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TL;DR: Processing Multi-session Calcium Imaging Data with CaliAli

This section is intended for users who have already read the rest of the documentation and want a general overview of the commands needed to fully process the data.

Run the following functions:

Note

The following functions use the default parameters assuming a frame rate of 10 frames per second.

1) Data Downsampling:

Downsample_avi(2)   

Downsample_tiff(2)      

Downsample_Inscopix(4)

2) Motion Correction:

% Choose the files to motion correct
MC_Batch();

3) Inter-session Alignment:

% Choose the sessions to align:
align_sessions_CaliAli();

% If it is only one session:
detrend_batch_and_calculate_projections()

4) Calcium Traces Extraction:

  • Run CNMFe_app.
  • Choose the video file with the concatenated data named <File_name>_Aligned.h5 or individual sessions named <File_name>_det.h5.
  • Select appropriate initialization parameters.
  • Run CNMFe_batch(parin).

5) Optional post-processing

  • Load the .mat file with the extracted data.
  • Label false positives with ix=postprocessing_app(neuron)
  • Run neuron.delete(ix) to check and delete labeled components.
  • Run save_workspace(neuron) to save results.