Zebrafish Atlas

With a wide variety of methods in molecular biology for generating transgenic fish, the number of of GFP-expressing expression patterns in the zebrafish brain is increasing on a daily basis. Comparing these patterns for the sake of understanding the connectivity and function of the fish brain is currently restrained by the missing framework of comparison. While very good anatomic works on the fish brain as the ‘Atlas of Zebrafish Development’ and ‘Brain atlas of the Medakafish’ do exist in print, the knowledge gained from these (and other) works still has to be correlated with new specimens in the scientist’s head. This effort not only limits the number of scientists capable of performing this comparison but also often is the source of misinterpretations and ‘wishful thinking’. Generating an atlas of standardized neuroanatomy has the goal to broaden the accessibility to zebrafish neuroanatomy as well as the generation and study of its connectome. Introducing high-resolution image data sets of expression patterns into a common coordinate system facilitates their direct comparison without previous descriptive interpretation as they currently have to be taken from publications. In close collaboration with VRVis Zentrum für Virtual Reality und Visualisierung Forschungs-GmbH (VRVis, http://www.vrvis.at), Vienna we are working on the transformation of their pre-existing software platform brain* (e.g. http://braingazer.org) to also work with high resolution image data of zebrafish. One of the biggest challenges thereby is the size of approx. 40GB per data set. This makes registration and rendering without resampling a demanding task.

However, first results on zebrafish larvae are coming in and can be visited online at zebrafish.tefor.net. This online database is aiming for the integration of our data with the data of our users and other labs and by this result in an compendium of zebrafish neuroanatomy. If you are interested, just get in contact with us.