Closed zhouyi0812 closed 6 months ago
If a batch item doesn't work it's usually due to the parameters.
Also, you don't need to create a new batch dataframe for each movie. I'd recommend learning pandas, you can filter based on values in columns etc.
Hello! May I ask if there is a way that I can get the optimal cor/pnr from the motion correction movie out from my 1500 movie efficiently? Like if there is a code that could detect the peak from the plot? Thank you very much!
You don't want the peak, you want the values such that the intersection of corr and pnr images captures neurons and excludes background/other activity. It's hard to get around visualization and be sure that you're not just capturing non-neuronal components.
Hello!!
I was trying to looping cnmfe by integrating the code together. However, sometimes it works, but most of the time it finished process the movie but the batch was not successful.
Here is my code and wonder if you could give me some guidance on how to adjust it? Thank you!
And the notification of running the cnmfe is: Start processing cnmfe: 016C5d7_B1_F2_1_00d00h00m Running 25ed74f2-722e-480d-8cd3-934e9e1a36fa with local backend cnmfe params: {'main': {'method_init': 'corr_pnr', 'K': None, 'gSig': (5, 5), 'gSiz': (21, 21), 'merge_thr': 0.75, 'p': 1, 'tsub': 1, 'ssub': 1, 'rf': 50, 'stride': 25, 'only_init': True, 'nb': 0, 'nb_patch': 0, 'method_deconvolution': 'oasis', 'low_rank_background': None, 'update_background_components': True, 'normalize_init': False, 'center_psf': True, 'ssub_B': 1, 'ring_size_factor': 1.4, 'min_corr': 0.75, 'min_pnr': 6.5, 'del_duplicates': True, 'bas_nonneg': True}} The local backend is an alias for the multiprocessing backend, and the alias may be removed in some future version of Caiman making memmap Performing CNMFE Finished processing cnmfe: 016C5d7_B1_F2_1_00d00h00m
Thank you very much!!