell-gene matrix chunks
Patch H 15000:20461, W 0:15000
(5461, 15000)
Reading filtered transcripts
3.2554653 9054.4 4.3321505 4342.8413
Transforming x_location
Transforming y_location
nan nan nan nan
Transforming x_location
Transforming y_location
nan nan nan nan
Extracting cell-gene matrix chunks
**Process Process-217:
Traceback (most recent call last):
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/pandas/core/indexes/range.py", line 1018, in getitem
return self._range[new_key]
IndexError: range object index out of range

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, self._kwargs)
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/bidcell/processing/cell_gene_matrix.py", line 27, in process_chunk
chunk_id = chunk.index[0]
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/pandas/core/indexes/range.py", line 1020, in getitem
raise IndexError(
IndexError: index 0 is out of bounds for axis 0 with size 0

...

Process Process-240:
Traceback (most recent call last):
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/pandas/core/indexes/range.py", line 1018, in getitem
return self._range[new_key]
IndexError: range object index out of range

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/bidcell/processing/cell_gene_matrix.py", line 27, in process_chunk
chunk_id = chunk.index[0]
File "/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/pandas/core/indexes/range.py", line 1020, in getitem
raise IndexError(
IndexError: index 0 is out of bounds for axis 0 with size 0
67%|██████▋ | 4/6 [04:13<01:29, 44.94s/it]/cluster/home/dabdrabb/miniforge3/envs/bidcell/lib/python3.10/site-packages/numpy/core/fromnumeric.py:59: FutureWarning: 'DataFrame.swapaxes' is deprecated and will be removed in a future version. Please use 'DataFrame.transpose' instead.
return bound(*args, **kwds)
Combining cell-gene matrix chunks
Patch H 15000:20461, W 15000:30000

Thanks.

[diala-ar]

Hello Bidcell team or @xhelenfu , any update on the above problem please? Thanks.