Written by Z. Dhanerawala and A. Hoag (zmd@princeton.edu, ahoag@princeton.edu).

• projects --> project-specific scripts written for Princeton Neuro researchers
• clearmap --> helper scripts and post-hoc processing for images analyzed using ClearMapCluster
• datajoint --> scripts to injest and curate lightsheet data in DataJoint databases; related to A. Hoag lightserv project
• lightsheet --> related to processing and analyzing raw or downsampled lightsheet images
• neuroglancer --> scripts to injest raw and downsampled lightsheet images into the Neuroglancer interface; related to A. Hoag lightserv project
• ontology_analysis --> scripts to assist in traversing an atlas hierarchy of structures; typically used for the Allen Mouse Brain Atlas
• registration --> helper scripts to do registration independent of the BrainPipe pipeline
• registration/annotation_volume_analysis --> scripts utilizing atlas annotation volumes for processing or to do volume analysis

In projects:

• braincogs --> general analysis scripts written for BRAIN CoGS members/labs
• esteban_engel --> analysis scripts related to Engel lab LAP promoter project in Maturana et al. (2020)
• jv --> cfos and general analysis scripts for J. Verpeut
• malaz --> analysis scripts to quantify clearing efficacy based on a summer undergraduate research project
• mkislin --> probe detection analysis scripts for M. Kislin in-vivo recording work
• rat_atlas --> scripts related to the Princeton Rat Atlas project in BRAIN CoGS
• scooter --> analysis scripts for Falkner lab's c-Fos projects
• seagravesk --> cfos and general analysis scripts for K. Seagraves
• tracing --> analysis for Wang lab tracing projects; includes the HSV and PRV scripts for Pisano et al. (2020)