iGluSnFR-registration-pipeline

This workflow leverages the Nextflow framework to automate and parallelize image registration tasks. It supports multiple registration algorithms, including:

• iGluSnFR Strip Registration GIT/CAPSULE
• CaImAn Suite2p Registration GIT/CAPSULE
• Matlab implementation of Strip Registration CAPSULE

• Matlab implementation of Strip Registration capsule has flags: -- maxshift 50 --clipShift 10 --removeLines 4 --ds_time 0
• CaImAn Suite2p Registration capsule needs flags -- caiman or -- suite2p to switch between CaImAn and Suite2p

Note:

This pipeline has multiple registration methods for comparing them for the upcoming iGluSnFR methods paper.

Output

The workflow generates registration results in the following directories:

• suite2p/: Results from Suite2p registration
• caiman/: Results from CaImAn registration
• stripRegisteration/: Results from strip registration
• stripRegisteration_matlab/: Results from matlab implementation strip registration