Brain Science

https://t.me/MBS_MedicalBooksStore

Noriko Kumazawa-Manita
Tsutomu Hashikawa
Atsushi Iriki

The 3D
Stereotaxic
Brain Atlas
of the Degu
With MRI and Histology Digital Model
with a Freely Rotatable Viewer
Brain Science
Series Editors
Hideyuki Okano
School of Medicine
Keio University
Shinjuku-ku, Tokyo, Japan

Atsushi Iriki
Laboratory for Symbolic Cognitive Development
RIKEN Brain Science Institute &
RIKEN Center for Biosystems
Dynamics Research
Wako-shi, Saitama 
Japan
The “Brain Science Series” provides critical and comprehensive discussions
of the most significant areas of neuroscience research, written by scientific
leaders and authorities. Each volume in the series presents the latest and most
complete information on its respective subject, making it an unrivalled
reference source. To analyze brain functions that have been preserved through
evolution, a reductive approach based on gene manipulation using models
such as genetically modified rodents were mainly used. At the same time, to
analyze high-order brain functions that are uniquely acquired only in non-­
human primates and humans, analyses of complex behaviors using a
psychological approach were mainly adopted. The Brain Science Series
focuses on clarifying the operating principles of the neural circuitry governing
the human mind, as well as the accompanying molecular mechanisms.

More information about this series at http://www.springer.com/series/13473

Noriko Kumazawa-­Manita
Tsutomu Hashikawa • Atsushi Iriki

The 3D Stereotaxic
Brain Atlas of the Degu
With MRI and Histology Digital
Model with a Freely Rotatable
Viewer
Noriko Kumazawa-Manita Tsutomu Hashikawa
Laboratory for Symbolic Cognitive RIKEN Brain Science Institute
Development Wako-shi, Saitama
RIKEN Brain Science Institute Japan
Wako-shi, Saitama
Japan

Atsushi Iriki
Laboratory for Symbolic Cognitive
Development
RIKEN Brain Science Institute &
RIKEN Center for Biosystems
Dynamics Research
Wako‐shi, Saitama
Japan

ISSN 2570-0197     ISSN 2570-0200 (electronic)

Brain Science
ISBN 978-4-431-56613-7    ISBN 978-4-431-56615-1 (eBook)
https://doi.org/10.1007/978-4-431-56615-1

Library of Congress Control Number: 2018946539

© Springer Japan KK, part of Springer Nature 2018

This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or
part of the material is concerned, specifically the rights of translation, reprinting, reuse of
illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way,
and transmission or information storage and retrieval, electronic adaptation, computer software,
or by similar or dissimilar methodology now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this
publication does not imply, even in the absence of a specific statement, that such names are
exempt from the relevant protective laws and regulations and therefore free for general use.
The publisher, the authors and the editors are safe to assume that the advice and information in
this book are believed to be true and accurate at the date of publication. Neither the publisher nor
the authors or the editors give a warranty, express or implied, with respect to the material
contained herein or for any errors or omissions that may have been made. The publisher remains
neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Printed on acid-free paper

This Springer imprint is published by the registered company Springer Japan KK part of Springer
Nature
The registered company address is: Shiroyama Trust Tower, 4-3-1 Toranomon, Minato-ku,
Tokyo 105-6005, Japan
Preface

In these decades, the availability of rodent degu, Octodon degus, has increased
in experimental medicine, representatively in the field of diabetes research. In
addition, recently much attention has been made in the fields of neuroscience
as well. Since they have characteristic social activities and behavior, they can
be one of the favorable animal models in the field of research of cognitive
brain functions. Aging-related brain dysfunction in humans, e.g., Parkinson’s
and Alzheimer’s diseases, also needs intensive studies in animal models.
Degu has been known certainly to be such a model. Under these circum-
stances and in order to facilitate researches in the field of neurosciences, it
seems necessary to provide a brain atlas specialized to this animal species.
Expanding an appreciation for a previous pioneer atlas by Wright and Kern
(1992), several useful functions are given in the present web-accessible atlas,
based on the powerful features of the three-dimensional and volume-­rendering
reconstructions. Taking into consideration of a modern examination with
magnetic resonance imaging (MRI) technologies, the present model is con-
structed by combining the architectonic information of Nissl sections with
that of MRI planes at corresponding levels.

Wako-shi, Japan Noriko Kumazawa-Manita

Wako-shi, Japan  Tsutomu Hashikawa
Wako-shi, Japan  Atsushi Iriki

v
Acknowledgments

We thank M. Katayama, R. Nakatomi, E. Kariya, R. Yanari, and Y. Sato (BSI)

for their excellent technical support. We thank Neuroinformatics Japan Center
for constructing this database with the Neuroinformatics Base Platform
System "XooNIps.” This database is supported by BSI-NI (BSI
Neuroinformatics) project. Supported by grants KAKENHI 18020035

vii
Contents

1 Introduction, Materials and Methods, and References����������������    1

2 Structure Lists����������������������������������������������������������������������������������    9
3 The Degu Brain Atlas in Stereotaxic Coordinates������������������������   21
4 Operation of Web-Accessible Volume-Rendering
Model of the Degu Brain����������������������������������������������������������������  109
Index of Structures��������������������������������������������������������������������������������  129
Index of Abbreviations��������������������������������������������������������������������������  137

ix
 Introduction, Materials
and Methods, and References
Introduction
Background
Degu (Octodon degus), a rodent native to the
Andes Mountains in South America, is commonly
known as the trumpet-tailed rat and belongs to the
parvorder Caviomorpha along with the chinchilla
and guinea pig. As experimental animal models,
degus contribute to a variety of medical research
fields, for example, those pertaining to diabetes,
hyperglycemia, pancreatic function, and adapta-
tion to high altitude (Bock et al. 2012; Braun et al.
1997; Colonnello et al. 2011; Ebensperger et al.
2011; Spear et al. 1984; Vosko et al. 2009). The
degu recently gained increasing importance in the
field of neuroscience, particularly in studies eval-
uating the relationship between sociality and cog-
nitive brain functions (Fuchs et al. 2010; Helmeke
© Springer Japan KK, part of Springer Nature 2018
N. Kumazawa-Manita et al., The 3D Stereotaxic Brain Atlas of the Degu, Brain Science,
https://doi.org/10.1007/978-4-431-56615-1_1
1
et  al. 2009) and studies pertaining to the evolu-
tional aspects of the acquisition of tool-use
­abilities (Braun et  al. 2012; Braidy et  al. 2012;
Kumazawa-Manita et al. 2013a; Lee et al. 2004;
Okanoya et al. 2008; Purger et al. 2009; Quirici
et  al. 2008; Uekita and Okanoya 2011).
Furthermore, aging-related brain dysfunction in
humans can be studied using this animal model, in
addition to some mammals with much longer life
spans than the degu (Inestrosa et  al. 2005; van
Groen et al. 2011).
The present degu brain atlas was constructed to
provide histological and volume-rendered informa-
tion simultaneously, fitting with any spatial coordi-
nation in brain positioning. It can be a useful guide
in degus as well as other rodents for studies of brain
structures conducted using magnetic resonance
imaging (MRI) or other contemporary examination
methods with volume-rendering functions.
1
2 1  Introduction, Materials and Methods, and References

