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.
Registration InterfaceAn example Jupyter notebook illustrating our registration procedure can be found here: https://github.com/neurodata/ndreg and a walkthrough can be found in Supplemental Materials. The registration procedure includes preprocessing, followed by registration at 2 different resolutions, using the lower resolution result as an initial guess for unknown parameters at higher resolution. The following figures shows an overview of the notebook, with user inputs, atlas processing, atlas orientation verification, tif processing, target orientation verification, and registration error at low and high resolution. Users can download this notebook and simply replace filenames with their data.