Re: Error while running minian pipeline on jupyter notebook

110 views
Skip to first unread message
Message has been deleted

Federico Sangiuliano

unread,
Feb 27, 2024, 5:23:55 PMFeb 27
to Miniscope
Hello Pranav. Did you activate the minan env before running the notebook?

On Tuesday, February 27, 2024 at 2:11:49 PM UTC-8 pranavs...@gmail.com wrote:
Greetings! I followed the installation guidelines for Minian from the GitHub page but I encountered an error when running the code in the Jupyter Notebook. When I run the import minian cell it gives me the following error: 

ModuleNotFoundError Traceback (most recent call last) Cell In[3], line 31 23 from minian.preprocessing import denoise, remove_background 24 from minian.utilities import ( 25 TaskAnnotation, 26 get_optimal_chk, (...) 29 save_minian, 30 ) ---> 31 from minian.visualization import ( 32 CNMFViewer, 33 VArrayViewer, 34 generate_videos, 35 visualize_gmm_fit, 36 visualize_motion, 37 visualize_preprocess, 38 visualize_seeds, 39 visualize_spatial_update, 40 visualize_temporal_update, 41 write_video, 42 ) File ~\.conda\envs\minian\lib\site-packages\minian\visualization.py:16 14 import numpy as np 15 import pandas as pd ---> 16 import panel as pn 17 import param 18 import scipy.sparse as scisps ModuleNotFoundError: No module named 'panel' Please let me know how can I remove this error. Thank you!
Message has been deleted

Jessica Tooley

unread,
May 30, 2024, 3:03:23 PMMay 30
to Miniscope

Unsure if this was ever solved, but just for other people's reference:

I was having this exact error and finally figured it out. I would get this ModuleNotFoundError: No module named 'panel' error no matter what I did - and I was setting up Minian on a completely new computer. I only just noticed today that for some reason, panel would be saved in site-packages in my main minian environment folder. Not in Lib/site-packages where everything else was. I just moved it into Lib/site-packages and everything has worked since then!

Pranav Sawant

unread,
May 30, 2024, 6:38:59 PMMay 30
to Miniscope
Hey! Yes this was resolved, you can refer to this 
https://github.com/denisecailab/minian/issues/266

The solution is quite similar to what you suggested. Thank you!
Reply all
Reply to author
Forward
0 new messages