Advantages of the Present Atlas the corresponding MR images. As a result, the

Nissl-stained images could be merged onto MR
Although all rodent brain atlases published so far images, and a three-dimensional (3D) brain atlas
(Aggarwal et al. 2011; Franklin and Paxinos could be constructed using both information
2008; Hjornevik et al. 2007; Toga et al. 1995, types simultaneously. The previously developed
1989; Purger et al. 2009), including one concern- stereotaxic brain atlas of the degu included only
ing degus (Schwarz et al. 2006; Wright and Kern line drawings without histology (Wright and
1992), can be used as references, this atlas has Kern 1992). In contrast, the present atlas includes
several advantages because it is a digital volume-­ a lot of information that facilitates the histologi-
rendered atlas that is web-accessible, and can be cal assessment of in  vivo MRI data. 3D recon-
freely rotated, permitting arbitrary sectioning and struction of serial Nissl-stained and digital MR
axis readjustment. In the present atlas, the origi- images of the degu brain is found at http://brain-
nal plane of histological sections for image atlas.brain.riken.jp/degu/modules/xoonips/list-
acquisition was coronal and perpendicular to the item.php?index_id=24 (Fig. 1.2).
longitudinal axis of the brain, which is common
in rodent brains, and its horizontal zero axis (a) Surface view
passed through the external acoustic meatus and The entire brain surface can be viewed from
maxillary incisor. In Chap. 3 (Figs. 3.1–3.84), any direction in this model (Fig. 1.2a). One
MR images, practical Nissl coronal images, and can rotate the surface images freely on the
line drawings, which are depicted with annota- display. This function may be convenient as
tions observable typical structures, are shown it enables a simple and rough localization of
with classical stereotaxic coordinates (Fig.  1.1 the brain areas in question.
left). (
b) Arbitrary sectioning
It is possible to reconstruct conventional ste- In this model, coronal, horizontal, sagittal,
reotaxic coordinates from this volume-rendered and any other planes of sectional images of
model. As shown in Chap. 3 (Figs. 3.85–3.86), brain structures can be cut arbitrarily.
the horizontal zero axis is inclined anteriorly Because the main structures are annotated in
upward 40°, so that it is adjusted to the AC–PC the volume-­rendered model, the composition
line (Wright and Kern 1992). Under this condi- of brain regions cut at any level and direction
tion, conventional coronal sections were obtained can be specified in such planes (Fig.  1.2b).
with stereotaxic coordinates and annotations in This function is also favorable for a 3D
the structures (Fig. 1.1 right). reconstruction of individual structures to
Because MR images of the brain fixed within understand their form and location in space
the skull were acquired, we assume that the brain in the brain.
structures would be in their correct positions. In (c) Adjustment to the stereotaxic coordinates
contrast, much finer information of the brain Expanding an arbitrary sectioning function,
structures in the same animal can be obtained the horizontal zero axis is adjusted to the
from Nissl-stained images because the original AC–PC line to construct an atlas with stereo-
resolution of Nissl-stained images (5214 × 5673, taxic coordinates, namely, zero levels of the
72 pixels/inch) is higher than that of MR images external acoustic foramen and the midline of
(512 × 512, 72 pixels/inch). The present volume-­ the hemisphere for coronal and sagittal
rendered model was constructed from histologi- planes. In Chap. 3 (Figs. 3.85–3.86), the
cal images obtained from 50-μm-thick adjusted stereotaxic histological planes are
Nissl-stained sections with 100-μm intervals. shown with the corresponding MR images
These histological images were aligned within (Kumazawa-Manita, et al. 2013b).
Introduction 3

Y
PC

Y Y
Z

AC

Z Z
X

40°

Fig. 1.1 Drawings showing the difference between around the interaural line of the “practical” brain position
­“practical” (left) and “conventional” (right) coordination results in its “conventional” position with the axis of the
in brain positioning. Forty-degree clockwise rotation AC–PC line as a horizontal zero (center)

