Atlas of the Postnatal Rat Brain in Stereotaxic Coordinates

The series of atlases of the developing rat brain in stereotaxic coordinates that we propose here1,2 has been conceived as a tool for the exploration of the rat brain in vivo during the postnatal period, offering a choice of bregma and lambda as the reference points. We suggest to use this atlas, which provides stereotaxic coordinates, in combination with other histological atlases, where brain structures and boundaries between them were assessed using histochemistry or quantative magnetic resonance techniques, but where stereotaxic coordinates are not available (Ramachandra and Subramanian, 2011; Calabrese et al., 2013; Ashwell and Paxinos, 2015) or provided (at P10, P21, and P39) but not within the bregma-lambda metrics (Sherwood and Timiras, 1970). The neonatal rat is a powerful model for the study of the early stages of central nervous system development. Comparative developmental studies suggest that the first two postnatal weeks in the rat roughly correspond to the second half of gestation and the early postnatal period in humans, with the electrical brain activity patterns expressed during this period and their developmental trajectories matching the patterns observed in premature human neonates (Clancy et al., 2001, 2007; Khazipov and Luhmann, 2006; Colonnese et al., 2010; Workman et al., 2013) (see also http://www.translatingtime.net/). Recent advances in the understanding of the developing brain functions largely came from the use of techniques to record brain activity from neonatal and adolescent rats in vivo, notably in head restrained animals (Leinekugel et al., 2002; Khazipov et al., 2004; Minlebaev et al., 2011; Tiriac et al., 2012; Yang et al., 2013). However, the rat brain grows rapidly and non-proportionally during the postnatal period and brain structures change their position in relation to the conventional skull marks such as bregma and lambda, making difficult to perform targeted recordings, stimulations, lesions, or local drug injections in precise anatomical locations. Hence the importance of a developmental atlas of the rat brain in stereotaxic coordinates. Several examples of histology atlases series of the developing rat brain have been published (Table ​(Table1). 1). The Atlas by Sherwood and Timiras “A Stereotaxic Atlas of the Developing Rat Brain” atlas includes three postnatal time points: postnatal days P10, P21, and P39 (Sherwood and Timiras, 1970). Ashwell and Paxinos' “Atlas of the Developing Rat Nervous System” provides photographs and accompanying diagrams of coronal and sagittal sections of rats aged E12, E13, E14, E16, E17, E19, and P0 (Ashwell and Paxinos, 2015). “Atlas of the Neonatal Rat Brain” by Ramachandra and Subramanian describes rat brains at P1, P7, and P14 (Ramachandra and Subramanian, 2011). More recently, Calabrese, Badea, Watson, and Johnson published their “Quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability” based on the study of P0, P2, P4, P8, P12, P18, P24, P40, and P80 rats (Calabrese et al., 2013). Among these atlases, only the atlas by Sherwood and Timiras (1970) provides stereotaxic coordinates and yet for only three postnatal days P10, 21, and P39. Stereotaxic atlases for the early postnatal period are not available, however. Table 1 Atlases of the developing rat brain. The series of atlases of the developing rat brain in stereotaxic coordinates that we propose here has been conceived as a tool for the exploration of the rat brain in vivo during the postnatal period, offering a choice of bregma and lambda as the reference points. Each atlas contains a series of microphotographs of wet, non-stained 200 micron coronal brain sections in oblique light, obtained from postnatal days P0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, and 21 rats, with an indication of the main brain structures. Wet non-stained sections were used to avoid deformation, shrinkage and lessening associated with staining and mounting procedures, particularly when manipulating immature tissue. Because we did not stain sections, the images do not provide cellular resolution and not all brain structures and boundaries between them can be easily identified. Therefore, only certain brain structures are labeled without boundaries. Used in combination with the existing high image resolution atlases of the developing rat brain (Sherwood and Timiras, 1970; Ramachandra and Subramanian, 2011; Calabrese et al., 2013; Ashwell and Paxinos, 2015), this atlas may be useful for targeted recordings, stimulations, and drug injections in different brain structures at various postnatal ages. This atlas has been successfully used in several previous studies (Minlebaev et al., 2011; Petit et al., 2014; Tyzio et al., 2014).