Iris Calliope

LL - Add F0 in proj_meta

Now generate_proj_meta.m saves also F0 (baseline fluorescence) for each ROI in ROIinfo(i).F0 (or .F0_ch525 or .F0_ch610)
This happens for WF and 2P data.
Changed generate_proj_meta.m for directly saving F0 and get_smoothed_ROIs.m for F0 in 2P data

"inhomogenous arrays" error when writing to matfile was caused by numpy version (we were at version 1.24.4, recommendations is numpy>=1.13.0, < 1.24). Reverting to numpy 1.23.5 resovled the error. Solution is to save to RAM instead of to a temp matfile, making the process independent of numpy versions.

removed the one layer case added on 08.09.2026 again.

Added a special case to deal with stacks that only have one z layer.

Problem: run_fissa was called with export_to_matfile, which routes the results through Python's savemat; for a single-layer/single-trial stack, FISSA returns per-ROI object arrays with differing component counts, and savemat crashed trying to pack those arrays into one homogeneous array (the (5,1) + inhomogeneous part ValueError).

Fix: branch when nLayers==1: instead of exporting to a matfile, it reads FISSA's returned tuple directly in MATLAB, pulling each ROI's separated neuron trace (row 1 of its 5×nFrames block) and storing it in activity_fissa_corrected. The existing 4-layer pipeline behaves exactly as before.

ROI_fissa could not handle stacks that only had one z-layer (Fissa worked fine, bug was relating to export_to_matfile).

Added variable nLayers to store the number of layers in the stack. Added nLayers as an input for the two times ROI_fissa is called.

LL - added plotBSTRP_multi to plot N traces and significance level between them

Set it back to a simpler option. User just needs to feed a vector of seed ROIs indices. Common seeds are used across siteIDs. TK

Edited the comment on manual seed specification. TK

modified the option to manually set seed ROIs - TK

TK: manually defining seed ROIs is now active.