a b

Fig. 1.2  Surface view of whole brain or individual internal exemplified here. (a) Lateral view (rostral on the left). (b)
structures can be reconstructed from the present 3D model. Arbitrary cut plane passing through the middle portion of
3D expansion of the cerebral cortex (yellow green), the hippocampus (blue)
­olfactory bulb (yellow), and hippocampus (green/blue) is
4 1  Introduction, Materials and Methods, and References
Materials and Methods
Subjects
The present brain atlas is based on an analysis of
the brains of six degus weighing 218.0–258.1 g
(mean ± SE, 235.9 ± 6.8) that were obtained from
colonies maintained in the Laboratory for
Symbolic Cognitive Development, BSI,
RIKEN. Each animal was housed in a steel cage
with its family (width  ×  length  ×  height,
90 × 45 × 45 cm) under environment-rich condi-
tions. Each cage contained running wheels, a
wood house, and a wood tunnel. The animals
were exposed daily to a 12-h/12-h light/dark
cycle at ambient temperatures close to 20°C. They
had ad libitum access to food and fresh water.
Because degus cannot generate certain vitamins
by themselves, the drinking water contained vita-
mins. The representative images presented in
Mini Atlas-a were obtained from a 22-month-old
male degu (body weight, 245 g).
Surgery
On the stereotaxic apparatus, on which horizontal
or coronal zero axes were adjusted to the line
through the maxillary incisor and external acous-
tic meatus or the interaural line, respectively, the
a b
Fig. 1.3  Surface anatomy of the degu’s fixed brain: (a)
View from the top, (b) View from the side. The first refer-
ence shaft was placed along the vertical plane 2.0  mm
lateral to the ear bar zero in the right hemisphere (a, right
white arrowhead). The second shaft was placed 50  mm
distance between coronal zero and the suture
bregma was calculated on their skull as an index
of brain size variation, ranging from 5.9  mm to
7.2 mm (6.8 ± 0.2 SE). All experimental protocols
were approved by the RIKEN Animal Experiment
Committee and performed in accordance with the
US National Institute of Health Guide for the
Care and Use of Laboratory Animals.
Each animal was deeply anesthetized with
sodium pentobarbital (200  mg/kg intraperitone-
ally), which was perfused through the left ven-
tricle with 20 ml 0.8% sodium chloride followed
by 200 ml 4% paraformaldehyde (PFA) in 0.1 M
phosphate buffer (pH 7.4), and placed on a ste-
reotaxic apparatus for small animals (Narishige,
Tokyo, Japan). The incisor bar was elevated
4.0  mm above the horizontal plane of the ear
bars, so that the horizontal zero plane passed
through the AC–PC line (Wright and Kern 1992).
Two reference tracts with carbon shafts (diame-
ter  =  0.2  mm) were made perpendicular to the
horizontal plane through the surface of the cere-
bral cortex: The first shaft was placed along the
vertical plane 1.0 mm and 2.0 mm lateral to the
midline in the right hemisphere and the second
one was placed 5.0 mm anteriorly to the first. An
additional reference was placed horizontally
through the cerebellum: 1.5  mm lateral to the
midline and 0.7  mm above the horizontal zero
(Fig. 1.3).
anterior to the first shaft (a, left white arrowhead). The
third shaft is placed perpendicular to the coronal plane
made from the posterior of the brain at 0.7 mm above the
horizontal zero and 1.5 mm lateral to the midline (a and b,
white arrow)
Materials and Methods
Histology
The animal’s head was then separated from the
body and stored for approximately 2 days in 4%
PFA at 4 °C. After the lower jaw and soft tissues
around the skull were removed, the skull with the
brain was transferred onto an MRI holder (see
below). Following the acquisition of MRI data,
the brain was removed from the skull and
­prepared for histological examination as follows.
The brain was immersed in 30% sucrose until it
sunk, followed by immersion in 10% gelatin at
60  °C for 1  h. Then, it was embedded in 10%
gelatin in the refrigerator. The gelatin-embedded
brain was immersed in 4% PFA for a few days
followed by immersion in 30% sucrose until it
sunk again. Serial subcoronal sections with
50-μm thickness were cut on a freezing micro-
tome. Nissl sections were stained with thionin.
Of note, in the present histological examination,
the subcoronal plane inclined the stereotaxic
plane anteriorly at a 40-degree angle. In this situ-
ation, the longitudinal line of the brain was
mostly parallel to the interaural line through the
maxillary incisor lines of the skull, a line that cor-
responds to a horizontal zero axis applied classi-
cally in rodent atlases. The present coronal plane
is more practical than that of their stereotaxic
coordinates because, in contrast to cutting sec-
tions adjusted to their stereotaxic coordinates,
coronal sections can easily be obtained, particu-
larly after removing the brain from the skull.
In the present materials, no prominent shrink-
age was observed based on the calculation of
positional changes of markers, probably due to
proper holding of the brain under gentle fixation
in the skull. If some partial shrinkage or wrinkles
were observed in sections, then Nissl-stained
images from such sections were replaced by a
neighboring image to avoid errors in image
rendering.
MRI
An MRI holder carrying the degu brain that was
simultaneously used in histological analysis was
transferred to an MRI machine. MRI scans were
5
performed using a 9.4-T Advance 400WB NMR
spectrometer (Bruker Biospin GmbH,
Rheinstetten, Germany) with a standard Micro
2.5 microimaging system. The inner diameter of
the integrated transmitting and receiving coil was
25 mm. Each scan took approximately 1.5 h. A
3D model of MR images was constructed using
“SG-eye” software, which was codeveloped by
Fiatlux (Tokyo, Japan).
Photography and Drawings
Photomicrographs were obtained as tif files from
the Nissl-stained sections using a virtual slide
scanner, the NanoZoomer 2.0-HT digital slide
(Hamamatsu Photonics, Hamamatsu, Japan). The
resolution of the original tif images was lowered
to 70% to ensure a maximum file size of
2  GB.  Mask images for each brain region were
prepared through Nissl-stained images using a
path function in Photoshop (Adobe, San Jose,
CA, USA), following which they were converted
using SG-eye (Fiatlux) to construct a 3D digital
volume-rendered brain model.
In the drawings, fiber tracts are outlined by
solid gray lines, and nuclei and cell groups are
outlined by solid lines with ID colors assigned to
each structure, as listed in Chap. 3. In general,
each abbreviation is placed in the center of the
structure to which it relates; where this is not pos-
sible, the abbreviation is placed alongside the
structure, and a leader line is used. (The abbrevi-
ations for fiber tracts and fissures are positioned
on the left side of the figure, and abbreviations
for nuclei and other cell groups are positioned on
the right side. The outlines of the ventricles and
aqueduct are filled in with solid color).
Nomenclature
Previously described brain atlases of the degu
were stereotaxic two-dimensional line-drawing
atlases using Latin anatomical terms (Wright and
Kern 1992). However, in the present atlas, we fol-
lowed the English anatomical terms adopted in
“The Rat Brain in Stereotaxic Coordinate”
6 1  Introduction, Materials and Methods, and References
(Paxinos and Watson 2009), which are currently
becoming popular terminology for rodent brain
structures. As control functional areas have not
been confirmed in this species, such areas are
identified tentatively by their cytoarchitectonic
features, following the control delineation in the
rat, and given in parentheses.
References
Aggarwal M, Zhang J, Mori S (2011) Magnetic resonance
imaging-based mouse brain atlas and its applications.
Methods Mol Biol 711:251–270
Bock J, Riedel A, Braun K (2012) Differential changes of
metabolic brain activity and interregional functional
coupling in prefronto-limbic pathways during dif-
ferent stress conditions: functional imaging in freely
behaving rodent pups. Front Cell Neurosci 6:19
Braidy N, Muñoz P, Palacios AG, Castellano-Gonzalez
G, Inestrosa NC, Chung RS, Sachdev P, Guillemin
GJ (2012) Recent rodent models for Alzheimer’s dis-
ease: clinical implications and basic research. J Neural
Transm 119:173–195
Braun K, Seidel K, Holetschka R, Groeger N, Poeggel
G (2012) Paternal deprivation alters the develop-
ment of catecholaminergic innervation in the pre-
frontal cortex and related limbic brain regions. Brain
Struct Funct 218(4):859–872. https://doi.org/10.1007/
s00429-012-0434-1
Braun S, Scheich H (1997) Influence of experience on
the representation of the “mothering call” in fron-
toparietal and auditory cortex of pups of the rodent
Octodon Degus: FDG mapping. J Comp Physiol A
181:697–709
Colonnello V, Iacobucci P, Fuchs T, Newberry RC,
Panksepp J (2011) Octodon Degus. A useful animal
model for social-affective neuroscience research: basic
description of separation distress, social attachments
and play. Neurosci Biobehav Rev 35:1854–1863
Ebensperger LA, Ramírez-Estrada J, León C, Castro
RA, Tolhuysen LO, Sobrero R, Quirici V, Burger JR,
Soto-Gamboa M, Hayes LD (2011) Sociality, gluco-
corticoids and direct fitness in the communally rearing
rodent, Octodon Degus. Horm Behav 60:346–352
Fuchs T, Iacobucci P, MacKinnon KM, Panksepp J (2010)
Infant-mother recognition in a social rodent (Octodon
degus). J Comp Psychol. 124:166–175
Franklin KBJ, Paxinos G (2008) The mouse brain in ste-
reotaxic coordinates compact third edition. Elsevier,
London
Helmeke C, Seidel K, Poeggel G, Bredy TW, Abraham
A, Braun K (2009) Paternal deprivation during
infancy results in dendrite- and time-specific changes
of ­dendritic development and spine formation in the
orbitofrontal cortex of the biparental rodent Octodon
Degus. Neuroscience 163:790–798
Hjornevik T, Leergaard TB, Darine D, Moldestad O, Dale
AM, Willoch F, Bjaalie JG (2007) Three-dimensional
atlas system for mouse and rat brain imaging data.
Front Neuroinform 1:4
Inestrosa NC, Reyes AE, Chacón MA, Cerpa W,
Villalón A, Montiel J, Merabachvili G, Aldunate R,
Bozinovic F, Aboitiz F (2005) Human-like rodent
amyloid-beta-­peptide determines Alzheimer pathol-
ogy in aged wild-­ type Octodon degu. Neurobiol
Aging 26:1023–1028
Kumazawa-Manita N, Hama H, Miyawaki A, Iriki A
(2013a) Tool use specific adult neurogenesis and syn-
aptogenesis in rodent (Octodon Degus) hippocampus.
PLoS One 8(3):e58649
Kumazawa-Manita N, Katayama M, Hashikawa T, Iriki
A (2013b) Three-dimensional reconstruction of brain
structures of the rodent Octodon Degus: a brain atlas
constructed by combining histological and magnetic
resonance images. Exp Brain Res 231(1):65–74
Lee TM (2004) Octodon Degus: a diurnal, social, and
long-lived rodent. ILAR J 45:14–24
Okanoya K, Tokimoto N, Kumazawa N, Hihara S, Iriki
A (2008) Tool-use training in a species of rodent: the
emergence of an optimal motor strategy and func-
tional understanding. PLoS One 3:e1860. https://doi.
org/10.1371/journal.pone.0001860
Paxinos G, Watson C (2009) The rat brain in stereotaxic
coordinate. Academic Press, Cambridge
Poeggel G, Braun K (1996) Early auditory filial learning
in degus (Octodon Degus): behavioral and autoradio-
graphic studies. Brain Res 743:162–170
Purger D, McNutt T, Achanta P, Quiñones-Hinojosa A,
Wong J, Ford E (2009) A histology-based atlas of
the C57BL/6J mouse brain deformably registered to
in vivo MRI for localized radiation and surgical target-
ing. Phys Med Biol 54:7315–7327
Quirici V, Castro RA, Oyarzún J, Ebensperger LA
(2008) Female degus (Octodon Degus) monitor their
environment while foraging socially. Anim Cogn
11:441–448
Schwarz AJ, Danckaert A, Reese T, Gozzi A, Paxinos G,
Watson C, Merlo-Pich EV, Bifone A (2006) A stereotaxic
MRI template set for the rat brain with tissue class distri-
bution maps and co-registered anatomical atlas: applica-
tion to pharmacological MRI. NeuroImage 32:538–550
Spear GS, Caple MV, Sutherland LR (1984) The pancreas
in the degu. Exp Mol Pathol 40:295–310
Toga AW, Santori EM, Hazani R, Ambach K (1995) A 3D
digital map of rat brain. Brain Res Bull 38:77–85
Toga AW, Samaie M, Payne BA (1989) Digital rat brain: a
computerized atlas. Brain Res Bull 22:323–333
Uekita T, Okanoya K (2011) Hippocampus lesions
induced deficits in social and spatial recognition in
Octodon Degus. Behav Brain Res 219:302–309
References
van Groen T, Kadish I, Popović N, Popović M, Caballero-­
Bleda M, Baño-Otálora B, Vivanco P, Rol MÁ, Madrid
JA (2011) Age-related brain pathology in Octodon
degu: blood vessel, white matter and Alzheimer-like
pathology. Neurobiol Aging 32:1651–1661
Vosko AM, Hagenauer MH, Hummer DL, Lee TM (2009)
Period gene expression in the diurnal degu (Octodon
7
Degus) differs from the nocturnal laboratory rat
(Rattus Norvegicus). Am J Physiol Regul Integr Comp
Physiol 296:R353–R361
Wright JW, Kern MD (1992) Stereotaxic atlas of the brain
of Octodon Degus. J Morphol 214:299–320
 Structure Lists
This annotated brain structure list, is a tool for
using the web-accessible brain atlas, as well as
for the Chapter 3 of this book. Structures are
arranged in a hierarchical organization, depicted
together with their abbreviations. Assigned
unique color for each brain region corresponds to
© Springer Japan KK, part of Springer Nature 2018
N. Kumazawa-Manita et al., The 3D Stereotaxic Brain Atlas of the Degu, Brain Science,
https://doi.org/10.1007/978-4-431-56615-1_2
2
the illustration in web-accessible brain atlas,
which has a function searching for structures by
the abbreviations. Further details can be referred
to “Operation manual of web-accessible volume-
rendering model of the Degu Brain” in the
Chapter 4 of this book.
9
10 2  Structure Lists

