A software tool to assist the planning of electrophysiological experiments on rat brain slices

We propose an interactive software tool for finding the plane which can be cut through the rat brain so as to contain maximum cross-section with a selected brain structure or combination of structures, i.e. a path of nerve fibers and the area they are known to connect to. A set of digitized coronal images from a stereotactic rat brain atlas is preprocessed: the images are registered, and the structures of interest plus the bulk of the brain are assigned specific gray levels. The Interactive Data Language (IDL) computing environment is used for volume reconstruction, visualization, and implementing the search procedure. Selected rat brain structures can be analyzed with our method, provided that the preprocessing of the atlas images is performed. As a first application of this method we have identified a set of parameters for which a plane (0.4 mm slice thickness) cut through the rat brain includes as many as possible intact connections between the fornix fibers and the mammilary bodies. Further development of the application will focus on automating the process and extending it to visualization of histochemical and autoradiographic data.

Duke Scholars

Author Cristian Tudorel Badea Radiology