Relaxing holiday at Club Med, Nea Makri, Greece (July 2004)
George Paxinos
Prince of Wales Medical Research Institute
The University of New South Wales
Sydney, Australia
g.paxinos@unsw.edu.au
www.powmri.edu.au/staff/paxinos.htm
Charles Watson
Division of Health Sciences
Curtin University of Technology
Perth, Australia
c.watson@curtin.edu.au
Relaxing holiday at Club Med, Nea Makri, Greece (July 2004)
We dedicate this book to Kosta Theodore Paxinos and Anwen Angharad Williams.
Preface
In the first four editions of this atlas, we relied on a coronal section set that
had some significant limitations; the section frequency proved over time to
be too wide, sections did not always appear at regular intervals, and a few
damaged sections had been replaced with sections from another brain. The
fifth edition is based on a new coronal set which includes 161 sections from a
single brain at regular 120µm intervals. This edition of the atlas is not simply
an incremental improvement on the previous edition, but a completely new
and far more comprehensive map of the rat brain.
Although the fifth edition features a different coronal section set, readers can
be assured that the stereotaxic coordinates in the new atlas match those in
previous editions. We have increased the scope of the atlas by incorporating
new anatomical concepts where appropriate, and have once again delineated
and named some areas not previously recognised.
Over the past decade our efforts at mapping the brain have been greatly
enhanced by the availability of sections stained with a wide range of different
chemical markers. A further contribution to the accuracy of our maps has
been the knowledge we have we have gained from comparative
neuroanatomical studies. One of us (GP) has published atlases of the human
(Paxinos and Huang, 1995; Mai et al. 2004), monkey (Paxinos et al. 2000),
and mouse brain (Paxinos and Franklin, 2004), and both of us are part of
a team that is in the final stages of preparing an atlas of the chicken brain
(Puelles et al. in press). Each of these atlas projects has provided us with
new insights that have enhanced our ability to interpret the anatomy of
the rat brain.
Acknowledgements
We thank Hongqin Wang for outstanding technical assistance from the
inception to the completion of the project. We are indebted to Lewis Tsalis for
speed, accuracy and brilliance in construction of diagrams and designing this
book; to Paul Halasz for his imagination in construction of the CD-Rom; to
Julia Tsalis for accurate labelling of diagrams; to Hongmei Liu for technical
assistance, and to Yvette Paxinos for the cover design.
We acknowledge with gratitude the intellectual contribution to delineations
made by Yuri Koutcherov (hypothalamus), Konrad Talbot (hippocampus),
Nicola Palomero-Gallagher and Karl Zilles (cortex), Brent Vogt (cingulate
cortex), Jan Vogt (cerebellum, precerebellar nuclei and vestibular nuclei),
George Alheid (basal forbrain), Pascal Carrive (periaqueductal gray and
hypothalamus), Glenda Halliday (substantia nigra and VTA), Ellen Covey and
Manolo Malmierca (auditory system), Joel Elmquist (hypothalamus), Ann
Goodchild and David Hopkins (rostroventrolateral and caudoventrolateral
medulla), Jose DeOlmos (amygdala), Henk Groenewegen (thalamus), Joseph
Travers (orofacial motor nuclei), John Mitrofanis (zona incerta), Pierre-Yves
Risold (septum), Miklos Palkovits (paralemniscal nuclei), Harvey Karten
(pretectal area), Chip Gerfen (basal ganglia), Terry Furlong (hypothalamus),
Jean Buettner-Ennever (oculomotor nuclei), Marina Bentivoglio
(parafascicular nucleus).
George Paxinos acknowledges the support he has received from the Australian
National Health and Medical Research Council (he holds an NHMRC
Principal Research Fellowship), as well as assistance from the Clive and Vera
Ramaciotti Foundation, the Rebecca Cooper Foundation, and the Brennan
Foundation.
We have appreciated the intelligent and enthusiastic support from our
Elsevier editor Johannes Menzel. His patience and consideration have made
a real difference to the successful completion of this project. We also thank
Maureen Twaig and other Elsevier staff for their willingness to help in solving
production problems.
Features of the Fifth Edition
• 161 coronal diagrams based on a single brain
• Diagrams spaced at constant 120 µm intervals giving scientists the most
comprehensive and convenient atlas of the rat brain
• The most accurate stereotaxic reference system available
• Outlines of figures and brain structures in blue, but labels and leader lines
in black for increased clarity of delineations
• All delineations re-examined in the light of recent findings
• Delineations of brain structures have been made with reference to sections
stained for Nissl substance, AChE, parvalbumin, calbindin, calretinin,
SMI-32, tyrosine hydroxylase, and NADPH diaphorase (Paxinos et al.
