Errors in Motion Correction when running .avi files in pipeline

[jtalley24]

• Windows 10, Python 3, Jupyter Notebook

• I am trying to run this pipeline with Miniscope data. Miniscope saves videos in the .avi format, and I receive the following error in the Motion Correction section when trying to run the pipeline:

• ---

  Exception Traceback (most recent call last)

  in () 6 dview=dview, 7 splits_rig=splits_rig, ----> 8 save_movie=not(do_motion_correction_nonrigid) 9 ) 10

~\Anaconda3\envs\caiman\lib\site-packages\caiman\motion_correction.py in motion_correct_oneP_rigid(filename, gSig_filt, max_shifts, dview, splits_rig, save_movie) 473 ''' 474 min_mov = np.array([cm.motion_correction.high_pass_filterspace( --> 475 m, gSigfilt) for m in cm.load(filename[0], subindices=range(400))]).min() 476 new_templ = None 477

~\Anaconda3\envs\caiman\lib\site-packages\caiman\base\movies.py in load(file_name, fr, start_time, meta_data, subindices, shape, var_name_hdf5, in_memory, is_behavior, bottom, top, left, right, channel, outtype) 1234 elif extension == '.avi': # load avi file 1235 if subindices is not None: -> 1236 raise Exception('Subindices not implemented') 1237 cap = cv2.VideoCapture(file_name) 1238 try:

Exception: Subindices not implemented

• Any help is greatly appreciated

[epnev]

@jtalley24 Support for .avi files was implemented as a response to issue https://github.com/flatironinstitute/CaImAn/issues/291 You should update to the latest version (see instructions on how to do this)

[jtalley24]

Could you provide a link to the relevant instructions?

[epnev]

It appears when you click to open a new issue but you deleted it. check the wiki

[jtalley24]

when attempting to remove the conda env in anaconda prompt:

"CondaEnvironmentError: cannot remove current environment. deactivate and run conda remove again"