WHOLE BRAIN WHOLE

1. FOREBRAIN (TELENCEPHALON and DIENCEPHALON) FORE
TELENCEPHALON TEL
OLFACTORY BULB OLB
Olfactory bulb OB
Accessory olfactory bulb AOB
Anterior olfactory nucleus AON
Ependyma & subependymal layer E
External plexiform layer of the accessory olfactory bulb EPlA
External plexiform layer of the olfactory bulb EPl
Glomerular layer of the accessory olfactory bulb GlA
Glomerular layer of the olfactory bulb Gl
Granule cell layer of the accessory olfactory bulb GrA
Granule cell layer of the olfactory bulb GrO
Internal plexiform layer of the olfactory bulb IPl
Mitral cell layer of the accessory olfactory bulb MiA
Mitral cell layer of the olfactory bulb Mi
Olfactory nerve layer ON
CEREBRUM/CEREBRAL CORTEX CER
Olfactory cortex OlfC
Tenia tecta TT
Olfactry tubercle Tu
Islands of Calleja ICj
Islands of Calleja/major island ICjM
Cortical areas CorA
Agranular insular cortex AI
Auditory cortex/primary area Au1
Cingulate cortex Cg
Dysgranular insular cortex DI
Entorhinal cortex Ent
Faciola cinereum FC
Granular insular cortex GI
Indusium griseum IG
Motor cortex/primary area M1
Navicular nucleus of the basal forebrain Nv
Orbital cortex Orb
Parasubiculum PaS
Piriform cortex Pir
Piriform cortex/layer 1 Pir 1
Piriform cortex/layer 2 Pir 2
Piriform cortex/layer 3 Pir 3
Postsubiculum Post
Presubiculum PrS
Retrosplenial dysgranular cortex RSD
Retrosplenial granular cortex RSG
Somatosensory cortex/primary area S1
Visual cortex/ primary area V1
Hippocampal formation HipF
Dentate gyrus DG
Granule cell layer of the dentate gyrus GrDG
Molecular layer of the dentate gyrus MoDG
Polymorph layer of the dentate gyrus PoDG
Hippocampus Hip
Field CA1 of the hippocampus CA1
Field CA2 of the hippocampus CA2
Field CA3 of the hippocampus CA3
Lacunosum moleculare layer of the hippocampus LMol
Oriens layer of the hippocampus Or
Pyramidal cell layer of the hippocampus Py
Radiatum layer of the hippocampus Rad
Stratum lucidum of the hippocampus SLu
Subiculum S
Dorsal subiculum DS
Ventral subiculum VS
2  Structure Lists 11

WHOLE BRAIN (cont’d) WHOLE

1. FOREBRAIN (TELENCEPHALON and DIENCEPHALON) (cont’d) FORE
䚷䕻TELENCEPHALON (cont’d) TEL
䚷䚷䖂 BASAL GANGLIA BG
Amygdala AMG
Amygdalohippocampal area AHi
Cortical amygdaloid group (corticomedial group) CoAG
Central amygdaloid nucleus Ce
Central amygdaloid nucleus/capular part CeC
Central amygdaloid nucleus/lateral part CeL
Central amygdaloid nucleus/medial part CeM
Cortical amygdaloid nucleus Co
Anterior amygdaloid area AA
Antrior cortical amygdaloid nucleus Aco
Nucleus of the lateral olfactry tract LOT
Posterolateral cortical amygdaloid nucleus PLCo
Posteromedial cortical amygdaloid nucleus PMCo
Medial amygdaloid nucleus Me
Extended amygdala EXA
Bed nucleus of the stria terminalis ST
Bed nucleus of the stria terminalis/lateral division STL
Bed nucleus of the stria terminalis/medial division STM
Intercalated nuclei of the amygdala I
Interstitial nucleus of the posterior limb of the anterior commissure IPAC
Sublenticular extended amygdala EA
Latero-basal nuclear complex (basolateral group) Lbn
Basolateral amygdaloid nucleus BL
Basolateral amygdaloid nucleus/anterior part BLA
Basolateral amygdaloid nucleus/posterior part BLP
Basolateral amygdaloid nucleus/ventral part BLV
Basomedial amygdaloid nucleus BM
Basomedial amygdaloid nucleus/anterior part BMA
Basomedial amygdaloid nucleus/posterior part BMP
Lateral amygdaloid nucleus La
Lateral amygdaloid nucleus/dorsolateral part LaDL
Lateral amygdaloid nucleus/ventrolateral part LaVL
Lateral amygdaloid nucleus/ventromedial part LaVM
Basal nucleus (Meynert) B
Claustrum Cl
Dorsal endopiriform nucleus DEn
Globus pallidus GP
External globus pallidus (globus pallidus) EGP
Internal globus pallidus (ento-/or intrapeduncular nucleus) IGP
Substantia innominata SI
Substantia innominata/basal part SIB
Substantia innominata/dorsal part SID
Susbtantia innominata/ventral part SIV
Substantia nigra SN
Substantia nigra/compact part SNC
Substantia nigra/lateral part SNL
Substantia nigra/reticular part SNR
Striatum St
Accumbens nucleus Acb
Accumbens nucleus/core AcbC
Accumbens nucleus/shell AcbSh
Caudate putamen (striatum) Cpu
Subthalamic nucleus STh
Ventral endopiriform nucleus VEn
Ventral pallidum VP
䚷䚷䖂SEPTUM SEP
Lateral septal nucleus LS
Lateral septal nucleus/dorsal part LSD
Lateral septal nucleus/intermediate part LSI
Lateral septal nucleus/ventral part LSV
Medial septal nucleus MS
Nucleus of the horizontal limb of the diagonal band HDB
Nucleus of the vertical limb of the diagonal band VDB
Septofimbrial nucleus SFi
Septohippocampal nucleus SHi
Triangular septal nucleus TS
12 2  Structure Lists

WHOLE BRAIN (cont'd) WHOLE

1. FOREBRAIN (TELENCEPHALON and DIENCEPHALON) (cont'd) FORE
DIENCEPHALON DIEN
THALAMUS THAL
Association nuclei ASN
Anterior nuclei ANN
Anterodorsal thalamic nucleus AD
Anteromedial thalamic nucleus AM
Anteroventral thalamic nucleus AV
Lateral nuclei LTN
Lateral posterior thalamic nucleus LP
Laterodorsal (or lateral dorsal) thalamic nucleus LD
Mediodorsal thalamic nucleus MD
Mediodorsal thalamic nucleus/lateral part MDL
Mediodorsal thalamic nucleus/medial part MDM
Paratenial thalamic nucleus PT
Auditory thalamus AuT
Medial geniculate nucleus MG
Medial geniculate nucleus/dorsal part MGD
Medial geniculate nucleus/medial part MGM
Medial geniculate nucleus/ventral part MGV
Midline and intralaminar nuclei MIN
Angular thalamic nucleus Ang
Central medial thalamic nucleus CM
Centrolateral thalamic nucleus CL
Interanterodorsal thalamic nucleus IAD
Interanteromedial thalamic nucleus IAM
Intermediodorsal thalamic nucleus IMD
Oval paracentral thalamic nucleus OPC
Paracentral thalamic nucleus PC
Parafascicular thalamic nucleus PaF
Retroreuniens area RRe
Reuniens thalamic nucleus Re
Rhomboid thalamic nucleus Rh
Xiphoid thalamic nucleus Xi
Motor thalamus MTT
Ventral anterior thalamic nucleus VA
Ventrolateral thalamic nucleus VL
Ventromedial thalamic nucleus VM
Somatosensory thalamus SST
Posterior thalamic nuclear group Po
Suprageniculate thalamic nucleus SG
Ventral posterolateral thalamic nucleus VPL
Ventral posteromedial thalamic nucleus VPM
Ventral thalamus VNT
Parasubthalamic nucleus PSTh
Reticular thalamic nucleus Rt
Subparafiscicular thalamic nucleus SPF
Zona incerta ZI
Zona incerta/caudal part ZIC
Zona incerta/dorsal part ZID
Zona incerta/rostral part ZIR
Zona incerta/ventral part ZIV
Visual thalamus VST
Dorsal lateral geniculate nucleus DLG
Ventral lateral geniculate nucleus VG
EPITHALAMUS EPI
Habenular nucleus Hb
Lateral habenular nucleus LHb
Medial habenular nucleus MHb
Paraventricular thalamic nucleus PV
Paraventricular thalamic nucleus/anterior part PVA
Paraventricular thalamic nucleus/posterior part PVP
2  Structure Lists 13