1999a,b)
• Extensive use was made of reference works, including the third edition
of The Rat Nervous System (Paxinos, 2004) and other recent
neuroanatomical literature
• Spinal cord drawings from the atlas of Molander and Grant(1995)
• Diagrams available on CD-ROM for printing.
Introduction
There are many reasons why the rat is the most commonly selected subject for
research in mammalian neuroscience. First, rats are the right size: neither too
small for accurate stereotaxic localization of discrete brain areas, nor too large
for cost-effective laboratory management. Second, rats are generally hardy
animals and are resistant to infections. Third, a number of inbred strains are
available commercially, so that animals of consistent size can be used for
stereotaxic procedures.
When the first edition of The Rat Brain in Stereotaxic Coordinates was
published in 1982, it was the first atlas to be based on the flat skull position.
It offered a choice of bregma, lambda, or the midpoint of the interaural line
as the reference point. Although the coordinates were developed from study
of adult male Wistar rats with weights ranging from 270 to 310 g, the atlas
can be successfully used with male or female rats, with weights ranging from
250 to 350 g (Paxinos et al., 1985).
With each new edition of the atlas, we have attempted to improve the
accuracy of our delineations and have incorporated new findings on brain
anatomy. However, our work has been hampered by the fact that our original
series of coronal sections suffered from a number of limitations. First of all,
our primary sections series showed sections at 0.5 mm intervals, which is
insufficient to adequately represent all major structures in the brain for
modern research purposes. Although we later attempted to better illustrate
some areas by using some intervening sections, we could never fully
compensate for the wide section interval in the primary series. In addition,
we lost some sections in some areas of the brain and were forced to interpolate
sections from another brain to compensate for the missing sections.
We were aware that the only real solution to these problems was to replace the
coronal section series with a new section set based on shorter intervals and
with all sections taken from the one brain. The new coronal section series is
presented in the present (fifth) edition of the atlas. It shows diagrams of
sections taken at regular intervals of 0.12 mm. Having constant intervals
between the sections shown in the atlas diagrams eliminates one of the
annoying features of many brain atlases – the fact that when the reader turns
a page they do not know how far they have advanced along the prime axis.
All sections are from the one brain.
The sections in our new coronal series were stained with cresyl violet or
with methods to demonstrate AChE or NADPH diaphorase because we found
that these three methods were compatible with using fresh (unfixed) tissue,
a requirement for deriving an accurate stereotaxic grid. However, we
consistently used other markers to confirm our delineations (Paxinos et al.,
1999a, Paxinos et al., 1999b).
We have once again been greatly assisted by the suggestions of many
colleagues in the delineation of structures. We welcome further advice that
might improve the accuracy of our diagrams in the future. Please email us
on g.paxinos@unsw.edu.au or c.watson@curtin.edu.au.
The present book will be followed by a comprehensive publication, which will
include accompanying photographs and revised diagrams of sagittal and
horizontal sections.
Methods
A fresh brain from a male 290 g Wistar rat was frozen, and coronal sections
were cut at 40 mm thickness. The sections were cut at right angles to the
horizontal plane joining bregma and lambda.
Stereotaxic surgery
We placed an anesthetized rats in a Kopf small-animal stereotaxic instrument,
and the incisor bar was adjusted until the heights of lambda and bregma were
equal. This flat-skull position was achieved when the incisor bar was lowered
3.3 ± 0.4 mm below horizontal zero (Table 1). Because the point of
intersection of the lambdoid and sagittal sutures is variable, we have chosen
to define lambda as the midpoint of the curve of best fit along the lambdoid
suture (see skull diagram). This redefined reference point is considerably
more reliable than the true lambda (the point of intersection of the sagittal
and lambdoid sutures), and it is located 0.3 ± 0.3 mm anterior to the
interaural line. We defined bregma as the point of intersection of the sagittal
suture with the curve of best fit along the coronal suture. When the two sides
of the coronal suture meet the sagittal suture at different points, bregma
usually falls midway between the two junctions. The anteroposterior position
of bregma was 9.1 ± 0.3 mm anterior to the coronal plane passing through
the interaural line, but for the brain represented in this atlas bregma is
deemed to lie at 9.0 mm. The top of the skull at bregma and lambda was
10.0 ± 0.2 mm dorsal to the interaural zero plane. To confirm the stereotaxic
orientation of sections in the brain used for this atlas, reference needle tracks
were made perpendicular to the horizontal and coronal planes. One
horizontal needle insertions perpendicular to the coronal plane were made
from the posterior of the brain at 4.0 mm above the interaural line and was
2.0 mm lateral to the midline. The reference track from the horizontal needle
appears as a small hole in coronal sections.
