The Zebrafish Brain Browser is a tool for 3D visualization of transgene and gene expression patterns in 6 dpf larval zebrafish. At present, the database includes expression patterns for 133 transgenic, enhancer trap or immunostained larvae, each scanned at high resolution and registered to a single reference brain. The browser enables expression patterns to be compared at near single cell resolution, and the identification of transgenic lines that express Gal4 in almost any selected set of neurons.
More information is available in Marquart (2015), and in the instruction manual (guide.pdf) included in the download (2.6 GB, ZBB1.2). Version 1.2 of ZBB includes brain scans and anatomical regions that were published in Z-Brain, which we aligned to the Brain Browser using the method described in Marquart (2016). Contact us if you want an older version for any reason.
The browser was designed to make it simple to add additional data. To do this you need to:
- Confocal scan your transgenic reporter, crossed to the vGlut:DsRed transgenic line: detailed imaging protocol here.
- Register your confocal stack to the vGlut:DsRed reference brain we used, either:
a. (good) by using CMTK - instructions on installing and using CMTK for brain registration in this protocol.
b. (better) by using ANTs, as described in Marquart (2016).
- Drag and drop the registered stack into the images directory of the browser.
We can provide additional help with each of these steps. We welcome feedback on bugs in the software and suggestions for new features. If you'd like to contribute transgenic lines or confocal scans, that would be great too.
Epifluorescent images for many lines are available from Zfin,which also contains links to ZIRC for ordering fish. Images of other enhancer trap lines (mostly labeling non-neuronal structures) are in our online database.
Virtual reality brain browser
See the zebrafish brain in 3D, using our virtual reality Brain Browser app for google cardboard: brainbrowser.apk (42 MB, Android).
The VR Browser was developed by Damian Dalle Nogare (NICHD).
Other valuable tools for brain registration and analysis in zebrafish:
- ViBE-Z: The Virtual Brain Explorer for Zebrafish, developed by the Driever lab.
- Z-Brain: A neuroanatomical reference atlas, developed by the Engert and Schier labs.