The advent of whole brain clearing and imaging methods have extended the breadth and depth at which neural populations can be studied. However, these methods have yet to be applied to larger brains, such as the brains of the common laboratory rat, despite the importance of these models in behavioral neuroscience research. Here we introduce an optimized iDISCO+ based immunolabeling and clearing methodology for application to adult rat brain hemispheres. We validate this methodology through the testing of common antibodies. In order to extend the accessibility of this methodology for general use, we have developed an open source platform for the registration of rat brain volumes to standard brain atlases for high throughput analysis.
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