Following surgery, the rat was decapitated and the whole head frozen on dry
ice. The frozen skull was then prised off the frozen brain, and the brain was
carefully mounted on the stage of microtome so that the sections would be
cut in the coronal stereotaxic plane.
Every third section was used for preparation of the atlas diagrams, so that the
interval between atlas diagrams is 0.12 mm. Exceptions to this rule are found
in the region rostral to the rostrum of the corpus collosum (Interaural AP
11.28) and in the region of the medulla caudal to the inferior olive (Interaural
AP -5.76 mm). In these two regions, sections were selected for presentation in
the atlas at 0.24 mm intervals. Finally, the olfactory bulb is depicted at only
three representative levels.
Histological methods
The ‘atlas’ sections were stained with either cresyl violet or for the
demonstration of AChE on an alternate basis, so that cresyl violet sections are
0.24 mm apart and AChE sections are also 0.24 mm apart. The two sections
that intervene between each ‘atlas’ section were stained with cresyl violet or
for the presence or AChE or NADPH diphorase, according to the following
sequence:
1. Cresyl violet ‘atlas’ section
2. AChE intervening section
3. NADPH intervening section
4. AChE ‘atlas’ section
5. Cresyl violet intervening section
6. NADPH diaphorase intervening sections
This sequence was repeated throughout the series of coronal section. This
arrangement ensures that every ‘atlas’ section is accompanied by two adjacent
sections, each of a different stain. For example, the ‘atlas’ AChE section
described as number four above is preceded by an NADPH diaphorase
section and followed by a cresyl violet section. This arrangement gave us
maximum information for each ‘atlas’ section from the three stains. Staining
was carried out on the same day as section cutting.
All sections, whether ‘atlas’ or intervening, were photographed on 4"x5" black
and white negatives and printed on 36"x24" photographic paper. Each ‘atlas’
section was then covered with a sheet of ‘Mylar’ tracing film and outlines of
structures were drawn in pencil. The final pencil drawings were scanned and
then digitized using Adobe Illustrator.
Quality of Sections
In some cases, the sections were slightly stretched or compressed in the
process of cutting and mounting on slides. We have compensated for this by
constructing diagrams which represent, as best we can judge from the study
of adjacent sections, the original shape of the brain section. In the worst cases,
the ‘atlas’ section was so badly damaged that we have taken our drawing from
an adjacent section.
Cresyl Violet Staining
Slides were immersed for 5 min in each of the following: xylene, xylene, 100%
alcohol, 100% alcohol, 95% alcohol, and 70% alcohol. They were dipped in
distilled water and stained in 0.5% cresyl violet for 15-30 min. They were
differentiated in water for 3-5 min and then dehydrated through 70% alcohol,
95% alcohol, 100% alcohol, and 100% alcohol. They were then put in xylene
and coverslipped.
To make 500 mL of 0.5% cresyl violet of about pH 3.9, mix 2.5 g of cresylecht
violet (Chroma Gesellschaft, Postfach 11 10, D-73257, Kongen, Germany, Fax
number: 49-7024-82660), 300 mL of water, 30 mL of 1.0 M sodium acetate
(13.6 g of granular sodium acetate in 92 mL of water), and 170 mL of 1.0 M
acetic acid (29 mL of glacial acetic acid added to 471 mL of water). Mix this
solution for at least 7 days on a magnetic stirrer, then filter.
AChE Histochemistry
The method for the demonstration of AChE followed the procedures of
Koelle and Friedenwald (1949) and Lewis (1961). Slides were incubated for
15 h in 100 mL of stock solution (see below) to which had been added
116 mg of S-acetylthiocholine iodide and 3.0 mg ethopropazine (May &
Baker). The slides were rinsed with tap water and developed for 10 min in
1% sodium sulphide (1.0 g in 100 mL of water) at pH 7.5. They were then
rinsed with water and immersed in 4% paraformaldehyde in phosphate
buffer for 8 h, and then allowed to dry. Subsequently, they were dehydrated
for 5 min in 100% alcohol, then immersed in xylene and coverslipped with
Permount. The stock solution was a 50 mM sodium acetate buffer at pH 5.0
which was made 4.0 mM with respect to copper sulphate and 16 mM with
respect to glycine. This was done by adding 6.8 g of sodium acetate, 1.0 g of
copper sulphate crystals, and 1.2 g of glycine to 1.0 L of water and lowering
the pH to 5.0 with HCl. We found that fresh, unfixed tissue from the frozen
brains showed a substantially stronger reaction for both stains than tissue
fixed with formalin, paraformaldehyde, glutaraldehyde, or alcohol.
