Key Features

Ninety-six coronal levels from the olfactory bulb to the pyramidal decussation are depicted. Delineations primarily made on the basis of direct observations on the MRI contrasts. Each of the 96 open book pages displays four items- top left the directionally colored fractional anisotropy image derived from DTI (DTI - FAC), top right the diffusion-weighted image (DWI), bottom left the gradient recalled echo (GRE), and bottom right the diagram. The diagram is the synthesis of the information derived from these three images and the two additional images, which we do not display (ARDC and RD). This is repeated for 96 coronal levels, which makes the levels 250 µm apart. The FAC images are shown in full color. The orientation of sections corresponds to that in Paxinos and Watson's The Rat Brain in Stereotaxic Coordinates (2014). The images have been obtained from 3D isotropic population averages (number of rats = 5). All abbreviations of structure names are identical to the Paxinos & Watson histologic atlas.

Reproduction of Atlas Figures in Other Publications

As authors, we give permission for the reproduction of any figure from the atlas in other publications, provided that the atlas is cited. Permission from the publisher may be sought directly on-line via the Elsevier homepage (http://elsevier.com/locate/permissions) or from Elsevier Global Rights Department in Oxford, UK: phone: (+44) 1865843830, fax: (+44) 1865 853333, email: permissions@elsevier.com.

Acknowledgments

This work was supported by NHMRC grant 1086643, the Australian Research Council Centre of Excellence for Integrative Brain Function (ARC Centre Grant CE140100007). All MR images were acquired at the Duke Center for In Vivo Microscopy, an NIH/NIBIB Biomedical Technology Resource Center (P41 EB015897). AB gratefully acknowledges support from NIH through K01AG041211. We thank Dr. Emma Schofield and Mark Foster for expert assistance in the organization of image sets.

Introduction

The development of atlases of the rat brain over the past 50 years can be mapped upon the successive introduction of new staining technologies and the development of more accurate stereotaxic coordinates. The early atlases of König and Klippel (1963) and Pellegrino et al. (1979) were based on either myelin or Nissl stained coronal sections of the brain. Both of these atlases offered a stereotaxic coordinate system, but each suffered from technical limitations. The Paxinos and Watson atlas of 1982 used acetlycholinesterase histochemical staining in addition to Nissl staining, and presented coronal, sagittal, and horizontal sections in an accurate stereotaxic system. The next step in atlas development was the introduction of a wide range of histochemical and immunohistochemical stains to assist anatomical delineation. The most comprehensive presentation of this method is represented by the atlas of Paxinos et al. (1996), now in its second edition (Paxinos et al., 2009). The later editions of the Paxinos and Watson rat brain atlas made use of additional immunohistochemical stains, even though these sections are not pictured in the atlas (Paxinos and Watson, 2005, 2007, 2014). Since the discovery of gene targeting in mice (Capecchi, 1989), data on gene expression in the rodent brain have made a contribution to anatomical mapping, through the use of mouse lineages based on site-specific recombinases. This has led to an era of what Alexandra Joyner (personal communications, 2013) calls "genetic neuroanatomy" in which the developmental origins of neuron groups can be visualized in post-natal brains (Joyner and Zervas, 2006). Over the past few decades, there have been predictions of the demise of classical histological neuroanatomical atlases and their imminent replacement by imaging atlases. However, there is no sign yet that these atlases are in fact replacing, or even complementing, the classical paper atlases. We believe that the reason for this is that the resolution and contrast of the images offered have not been sufficient, and the neuroanatomical delineations were scanty. The present atlas offers two major enhancements when compared with earlier attempts to make MRI/DTI rat brain atlases. Firstly the MRI/DTI resolution/contrast obtained at the Duke Center for In Vivo Microscopy has surpassed that obtained by any other lab by nearly 400×. Secondly, the comprehensive set of contrasts provided by the DTI images has enabled us to identify more than 80% of structures identified in The Rat Brain in Stereotaxic Coordinates. MRI mapping will not quickly replace histological methods, but rapid improvements in resolution and contrast have already established a secure place for MRI technologies in brain mapping and we submit this book as an example. Since the publication of the first (MRI) atlas of the live rat in 1987 (Johnson et al., 1987), a series of important technical improvements have enabled the production of high quality image series, such as has been employed in the construction of this atlas. Since the atlas of Johnson et al. (1987), MR images of rat brain have progressively acquired higher spatial resolution, 3D acquisitions with isotropic voxels (Suddarth and Johnson, 1991), and a valuable set of contrast mechanisms. The major developments since 1987 include the following: 1. An increase in magnetic field from 1.5 T to 7.1 T allowing the acquisition of images at higher resolution. 2. An increased number of sequences to emphasize different contrasts in the tissue (T1-emphasizing difference in spin lattice relaxation time; T2-emphasizing difference in spin relaxation time; PD-based on differences in proton density; and diffusion tensor images (DTI)-providing a suite of contrast parameters based on tissue-specific diffusion of water). 3. The development of isotropic imaging through the use of three-dimensional (3D) imaging sequences with large arrays (Suddarth and Johnson, 1991). 4. Active staining of tissues with gadolinium contrast agents to reduce T1 (and allow shorter acquisitions) (Johnson et al., 2002). 5. The development of an extended dynamic range (Johnson et al., 2007). 6. The registration of multiple data sets to produce an average atlas with enhanced signal-to-noise and contrast-to-noise ratios.

