Motivation

• The previous XY-fusion logic could reject overlapping stacks based on a single z slice, causing false negatives when that slice was blank, damaged, or feature-poor.
• Improve robustness of SIFT-based overlap detection by sampling multiple representative slices across the shared z-range.
• Provide clearer diagnostic logging so users can see which z slices were tried and why SIFT matching succeeded or failed.

Description

• Add helper functions _candidate_overlap_slices, _load_resampled_ref_slice, _has_valid_xy_overlap, and _format_sift_metrics to select representative z indices, load/resample slices, run multi-slice SIFT checks, and format SIFT diagnostics.
• Update create_configs_fused_stacks to call _candidate_overlap_slices and to test pairwise overlaps by trying several candidate slices before deciding that a pair does not overlap.
• Enhance logging to include the matched z slice and compact SIFT metrics on success and the list of tested z slices plus diagnostics on failure.
• Changes made in emalign/align_xy/prep.py (adds ~84 lines, removes ~14 lines) to implement the above behavior.

Testing

• Ran syntax check with python -m py_compile emalign/align_xy/prep.py and it succeeded.
• Ran git diff --check and there were no whitespace or diff-check issues.
• The change was committed with the message Improve XY fusion overlap detection.

Codex Task