NADPH diaphorase
The sections were washed in phosphate buffer for 10 minutes and incubated
in 10 ml of a phosphate buffer solution containing 0.0125% nitroblue
tetrazolium, 0.05% NADPH, 0.5% Triton X-100, and 1 mM magnesium
chloride. The pH of the solution was adjusted to 7.6. The sections were
incubated at 4ºC for 48 hours. The incubation was stopped with a wash in
phosphate buffer.
Photography and drawings
Photography
The photographs of stained brain sections were taken with a Nikon Multiplot
macrophotographic apparatus using 4"x5" Kodax Plus X film. High contrast
paper was used to print the photographs of Nissl sections, whereas lower
contrast paper was used to print the photographs of AChE and NADPH
sections.
Drawings
Drawings, which later formed the basis of the figures, were made by tracing
the photographs of sections. We drew only the right side of each section and
derived the outline of structures on the left side by mirror image construction
using Adobe Illustrator.
Fiber tracts in the drawings are outlined by solid lines, and nuclei and cell
groups are outlined by broken lines. In general, each abbreviation is placed in
the center of the structure to which it relates; where this is not possible, the
abbreviation is placed alongside the structure and a leader line is used. The
abbreviations for fiber tracts and fissures are almost always positioned on the
left side of the figure, and the abbreviations for nuclei and other cell groups
are generally positioned on the right side. The outlines of the ventricles and
aqueduct are filled in with solid color.
Stereotaxic Reference System
The stereotaxic reference system is based on the flat skull position, in which
bregma and lambda lie in the same coronal plane. Two coronal and two
horizontal zero-reference planes are referred to in these drawings. One
reference coronal plane cuts through bregma and the other cuts through the
interaural line. Similarly, one horizontal plane is at the level of bregma on the
top of the skull and the other is at the level of the interaural line. Lambda is
usually located 0.3 mm anterior to the interaural line, and it can be used as
an alternative reference point in conjunction with the dorsoventral
coordinate of bregma. The position of the stereotaxic reference points and
planes are indicated on the skull diagram. The stereotaxic reference grid
shows 0.2 mm intervals.
Drawings of coronal brain sections
In each of the coronal drawings, the large number at the bottom left shows
the anteroposterior distance of the section from the vertical coronal plane
passing through the interaural line. The large number at bottom right shows
the anteroposterior distance of the plate from a vertical coronal plane passing
through bregma. Note that these two coronal planes are 10 mm apart, so the
two numbers on any one plate add up to 10 mm. The small numbers on the
left margin show the dorsoventral distance from the horizontal plane passing
through the interaural line. The numbers on the right margin show the
dorsoventral distance from the horizontal plane passing through bregma and
lambda on the surface of the skull. The numbers on the top and bottom
margins show the distance of structures from the midline sagittal plane.
Skull Diagram Dorsal and lateral views of the skull of a 290 g Wistar rat. The positions of bregma, lambda and the plane
of the interaural line are shown above the lateral view. The distance between the horizontal plane passing through the
interaural line is shown on the right of the lateral view. The distance between the incisor bar and the horizontal plane
passing through the interaural line is shown on the left of the lateral view. Lambda (midpoint of the curve of best fit
along the lambdoid suture) is 0.3 mm anterior to the coronal plane passing through the interaural line.
290 g Male Wistar
Interaural Line
Incisor Bar
Lambda
Lambda
Bregma
Bregma
10.0 mm
3.3 mm
9.0 mm
Accuracy of the stereotaxic coordinates
In almost all cases, the potential error in defining the position of any point
in the brain is less than 0.5 mm. Although we used medium-sized (average
290 g) male Wistar rats in the construction of this atlas, we recognize that
researchers often use animals of different sex, strain, and weight. Because
of this, we have estimated the error that may occur if this atlas is used with
female Wistar rats, male hooded (Long Evans) rats, male Sprague Dawley rats
of 300-g weight, juvenile (180 g) Wistar rats, and mature (436 g) Wistar rats.
The results of these estimations are shown in Table 1 (reproduced from
Paxinos et al., 1985).
I
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