Helper scripts to assist with Wang lab lightsheet & tracing projects & Princeton BRAIN CoGS Histology Core.

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

Module functions:

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)