WHOLE BRAIN (cont'd) WHOLE

1. FOREBRAIN (TELENCEPHALON and DIENCEPHALON) (cont'd) FORE
䚷䚷䚷㻌䖂DIENCEPHALON (cont'd) DIEN
HYPOTHALAMUS HYPO
Anterior hypothalamic area AH
Arcuate hypothalamic nucleus Arc
Dorsomedial hypothalamic nucleus DM
Dorsomedial hypothalamic nucleus/compact part DMC
Dorsomedial hypothalamic nucleus/dorsal part DMD
Lamina terminalis Lter
Lateral hypothalamic area LH
Lateral mammillary nucleus LM
Mamillary body MB
Medial mamillary nucleus/lateral part ML
Medial mamillary nucleus/medial part MM
Medial mamillary nucleus/median part MnM
Medial preoptic nucleus MPO
Medial tuberal nucleus MTu
Nucleus of the stria medullaris SM
Paraventricular hypothalamic nucleus Pa
Periventricular hypothalamic nucleus Pe
Posterior hypothalamic area PHA
Posterior hypothalamic nucleus PH
Premamillary nucleus PrM
Preoptic area PO
Lateral preoptic area LPO
Medial preoptic area MPA
Medial preoptic nucleus MPO
Median preoptic nucleus MnPO
Ventrolateral preoptic nucleus VLPO
Ventromedial preoptic nucleus VMPO
Suprachiasmatic nucleus SCh
Suprachiasmatic nucleus/ventromedial part SChVM
Suprachiasmatic nucleus/dorsolateral part SChDL
Supraoptic nucleus SO
Ventromedial hypothalamic nucleus VMH
Ventral tuberomamillary nucleus VTM
Terete hypothalamic nucleus Te
䚷䚷䚷㻌䖂PRETECTUM Pt
Anterior pretectal nucleus APT
Magnocellular nucleus of the posterior commissure MCPC
Medial pretectal nucleus MPT
Olivary pretectal nucleus OPT
Nucleus of the optic tract OT
Posterior pretectal nucleus PPT
14 2  Structure Lists

WHOLE BRAIN (cont’d) WHOLE

2䠊BRAIN STEM (MIDBRAIN+PONS+MEDULLA OBLONGATA) STEM
䕻MIDBRAIN (MESENCEPHALON) MID
Commissural nucleus of the inferior colliculus Com
Edinger-Westphal nucleus EW
Inferior colliculus IC
Central nucleus of the inferior colliculus CIC
Dorsal cortex of the inferior colliculus DCIC
External cortex of the inferior colliculus ECIC
Interpeduncular nucleus IP
Interpeduncular nucleus/caudal subnucleus IPC
Interpeduncular nucleus/intermediate subnucleus IPI
Interpeduncular nucleus/lateral subnucleus IPL
Interpeduncular nucleus/rostrall subnucleus IPR
Interstitial nucleus of Cajal InC
Mesencephalic trigeminal nucleus Me5
Nucleus of Darkschewitsch Dk
Nuclus of the brachium of the inferior colliculus BIC
Nucleus of the posterior commissure PCom
Oculomotor nucleus 3N
Oculomotor nucleus/parvicellular part 3PC
Periaqueductal gray PAG
Supraoculomotor cap Su3C
Supraoculomotor periaqueductal gray Su3
Raphe nuclei RaMID
Dorsal raphe nucleus DR
Dorsal raphe nucleus/caudal part DRC
Dorsal raphe nucleus/dorsal part DRD
Dorsal raphe nucleus/lateral part DRL
Dorsal raphe nucleus/ventral part DRV
Rostral linear nucleusof the raphe RLi
Red nucleus R
Red nucleus/magnocellular part RMC
Red nucleus/parvocellular part RPC
Reticular formation RtMID
Cuneinform nucleus CnF
Mesencephalic reticular formation MeRt
Substantia nigra SNMID
Superior colliculus SC
Deep gray layer of the superior colliculus DpG
Deep white layer of the superior colliculus DpWh
Intermediate gray layer of the superior colliculus InG
Intermediate white layer of the superior colliculus InWh
Optic nerve layer of the superior colliculus Op
Superficial gray layer of the superior colliculcus SuG
Zonal layer ofthe superior colliculus Zo
Trochlear nucleus 4N
Ventral tegmental area VTA
䚷䚷䚷 䖂 PONS (METENCEPHALON) PONS
Abducens nucleus 6N
Central gray CG
Cochlear nuclei C
Dorsal cochlear nucleus DC
Dorsal cochlear nucleus/deep core DCDp
Dorsal cochlear nucleus/fusiform layer DCFu
Dorsal cochlear nucleus/molecular layer DCMo
Granule cell layer of the cochlear nuclei GrC
Ventral cochlear nucleus VC
Ventral cochlear nucleus/anterior part VCA
Ventral cochlear nucleus/posterior part VCP
Dorsal nucleus of the lateral lemniscus DLL
Dorsal tegmental nucleus DTgp
Facial nucleus 7N
Intermediate nucleus of the lateral lemniscus ILL
Lateral parabrachial nucleus LPB
Laterodorsal tegmental nucleus LDTg
Locus coeruleus LC
Medial parabrachial nucleus MPB
Motor trigeminal nucleus 5N
Nucleus of the spinal trigeminal tract Sp5PONS
Nucleus of the trapezoid body Tz
Parabigeminal nucleus PBG
Pontine nuclei Pn
Principal sensory trigeminal nucleus Pr5
2  Structure Lists 15

WHOLE BRAIN (cont’d) WHOLE

2䠊BRAIN STEM (MIDBRAIN+PONS+MEDULLA OBLONGATA) (cont’d) STEM
MIDBRAIN (MESENCEPHALON) (cont’d) MID
PONS (METENCEPHALON) (cont’d) PONS
Raphe nuclei RaPONS
Caudal linear nucleus of the raphe CLi
Dorsal raphe nucleus/caudal part DRC
Median raphe nucleus MnR
Paramedian raphe nucleus PMnR
Raphe interpositus nucleus RIP
Raphe magnus nucleus RMg
Rhabdoid nucleus Rbd
Reticular formation RtPONS
Pontine reticular nucleus/caudal part PnC
Pontine reticular nucleus/oral part PnO
Pontine reticular nucleus/ventral part PnV
Reticulotegmental nucleus of the pons RtTg
Reticulotegmental nucleus of the pons/lateral part RtTgL
Retroisthmic nucleus RIs
Retrolemniscal nucleus RL
Sagulum nucleus Sag
Subcoeruleus nucleus SubC
Subcoeruleus nucleus/alpha part SubCA
Subcoeruleus nucleus/dorsal part SubCD
Subcoeruleus nucleus/ventral part SubCV
Subpeduncular tegmental nucleus SPTg
Superior olive SOl
Dorsal periolivary region DPO
Lateral superior olive LSO
Lateroventral periolivary nucleus LVPO
Medial superior olive MSO
Medioventral periolivary nucleus MVPO
Superior paraolivary nucleus SPO
Supratrigeminal nucleus Su5
Triangular nucleus of the lateral lemniscus Tr
Ventral nucleus of the lateral lemniscus VLL
Ventral tegmental nucleus VTg
Vestibular nuclei VePONS
3䠊MEDULLA OBLONGATA (MYELENCEPHALON) MED
A1 noradrenaline cells A1
A2 noradrenaline cells A2
A5 noradrenaline cells A5
Accessory nerve nucleus 11N
Ambiguus nucleus Amb
Ambiguus nucleus/compact part AmbC
Ambiguus nucleus/loose part AmbL
C1 adrenaline cells C1
C2 adrenaline cells C2
C3 adrenaline cells C3
Central cervical nucleus CeCv
Conterminal nucleus Ct
Cuneate nucleus Cu
Dorsal motor nucleus of vagus 10N
Dorsal tegmental nucleus DTgm
Dorsal tegmental nucleus/central part DTgC
Dorsal tegmental nucleus/pericentral part DTgP
Dorsomedial tegmental area DMTg
Epifacicular nucleus EF
External cuneate nucleus ECu
Gracile nucleus Gr
Hypoglossal nucleus 12N
Intercalated nucleus of the medulla In
Interstitial nucleus of the vestibular part of the 8th nerve I8
Inferior olive IO
16 2  Structure Lists

