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Getting Started

This guide explains the CaliAli pipeline using the demo sessions in Demos, but the same workflow applies to your own data.

Installation

First follow the CaliAli installation notes Installation and System Requirements

CaliAli Processing Steps Overview

This guide is based on Demo_pipeline.mlx. In MATLAB, run:

open Demo_pipeline.mlx
How long it takes to process the Demo data?

Processing the demo data is expected to take approximately 5 minutes on a standard desktop computer.

CaliAli runs in five steps:

  1. Setting CaliAli Parameters

  2. Downsampling and File Conversion

  3. Motion Correction

  4. Inter-session Alignment

  5. Signal Extraction From Concatenated Sessions

Workflow:
sequenceDiagram
    participant U as User
    participant DS as CaliAli_downsample()
    participant MC as CaliAli_motion_correction()
    participant AT as CaliAli_align_sessions()
    participant CN as CaliAli_cnmfe()
    participant PP as Postprocessing

    U->>DS: Select input video(s)
    DS->>U: Downsampled .mat files output
    U->>MC: Provide downsampled files for motion correction
    MC->>U: Motion corrected video saved
    U->>AT: Initiate inter-session alignment
    AT->>U: Updated transformation parameters
    U->>CN: Run CNMF‐e extraction on aligned videos
    CN->>U: Neuronal components extracted and saved
    U->>PP: Launch postprocessing for residual updates and manual review
    PP->>U: Updated neuron data ready for further analysis

Can I automate this process without manually selecting files?

Yes. If you pass file lists through CaliAli_options, you can run the pipeline without file-selection popups:

CaliAli_options = CaliAli_demo_parameters();
CaliAli_options = CaliAli_downsample_batch(CaliAli_options);
CaliAli_options.motion_correction.input_files = CaliAli_options.downsampling.output_files;
CaliAli_options = CaliAli_motion_correction(CaliAli_options);
CaliAli_options.inter_session_alignment.input_files = CaliAli_options.motion_correction.output_files;
CaliAli_options = CaliAli_align_sessions(CaliAli_options);
File_path = CaliAli_cnmfe(CaliAli_options.inter_session_alignment.out_aligned_sessions);

Proceed to Setting CaliAli Parameters