Inter-Session Alignment and Projection Calculation

After motion correction, CaliAli calculates session projections, aligns sessions, and concatenates them for extraction.

Alignment and ConcatenationSingle File Processing

Run:

matlab CaliAli_align_sessions(CaliAli_options);

Output File

This step creates one *_Aligned.mat file plus per-session *_det.mat files. For naming and save-location details, see FAQ output naming.

If you do not need inter-session alignment, you can still calculate detrended projections for each file:

matlab detrend_batch_and_calculate_projections(CaliAli_options);

Output File

This step creates *_det.mat files.

Evaluating Alignment Performance

While running CaliAli_align_sessions(), check the reported:

Blood-vessel similarity score
Spatial correlation after alignment

Quick post-alignment check:

```matlab fprintf('BV Score: %.4f\n', CaliAli_options.inter_session_alignment.BV_score); Alignment_metrics = CaliAli_options.inter_session_alignment.alignment_metrics plot_alignment_scores(CaliAli_options)

P = CaliAli_options.inter_session_alignment.P; frame = plot_P(P); ```

BV+Neurons

Important

Always visually verify alignment quality before CNMF-E. If sessions remain visibly displaced, downstream extraction quality will be affected.

For advanced details about alignment internals and stored fields, see CaliAli_align_sessions().