Georg

updated change log to include description of zeroing out deleted rois in self.roi_map, as well as in self.rois.

bug fix: when ROIs where deleted, they were only removed from self.rois, but not self.rois_map. Since we export the roi map for our analysis purposes, we were actually still exporting deleted rois. This has now been fix - deleted ROI's voxels are zeroed out in roi_map. this is the same principle as is used in rois.

two bug fixes. 1.) if analysis through deepd3 is run again, the spines in adata can now be overriden. 2.) There was a bug in DeepD3 where deleted ROIs were removed from self.rois but not self.rois_map. This meant the roi_map we were exporting still included the rois I had deleted. This has now been fixed, so deleted ROIs are empty voxel arrays in self.rois_map. The fix here removes those empty voxel arrays.

bugfix to create_submissionArchive.m / GK

added option to include .mat that are temp_AnalysisFiles in submission archive code

"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.