CaliAli parameters

function opt=CaliAli_parameters(varargin)

Description

CaliAli_parameters: Initialize and configure parameters for CaliAli processing.

This function initializes and returns a structured set of parameters for different stages of the CaliAli processing pipeline, including downsampling, preprocessing, motion correction, inter-session alignment, and CNMF-E.

Function Inputs:

Parameter Name	Type	Description
varargin	array	Variable input arguments, which can be an existing structure or key-value pairs specifying parameters.

Function Outputs:

Parameter Name	Type	Description
opt	struct	Structure containing all processing parameters.

Example usage:

opt = CaliAli_parameters();   % Default parameter initialization
opt = CaliAli_parameters(existing_opt);   % Use existing parameter structure

Notes:

• Each processing module (downsampling, preprocessing, motion correction, inter-session alignment, and CNMF-E) has its own sub-structure with configurable parameters.
• The details of these structures can be found in CaliAli_demo_parameters().