Methods

Preparation of brains for MR image acquisition of data was carried out at the Duke Center for In Vivo Microscopy. The end result of image acquisition and processing pipelines is a final image set comprising averaged data from five adult male Wistar rats. The experimental procedures have been described in detail in a recent publication (Johnson et al., 2012) and will be summarized here. All experiments and procedures were carried out with the approval of the Duke University Institutional Animal Care and Use Committee. Five male Wistar rats (Charles River Laboratories, Wilmington, MA, USA), 80 days old and weighing approximately 250 g were selected for imaging studies. Rats were perfusion-fixed using the active staining technique (Johnson et al., 2002) to introduce the gadolinium-based MRI contrast agent Gadoteridol (ProHance, Bracco Diagnostics Inc., Princeton, NJ, USA) into the brain parenchyma. After flushing the vasculature with normal saline, perfusion fixation was achieved using a 10% solution of neutral buffered formalin (NBF) containing 10% (50 mM) gadoteridol. After perfusion fixation, rat heads were removed from the body and immersed in 10% NBF for 24 h. Finally, fixed rat heads (i.e., with brains still in the cranium) were transferred to a 0.1 M solution of phosphate buffered saline containing 1% (5mM) gadoteridol at 4°C for 5-7 days to ensure equilibration of contrast agent and tissue rehydration. Prior to imaging, specimens were placed in custom-made, MRI-compatible tubes and immersed in liquid fluorocarbon (Fomblin perfluoropolyether, Ausimont, Thorofare, NJ, USA) to reduce susceptibility artifacts at tissue/air interfaces, and to prevent specimen dehydration. All imaging experiments were performed with the brain in the cranium to preserve its integrity and natural shape.

Acquisition of gradient recalled echo (GRE) images

GRE images were acquired on a 7 T small animal MRI system (Magnex Scientific, Yarnton, Oxford, UK) equipped with 750 mT/m Resonance Research gradient coils (Resonance Research, Inc., Billerica, MA, USA), and controlled with a General Electric Signa console (GE Medical Systems, Milwaukee, WI, USA). RF excitation and reception were accomplished using a custom-made 30-mm diameter × 50-mm long solenoid RF coil. T2*-weighted structural images were acquired using a 3D gradient recalled echo (GRE) sequence (flip angle a = 60°, TR = 50 ms, TE = 8.3 ms, NEX = 2) with a strategy designed to provide the wide dynamic range required for large 3D arrays, described in more detail in Johnson et al. (2007). The data were fully sampled in Fourier space with an acquisition matrix of 1600 (frequency)×800 (phase 1)×800 (phase 2) over a 40×20×20 mm field of view (FOV), yielding a Nyquist limited isotropic voxel size of 25 µm3 (voxel volume = 15.6 pl). The data were not interpolated by zero filling. Approximate scan time was 13 h per specimen.

Diffusion-weighted images

Diffusion-weighted...