Check initialization parameters

Check_initialization_parameters

function Check_initialization_parameters(CaliAli_options)

Description

Check_initialization_parameters previews how many neurons will be seeded before running CNMF-E. It inspects the stored correlation (Cn) and peak-to-noise (PNR) projections, applies the current min_corr, min_pnr, and seed_mask thresholds, and reports the total count while overlaying the candidate locations on the correlation image. Use this helper after alignment to decide whether initialization parameters need adjustment.

Function Inputs

Name	Type	Description
CaliAli_options	struct	Options structure loaded from a _det or _Aligned file; must contain inter_session_alignment.Cn/PNR and CNMF settings.

Behaviour

• Validates that the required Cn and PNR projections are present.
• Computes the local maxima mask used during CNMF-E initialization and applies correlation/PNR thresholds together with the seed mask.
• Displays the correlation image with the proposed seeds highlighted and prints a colour-coded summary of the neuron count.
• Reminds you to re-run CaliAli_set_initialization_parameters if the count looks too high or too low.

Example Usage

% After running CaliAli_align_sessions, preview initialization density
Check_initialization_parameters(CaliAli_options);