Error while running cnmf

[Mtkostecki]

1. Operating system (Linux/macOS/Windows): Wind

2. Python version (3.x): 3.7.10

3. Working environment (Python IDE/Jupyter Notebook/other): Spyder

4. Which of the demo scripts you're using for your analysis (if applicable): https://github.com/flatironinstitute/CaImAn/blob/master/demos/notebooks/demo_pipeline_cnmfE.ipynb

5. CaImAn version*: 1.9.1

6. CaImAn installation process (pip install ./pip install -e ./conda): conda

• Describe the issue that you are experiencing Hi! While running cnf in a one photon pipeline I got an error. What may be the cause?

• Copy error log below

  File "C:\Users\MKOSTE~1\AppData\Local\Temp/ipykernel_17900/3502115709.py", line 2, in cnm.fit(images)

  File "C:\Users\mkostecki\anaconda3\envs\caiman\lib\site-packages\caiman\source_extraction\cnmf\cnmf.py", line 607, in fit indices=indices)

  File "C:\Users\mkostecki\anaconda3\envs\caiman\lib\site-packages\caiman\source_extraction\cnmf\map_reduce.py", line 249, in run_CNMF_patches file_res = dview.map_async(cnmf_patches, args_in).get(4294967)

  File "C:\Users\mkostecki\anaconda3\envs\caiman\lib\multiprocessing\pool.py", line 657, in get raise self._value

IndexError: index 16 is out of bounds for axis 0 with size 16

[pgunn]

Hello, Is this one of the demos? Your own data?

[Mtkostecki]

It's my own (UCLA miniscope v4, avi,, 1000 frames)

[pgunn]

What's the dimensionality of your data, and what changes did you make to the demos (or otherwise how are you getting it into Caiman) for load?

[Mtkostecki]

Its 608 x 608 x 1000; I just use fnames = ['m13test.avi'] , etc. Motion correction works well.

[Mtkostecki]

Otherwise I did not make any changes!

[pgunn]

Are you doing it with a single file? Is this something you would mind sharing with us (over dropbox, perhaps)? If that'd work I can share my email for a share.

[Mtkostecki]

It started working for no really clear reason (I didn't change anything, just tested for the third time today), thanks anyway!

wt., 24 sie 2021 o 18:10 Pat Gunn @.***> napisał(a):

Are you doing it with a single file? Is this something you would mind sharing with us (over dropbox, perhaps)? If that'd work I can share my email for a share.

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