WHOLE BRAIN (cont’d) WHOLE

3䠊MEDULLA OBLONGATA (MYELENCEPHALON) (cont’d) MED
Inferior olive/beta subnucleus of the medial nucleus IOBe
Inferior olive/cap of Kooy of the medial nucleus IOK
Inferior olive/dorsal nucleus IOD
Inferior olive/dorsomedial cell group IODM
Inferior olive/medial nucleus IOM
Inferior olive/principal nucleus IOPr
Inferior olive/subnucleus A of medial nucleus IOA
Inferior olive/subnucleus B of medial nucleus IOB
Inferior olive/subnucleus C of medial nucleus IOC
Inferior olive/ventrolateral prorusion IOVL
Inferior salivatory nucleus IS
Kolliker-Fuse nucleus KF
Lateral terminal nucleus of the accessory optic tract LT
Linear nucleus of the medulla Li
Matrix region of the medulla Mx
Median accessory nucleus of the medulla MnA
Nucleus of Roller Ro
Nucleus of the solitary tract Sol
Nucleus of the solitary tract/central part SolCe
Nucleus of the solitary tract/commissural part SolC
Nucleus of the solitary tract/dorsolateral part SolDL
Nucleus of the solitary tract/dorsomedial part SolDM
Nucleus of the solitary tract/gelatinous part SolG
Nucleus of the solitary tract/interstitial part SolI
Nucleus of the solitary tract/intermediate part SolIM
Nucleus of the solitary tract/lateral part SolL
Nucleus of the solitary tract/medial part SolM
Nucleus of the solitary tract/rostrolateral part SolRL
Nucleus of the solitary tract/ventral part SolV
Nucleus of the solitary tract/ventrolateral part SolVL
Nucleus of the spinal trigeminal tract Sp5MED
Spinal trigeminal nucleus/caudal part Sp5C
Spinal trigeminal nucleus/interpolar part Sp5I
Spinal trigeminal nucleus/oral part Sp5O
Nucleus X X
Parasolitary nucleus PSol
Prepositus nucleus Pr
Raphe nuclei RaMED
Raphe obscurus nucleus ROb
Raphe pallidus nucleus RPa
Reticular formation RtMED
Gigantocellular reticular nucleus Gi
Intermediate reticular nucleus IRt
Lateral paragigantocellular nucleus LPGi
Lateral reticular nucleus LRt
Lateral reticular nucleus/parvicellular part LRtPC
Medullary reticular nucleus MRt
Paramedian reticular nucleus PMn
Parvicellular reticular nucleus PCRt
Retroambiguus nucleus RAmb
Subpostrema area SubP
Superior salivatory nucleus SuS
Vestibular nuclei VeMED
Lateral vestibular nucleus LVe
Medial vestibular nucleus MVe
Medial vestibular nucleus/magnocellular part MVeMC
Medial vestibular nucleus/parvicellular part MVePC
Spinal vestibular nucleus SpVe
Superior vestibular nucleus SuVe
2  Structure Lists 17

WHOLE BRAIN (cont’d) WHOLE

4䠊CEREBELLUM (METENCEPHALON) CB
䚷䕻 Cerebellar cortex Cb
Copula of the pyramis Cop
Crus1 of the ansiform lobule Crus1
Crus2 of the ansiform lobule Crus2
Flocculus Fl
Lobule 1 of cerebellar vermis (lingula) 1Cb
Lobule 2 of cerebellar vermis 2Cb
Lobule 3 of cerebellar vermis 3Cb
Lobule 4 of cerebellar vermis 4Cb
Lobule 5 of cerebellar vermis 5Cb
Lobule 6 of cerebellar vermis 6Cb
Lobule 7 of cerebellar vermis 7Cb
Lobule 8 of cerebellar vermis 8Cb
Lobule 9 of cerebellar vermis (uvula) 9Cb
Lobule 10 of cerebellar vermis (nodule) 10Cb
Paraflocculus PFl
Paramedian lobule PM
Simple lobule Sim
Deep cerebellar nuclei Dc
Anterior interposed cerebellar nucleus IntA
Nucleus Y of the vestibular complex Y
Lateral (dentate) cerebellar nucleus Lat
Medial (fastigal) cerebellar nucleus Med
Posterior interposed cerebellar nucleus IntP
Vestibulocerebellar nucleus VeCb
Superior medullary velum SMV
18 2  Structure Lists

䕔 FIBER BUNDLE FB
Anterior commissure ac
Anterior commissure/anterior part aca
Anterior commissure/intrabulbar part aci
Anterior commissure/posterior limb acp
Alveus of the hippocampus alv
Ascending fibers of the facial nerve asc7
Brachium of the inferior colliculus bic
Brachium of the superior colliculus bsc
Cerebral peduncle cp
Cingulum cg
Commissure of the inferior colliculus cic
Commissure of the superior colliculus csc
Corpus callosum cc
Cuneate fasciculus cu
Decussation of the medial lemniscus mlx
Decussation of the superior cerebellar peduncle scpx
Dosal acoustic atria das
Dorsal corticospinal tract dcs
Dorsal spinocerebellar tract dsc
Dorsal tegmental decussation dtgx
External capsule ec
External medullary lamina eml
Fasciculus retroflexus fr
Fimbria of the hippocampus fi
Forceps major of the corpus callosum fmj
Forceps minor of the corpus callosum fmi
Fornix f
Genu of the corpus callosum gcc
Genu of the facial nerve g7
Gracile fasciculus gr
Habenular commissure hbc
Inferior cerebellar peduncle (restiform body) icp
Internal capsule ic
Internal medullary lamina iml
Lateral lemniscus ll
Lateral olfactory tract lo
Longitudinal fasciculus of the pons lfp
Mamillary peduncle mp
Mamillothalamic tract mt
Mamillotegmental tract mtg
Medial lemniscus ml
Medial longitudinal faciculcus mlf
Mesencephalic trigeminal tract me5
Middle cerebellar peduncle mcp
Motor root of the trigeminal nerve m5
Optic chiasm och
Optic tract opt
Posterior commissure pc
Pyramidal decussation pyx
Pyramidal tract py
Rostrum of the corpus callosum rcc
Rubrospinal tract rs
Sensory root of the trigeminal nerve s5
Solitary tract sol
Spinal trigeminal tract sp5
Splenium of the corpus callosum scc
Stria medullaris of the thalamus sm
Stria terminalis st
Superior cerebellar peduncle (brachium conjunctivum) scp
Tectospinal tract ts
Transverse fibers of the pons tfp
Trapezoid body tz
Uncinate fasciculus of the cerebellum un
Ventral hippocampal commissure vhc
Ventral spinocerebellar tract vsc
Ventral tegmental decussation vtgx
2  Structure Lists 19

CRANIAL NERVE CN
Abducens nerve 6n
Cochlear root of the vestibulocochlear nerve 8cn
Facial nerve 7n
Hypoglossal nerve 12n
Occulomotor nerve 3n
Trochlear nerve 4n
Trigeminal nerve 5n
Vagus nerve 10n
Vestibulocochlear nerve 8n
Vestibular root of the vestibulocochlear nerve 8vn
CIRCUMVENTRICULAR ORGAN CvO
Area postrema AP
Median eminence ME
Pineal gland Pi
Subcommissural organ SCO
Subfornical organ SFO
Vascular organ of the lamina terminalis VOLT
VENTRICLE V
Aqueduct Aq
Central canal CC
Fourth ventricle 4V
Interventricular foramen IVF
Lateral recess of the 4th ventricle LR4V
Lateral ventricle LV
Mamillary recess of the 3rd ventricle MRe
Olfactory ventricle (olfactory part of lateral ventricle) OV
Third ventricle 3V
SULCUS SUL
Ansoparamedian fissure ampf
Hippocampal fissure hif
Intercrural fissure icf
Parafloccular sulcus pfs
Posterior superior fissure psf
Posterolateral fissure plf
Preculminate fissure pcuf
Prepyramidal fissure ppf
Primary fissure prf
Simplex fissure simf
Rhinal fissure rf
 The Degu Brain Atlas
in Stereotaxic Coordinates 3

Fig. 3.1 through Fig. 3.84 Fig. 3.85, Fig. 3.86

Representative coronal Nissl sections and MRI Reconstructed coronal, horizontal and parasagit-
profiles. “Practical” plane with an interaural-inci- tal Nissl and MRI profiles. “Conventional” plane
sor line as a horizontal zero axis. with an AC-PC line as a horizontal zero axis.
Left pages (odd numbered pages) – Nissl Fig. 3.85 –Reconstructed coronal images.
images. Fig. 3.86 –Reconstructed horizontal (a) and
Right pages (even numbered pages) – Line para sagittal (b) images.
drawings overlaid on pale Nissl images, together
with corresponding MR images at top left corner.
Levels of sections (common with left pages) are
indicated by red line on the surface rendered
brain model on the left bottom corner.

