Adult neurogenesis occurs in proliferative zones of the brain that contain neural progenitor cell populations capable of differentiating into specific cell types. However, we remain limited in our understanding of the signals that regulate neural progenitor cell proliferation and differentiation in adults. Recently zebrafish (Danio rerio) have emerged as an excellent model for studying the molecular mechanisms behind adult neurogenesis, because sixteen proliferative zones remain active in the adult brains. Thousands of fluorescent transgenic reporter lines have been generated in zebrafish that reveal gene expression patterns of cell-cell signaling systems, some of which may regulate neurogenesis in these brain regions. Using a new tissue clearing technique and whole brain imaging with fluorescent light sheet microscopy (FLSM) we have generated the first 3-Dimensional atlas of gene expression in an intact adult zebrafish brain. So far we have created a reference brain image and have aligned the expression patterns from three transgenic lines. This work is a preliminary step in the generation of a new, open access brain atlas called the Zebrafish Adult Brain Browser (ZABB). While generating this atlas we focused on documenting the adult brain regions responsive to Sonic Hedgehog (Shh), a cell-cell signaling system known to regulate neurogenesis during embryonic development. We used two Shh-reporter lines to create another atlas comparing reporter transgene expression in whole brain and sectioned tissue to the expression of the Hedgehog (Hh) target gene ptch2 using in situ hybridization. We show that the reporter lines reveal different Hh responsive domains, but together identify fourteen Hh responsive regions in the brain, nine of which are known proliferative zones. Thus, it appears that subsets of both proliferating neural progenitors and non-proliferative cells remain Hh responsive in adult brains. Our data suggests that Hh signaling contributes to the regulation of neural progenitor cells in nine of the sixteen proliferative zones. Uncovering the molecular mechanisms behind adult neurogenesis and forming a greater understanding of adult neural stem cell regulation has the potential to influence the treatment of many neurodegenerative diseases and cancers.