Skip to content

postprocessDeconvolvedTraces

function neuron = postprocessDeconvolvedTraces(neuron, method, type, smin)

Description

This function applies deconvolution to calcium traces and performs post-processing to denoise the traces based on specified options. It allows users to change the autoregressive model (ar1, ar2, etc.) at the end of CNMF iterations for refined neuronal activity estimation.

Function Inputs:
Parameter Name Type Description
neuron struct A struct containing the raw calcium traces (neuron.C_raw).
method string The deconvolution method to use (default is 'foopsi').
type string The type of deconvolution (default is 'ar2').
smin double Minimum threshold for deconvolution (default is -5).
Function Outputs:
Parameter Name Type Description
neuron struct Updated struct with processed calcium traces (neuron.C and neuron.S).
Example usage:
neuron = postprocessDeconvolvedTraces(neuron);
neuron = postprocessDeconvolvedTraces(neuron, 'thresholded', 'ar1', -3);
  • It allows users to change the autoregressive model (ar1, ar2, etc.) at the end of CNMF iterations for refined neuronal activity estimation.
  • This is particularly useful if a fast deconvolution method (e.g., foopsi) was used during CNMF iterations, and a more precise but slower thresholded method is desired for final processing.

Warning

  • Running this function modifies the temporal traces in a way that makes them unsuitable for further CNMF iterations. If additional CNMF iterations are needed, neuron=CNMF_CaliAli_update('Temporal',neuron); must be rerun to restore a compatible state.