microscopcy_scripts

Collection of scripts to automate microscopy collection/processing

QuPath

run scripts for all images in project with: QuPath script <full_path_to_script.groovy> -p <full_path_to_project_file.qpproj>

2D registrations

• require nighres and additional tools
• depend on multiple iterations of forward and back registrations

2d_slice_registration_all_fns.py

• full registration approach, but not full resolution so that you can test this relatively quickly before pushing to full reg

2d_slice_registration_all_fns_fullres.py

• as above, but in full res to generate 50um images (rescale value is set differently)