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detrend Ca traces

detrend_Ca_traces

function out=detrend_Ca_traces(nums,obj,F)

Description

detrend_Ca_traces: Removes slow baseline fluctuations from calcium traces.

Function Inputs:
Parameter Name Type Description
nums double The window size factor used for median filtering and erosion.
obj matrix The calcium activity traces (matrix of size [neurons x frames]).
F double (Optional) The number of frames per batch. Defaults to size(obj,2).
Function Outputs:
Parameter Name Type Description
out matrix The detrended calcium traces with baseline fluctuations removed.
Example usage:
out = detrend_Ca_traces(10, neuron.C_raw);
out = detrend_Ca_traces(nums,neuron.C_raw, 1000);

Functionality

  • Applies a median filter (medfilt1) to smooth the signal over nums*10 frames.
  • Refines the baseline using morphological erosion (imerode).
  • Computes detrended traces by subtracting the estimated baseline from the original signal.
  • Handles multi-batch datasets by processing each segment separately and concatenating results if needed.

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.