Widefield alignment

AP_align_widefield

Usage:

0. Set path to save alignments (first line in AP_align_widefield)
1. Create master alignment reference ('create_master') from average aligned vfs's from multiple animals

• Example is already included (master_vfs.mat) at 20.6 um per pixel across 11 mice
• This also aligns the Allen CCF to the master vfs

2. Across-day align ('new_days') using vasulature from all days of one animal

• Days first-pass rigid aligned using whole images
• First-pass rigid aligned again using user-selected stable area

3. Across-animal align ('new_animal) using the aligned average vfs from new animal

• Animal vfs affine aligned to the master vfs

4. Apply saved alignments to any images (specifying animal and day source)

• Regular usage after creating and saving alignments