© Springer Japan KK, part of Springer Nature 2018

N. Kumazawa-Manita et al., The 3D Stereotaxic Brain Atlas of the Degu, Brain Science, 21
https://doi.org/10.1007/978-4-431-56615-1_3
22 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 16.18

Fig. 3.1 
3  The Degu Brain Atlas in Stereotaxic Coordinates 23

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.2  Images for I:16.18. E/OV Ependyma and subep- GrO Granule cell layer of the olfactory bulb, IPl Internal
endymal layer/olfactory ventricle, EPl External plexiform plexiform layer of the olfactory bulb, Mi Mitral cell layer
layer of the olfactory bulb, GI Granular insular cortex, of the olfactory bulb, olf Olfactory nerve
24 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 15.52

Fig. 3.3 
3  The Degu Brain Atlas in Stereotaxic Coordinates 25

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.4  Images for I:15.52. aci Anterior commissure/ Granule cell layer of the accessory olfactory bulb, GrO
intrabulbar part, E/OV Ependyma and subependymal Granule cell layer of the olfactory bulb, IPl Internal plexi-
layer/olfactory ventricle, EPl External plexiform layer of form layer of the olfactory bulb, Mi Mitral cell layer of the
the olfactory bulb, GI Granular insular cortex, GrA olfactory bulb, olf Olfactory nerve
26 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 14.86

Fig. 3.5 
3  The Degu Brain Atlas in Stereotaxic Coordinates 27

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.6  Images for I: 14.86. aci Anterior commissure/
intrabulbar part, AO Anterior olfactory nucleus, dlo
Dorsal olfactory tract, E/OV Ependyma and subependy-
mal layer/olfactory ventricle, EPl External plexiform
layer of the olfactory bulb, EPlA External plexiform layer
of the accessory olfactory bulb, FrA Frontal associational
cortex, GI Granular insular cortex, GlA Glomerular layer
of the accessory olfactory bulb, GrA Granule cell layer of
the accessory olfactory bulb, GrO Granule cell layer of
the olfactory bulb, IPl Internal plexiform layer of the
olfactory bulb, lo Lateral olfactory tract, Mi Mitral cell
layer of the olfactory bulb, MiA Mitral cell layer of the
accessory olfactory bulb, rf rhinal fissure, ri rhinal
incisures
28 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 14.20

Fig. 3.7 
3  The Degu Brain Atlas in Stereotaxic Coordinates 29

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.8  Images for I: 14.20. aci Anterior commissure/
intrabulbar part, AOE Anterior olfactory nucleus/external
part, AOL Anterior olfactory nucleus/lateral part, dlo
Dorsal olfactory tract, E/OV Ependyma and subependy-
mal layer/olfactory ventricle, EPl External plexiform
layer of the olfactory bulb, EPlA External plexiform layer
of the accessory olfactory bulb, FrA Frontal associational
cortex, GI Granular insular cortex, GlA Glomerular layer
of the accessory olfactory bulb, GrA Granule cell layer of
the accessory olfactory bulb, GrO Granule cell layer of
the olfactory bulb, IPl Internal plexiform layer of the
olfactory bulb, lo Lateral olfactory tract, Mi Mitral cell
layer of the olfactory bulb, MiA Mitral cell layer of the
accessory olfactory bulb, rf rhinal fissure, ri rhinal
incisures
30 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 13.65

Fig. 3.9 
3  The Degu Brain Atlas in Stereotaxic Coordinates 31

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.10  Images for I: 13.65. AOD Anterior olfactory
nucleus/dorsal part, AOE Anterior olfactory nucleus/
external part, AOL Anterior olfactory nucleus/ lateral part,
AOM Anterior olfactory nucleus/  medial part, E/OV
Ependyma and subependymal layer/olfactory ventricle,
EPl External plexiform layer of the olfactory bulb, EPlA
External plexiform layer of the accessory olfactory bulb,
FrA Frontal associational cortex, GI Granular insular cor-
tex, GrO Granule cell layer of the olfactory bulb, IPl
Internal plexiform layer of the olfactory bulb, lo Lateral
olfactory tract, LO Lateral orbital cortex, Mi Mitral cell
layer of the olfactory bulb, MiA Mitral cell layer of the
accessory olfactory bulb, MO Medial orbital cortex, rf rhi-
nal fissure, ri rhinal incisure, VO Ventral orbital cortex
32 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 12.88

Fig. 3.11 
3  The Degu Brain Atlas in Stereotaxic Coordinates 33

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.12  Images for I: 12.88. aci Anterior commissure/
intrabulbar part, AOD Anterior olfactory nucleus/dorsal
part, AOL Anterior olfactory nucleus/ lateral part, AOM
Anterior olfactory nucleus/medial part, AOVP Anterior
olfactory nucleus/ventroposterior part, E/OV Ependyma
and subependymal layer/olfactory ventricle, lo Lateral
olfactory tract, LO Lateral orbital cortex, MO Medial
orbital cortex, PrL Prelimbic cortex, rf rhinal fissure, ri
rhinal incisure, VO Ventral orbital cortex, VTT 1-2 Ventral
tenia tecta/layer 1-2
34 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 12.22

Fig. 3.13 
3  The Degu Brain Atlas in Stereotaxic Coordinates 35

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.14  Images for I: 12.22. aci Anterior commissure/
intrabulbar part, AI Agranular insular cortex, AOD
Anterior olfactory nucleus/dorsal part, AOL Anterior
olfactory nucleus/lateral part, AOVP Anterior olfactory
nucleus/ventroposterior part, Cg Cingulate cortex, E/OV
Ependyma and subependymal layer/olfactory ventricle,
fmi Forceps minor of the corpus callosum, lo Lateral
olfactory tract, LO Lateral orbital cortex, MO Medial
orbital cortex, PrL Prelimbic cortex, rf rhinal fissure, ri
rhinal incisure, VO Ventral orbital cortex, VTT 1-2 Ventral
tenia tecta/layer 1-2
36 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 11.56

Fig. 3.15 
3  The Degu Brain Atlas in Stereotaxic Coordinates 37

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.16  Images for I: 11.56. aca Anterior commissure/
anterior part, AI Agranular insular cortex, AOP Anterior
olfactory nucleus/posterior part, AOVP Anterior olfactory
nucleus/ventroposterior part, Cg Cingulate cortex, Cl
Claustrum, DI Dysgranular insular cortex, DP Dorsal
peduncular cortex, DTr Dorsal transition zone, DTT 1-3
Dorsal tenia tecta/layer 1-3, E/OV Ependyma & subepen-
dymal layer/olfactory ventricle, fmi Forceps minor of the
corpus callosum, GI Granular insular cortex, IL
Infralimbic cortex, lo Lateral olfactory tract, LO Lateral
orbital cortex, M1 Motor cortex/primary area, Pir 1-3
Piriform cortex/layer 1-3, PrL Prelimbic cortex, rf rhinal
fissure, S1 Somatosensory cortex/primary area, VO
Ventral orbital cortex
38 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 10.90

Fig. 3.17 
3  The Degu Brain Atlas in Stereotaxic Coordinates 39

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.18  Images for I: 10.90. aca Anterior commissure/
anterior part, AI Agranular insular cortex, AOP Anterior
olfactory nucleus/posterior part, AOVP Anterior olfactory
nucleus/ventroposterior part, Cg Cingulate cortex, Cl
Claustrum, DEn Dorsal endopiriform nucleus, DI
Dysgranular insular cortex, DP Dorsal peduncular cortex,
DTr Dorsal transition zone, DTT 1-3 Dorsal tenia tecta/
layer 1-3, E/OV Ependyma and subependymal
layer/olfactory ventricle, fmi Forceps minor of the corpus
callosum, GI Granular insular cortex, IL Infralimbic cortex,
lo Lateral olfactory tract, LO Lateral orbital cortex, M1
Motor cortex/primary area, Pir 1-3 Piriform cortex/layer
1-3, PrL Prelimbic cortex, rf rhinal fissure, S1
Somatosensory cortex/primary area, VEn Ventral endopiri-
form nucleus, VO Ventral orbital cortex
40 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 10.24

Fig. 3.19 
3  The Degu Brain Atlas in Stereotaxic Coordinates 41

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.20  Images for I: 10.24. aca Anterior commissure/
anterior part, AcbC Accumbens nucleus/core, AcbSh
Accumbens nucleus/shell, AI Agranular insular cortex, cg
Cingulum, Cg Cingulate cortex, Cl Claustrum, CPu Caudate
putamen (striatum), DEn Dorsal endopiriform nucleus, DI
Dysgranular insular cortex, DP Dorsal peduncular cortex,
DTT 1-2 Dorsal tenia tecta/layer 1-2, E/LV Ependyma and
subependymal layer/lateral ventricle, gcc Genu of the
corpus callosum, GI Granular insular cortex, ICj Islands of
Calleja, IG Indusium griseum, IL Infralimbic cortex, LO
Lateral orbital cortex, M1 Motor cortex/primary area, Pir
1-3 Piriform cortex/layer 1-3, PrL Prelimbic cortex, rf rhinal
fissure, S1 Somatosensory cortex/primary area, Tu 1-3
Olfactory tubercle/layer 1-3, VEn Ventral endopiriform
nucleus
42 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 9.58

