At ZebrafishBrain we use the ontology developed by ZFIN. Using a common ontology across the zebrafish community is very important, as then we know we are all talking about the same structure!
A good website for exploring the zebrafish ontology is the ontology lookup service(OLS). For a pictorial representation of where any of the brain regions sit within the zebrafish ontology click the accompanying OLS link.
Vibe-Z
Throughout the brain region tutorials we make use of another fantastic neuroanatomical resource, the Vibe-Z anatomical segmentation of 3 day old zebrafish larval brain by Thomas Müller, Olaf Ronneberger, Wolfgang Driever and colleagues. For details see Ronneberger et al., Nat. Meth. 2012 and http://vibez.informatik.uni-freiburg.de. This segmented brain allows us to illustrate where the different brain regions lie in relation to each other in 3 dimensions. Details for how to download the original stack and view this segmented brain using Image J can be found in the supplementary data accompanying the Ronneberger et al., Nat. Meth. 2012 paper.
If you would like to look through some serial sections of the segmented Vibe-Z brain from three different orientations click the button below.
Zebrafish Brain Browser (ZBB)
We also use stills from the ZBB to illustrate our tutorials. Both the anatomical segmentation and where appropriate transgenic lines that label particular structures. These stills are no match for the real thing, so we urge you to visit the ZBB and use their 3D online viewer to browse zebrafish anatomy and their huge collection of transgenic lines. It is a brilliant and ever growing resource for the zebrafish community. It is also possible to morph your own data to ZBB. You can read more about ZBB here.
We are very grateful to Wolfgang Driever and Harry Burgess for allowing us to use their fantastic resources to illustrate our tutorials.