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Elife. 2019 Feb 8;8. pii: e42687. doi: 10.7554/eLife.42687.

Brain-wide cellular resolution imaging of Cre transgenic zebrafish lines for functional circuit-mapping.

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Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, United States.
Neuroscience and Cognitive Science Program, University of Maryland, College Park, United States.
Advanced Research Computing, Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, United States.
Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, Bethesda, United States.


Decoding the functional connectivity of the nervous system is facilitated by transgenic methods that express a genetically encoded reporter or effector in specific neurons; however, most transgenic lines show broad spatiotemporal and cell-type expression. Increased specificity can be achieved using intersectional genetic methods which restrict reporter expression to cells that co-express multiple drivers, such as Gal4 and Cre. To facilitate intersectional targeting in zebrafish, we have generated more than 50 new Cre lines, and co-registered brain expression images with the Zebrafish Brain Browser, a cellular resolution atlas of 264 transgenic lines. Lines labeling neurons of interest can be identified using a web-browser to perform a 3D spatial search ( This resource facilitates the design of intersectional genetic experiments and will advance a wide range of precision circuit-mapping studies.


Cre; Gal4; brain atlas; imaging; intersectional genetics; neuroscience; registration; zebrafish

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