Fig. 3.21 
3  The Degu Brain Atlas in Stereotaxic Coordinates 43

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.22  Images for I: 9.58. aca Anterior commissure/
anterior part, AcbC Accumbens nucleus/core, AcbSh
Accumbens nucleus/shell, AI Agranular insular cortex, cc
Corpus callosum, cg Cingulum, Cg Cingulate cortex, CPu
Caudate putamen (striatum), DEn Dorsal endopiriform
nucleus, DI Dysgranular insular cortex, DP Dorsal pedun-
cular cortex, DTT 1-2 Dorsal tenia tecta/layer 1-2, E
Ependyma and subependymal layer, GI Granular insular
cortex, ICj Islands of Calleja, IG Indusium griseum, lo
Lateral olfactory tract, LSI Lateral septal nucleus/interme-
diate part, LV Lateral ventricle, M1 Motor cortex/primary
area, Nv Navicular nucleus of the basal forebrain, Pir 1-3
Piriform cortex/layer 1-3, rf rhinal fissure, S1
Somatosensory cortex/primary area, Tu 1-3 Olfactory
tubercle/layer 1-3, VCl Ventral part of claustrum, VEn
Ventral endopiriform nucleus, VP Ventral pallidum
44 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 8.92

Fig. 3.23 
3  The Degu Brain Atlas in Stereotaxic Coordinates 45

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.24  Images for I: 8.92. aca Anterior commissure/
anterior part, AcbC Accumbens nucleus/core, AcbSh
Accumbens nucleus/shell, AI Agranular insular cortex, cc
Corpus callosum, cg Cingulum, Cg Cingulate cortex, CPu
Caudate putamen (striatum), DCl Dorsal part of claus-
trum, DEn Dorsal endopiriform nucleus, DI Dysgranular
insular cortex, DP Dorsal peduncular cortex, E Ependyma
and subependymal layer, ec External capsule, GI Granular
insular cortex, ICj Islands of Calleja, ICjM Islands of
Calleja/major island, IG Indusium griseum, lo Lateral
olfactory tract, LSD Lateral septal nucleus/dorsal part, LSI
Lateral septal nucleus/intermediate part, LSV Lateral sep-
tal nucleus/ventral part, LV Lateral ventricle, M1 Motor
cortex/primary area, MS Medial septal nucleus, Pir 1-3
Piriform cortex/layer 1-3, rf rhinal fissure, S1
Somatosensory cortex/primary area, Tu 1-3 Olfactory
tubercle/layer 1-3, VCl Ventral part of claustrum, VDB
Nucleus of the vertical limb of the diagonal band, VEn
Ventral endopiriform nucleus, VP Ventral pallidum
46 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 8.26

Fig. 3.25 
3  The Degu Brain Atlas in Stereotaxic Coordinates 47

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.26  Images for I: 8.26. aca Anterior commissure/
anterior part, AcbC Accumbens nucleus/core, AcbSh
Accumbens nucleus/shell, AI Agranular insular cortex, cc
Corpus callosum, cg Cingulum, Cg Cingulate cortex, CPu
Caudate putamen (striatum), DCl Dorsal part of claus-
trum, DEn Dorsal endopiriform nucleus, DI Dysgranular
insular cortex, GI Granular insular cortex, ICj Islands of
Calleja, ICjM Islands of Calleja/major island, IG Indusium
griseum, lo Lateral olfactory tract, LSD Lateral septal
nucleus/dorsal part, LSI Lateral septal nucleus/intermedi-
ate part, LSS Lateral stripe of the striatum, LSV Lateral
septal nucleus/ventral part, LV Lateral ventricle, M1
Motor cortex/primary area, MS Medial septal nucleus, Pir
1-3 Piriform cortex/layer 1-3, rf rhinal fissure, S1
Somatosensory cortex/primary area, Tu 1-3 Olfactory
tubercle/layer 1-3, VCl Ventral part of claustrum, VDB
Nucleus of the vertical limb of the diagonal band, VEn
Ventral endopiriform nucleus, VP Ventral pallidum
48 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 7.60

Fig. 3.27 
3  The Degu Brain Atlas in Stereotaxic Coordinates 49

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.28  Images for I: 7.60. aca Anterior commissure/
anterior part, AI Agranular insular cortex, cc Corpus cal-
losum, cg Cingulum, Cg Cingulate cortex, CPu Caudate
putamen (striatum), CxA 1-3 Cortex-amygdala transition
zone/layer 1-3, DCl Dorsal part of claustrum, DEn Dorsal
endopiriform nucleus, DI Dysgranular insular cortex, ec
External capsule, fi Fimbria of the hippocampus, GI
Granular insular cortex, HDB Nucleus of the horizontal
limb of the diagonal band, ic Internal capsule, ICj Islands
of Calleja, IG Indusium griseum, IPAC Interstitial nucleus
of the posterior limb of the anterior commissure, lo
Lateral olfactory tract, LPO Lateral preoptic area, LSD
Lateral septal nucleus/dorsal part, LSI Lateral septal
nucleus/intermediate part, LSS Lateral stripe of the stria-
tum, LSV Lateral septal nucleus/ventral part, LV Lateral
ventricle, M1 Motor cortex/primary area, MCPO
Magnocellular preoptic nucleus, MnPO Median preoptic
nucleus, MS Medial septal nucleus, och Optic chiasm, Pir
1-3 Piriform cortex/layer 1-3, rf Rhinal fissure, S1
Somatosensory cortex/primary area, SFi Septofimbrial
nucleus, SHy Septohypothalamic nucleus, SIB Substantia
innominata/basal part, SO Supraoptic nucleus, STL Bed
nucleus of the stria terminalis/lateral division, STM Bed
nucleus of the stria terminalis/medial division, Tu
Olfactory tubercle, VCl Ventral part of claustrum, VEn
Ventral endopiriform nucleus, VOLT Vascular organ of
the lamina terminalis, VP Ventral pallidum
50 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 6.94

Fig. 3.29 
3  The Degu Brain Atlas in Stereotaxic Coordinates 51

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.30  Images for I: 6.94. AA Anterior amygdaloid
area, ac Anterior commissure, acp Anterior commissure/
posterior limb, AI Agranular insular cortex, cc Corpus cal-
losum, cg Cingulum, Cg Cingulate cortex, CPu Caudate
putamen (striatum), CxA1 Cortex-amygdala transition
zone/layer 1-3, DCl Dorsal part of claustrum, DEn Dorsal
endopiriform nucleus, DI Dysgranular insular cortex, ec
External capsule, fi Fimbria of the hippocampus, GI
Granular insular cortex, GP Globus pallidus, ic Internal
capsule, IG Indusium griseum, IPACL Interstitial nucleus
of the posterior limb of the anterior commissure/lateral
part, IPACM Interstitial nucleus of the posterior limb of
the anterior commissure/medial part, lo Lateral olfactory
tract, LPO Lateral preoptic area, LSD Lateral septal
nucleus/dorsal part, LSV Lateral septal nucleus/ventral
part, LV Lateral ventricle, M1 Motor cortex/primary area,
MCPO Magnocellular preoptic nucleus, MnPO Median
preoptic nucleus, MPA Medial preoptic area, MPO Medial
preoptic nucleus, och Optic chiasm, Pe Periventricular
hypothalamic nucleus, Pir 1-3 Piriform cortex/layer 1-3,
rf rhinal fissure, S1 Somatosensory cortex/primary area,
SFi Septofimbrial nucleus, SHy Septohypothalamic
nucleus, SIB Substantia innominata/basal part, SO
Supraoptic nucleus, st Stria terminalis, STL Bed nucleus
of the stria terminalis/lateral division, STM Bed nucleus
of the stria terminalis/medial division, TS Triangular sep-
tal nucleus, VCl Ventral part of claustrum, VEn Ventral
endopiriform nucleus, VP Ventral pallidum
52 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 6.28

Fig. 3.31 
3  The Degu Brain Atlas in Stereotaxic Coordinates 53

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.32  Images for I: 6.28. 3V Third ventricle, AA
Anterior amygdaloid area, AI Agranular insular cortex,
AM Anteromedial thalamic nucleus, AV Anteroventral
thalamic nucleus, B Basal nucleus (Meynert), C Cochlear
nuclei, cc Corpus callosum, Cg Cingulate cortex, cg
Cingulum, chp Choroid plexus, CPu Caudate putamen
(striatum), CxA1 Cortex-­amygdala transition zone/layer
1, DCl Dorsal part of claustrum, DEn Dorsal endopiri-
form nucleus, df Dorsal fornix, DI Dysgranular insular
cortex, EAC Sublenticular extended amygdala/central
part, ec External capsule, fi Fimbria of the hippocampus,
GI Granular insular cortex, GP Globus pallidus, HDB
Nucleus of the horizontal limb of the diagonal band, ic
Internal capsule, IG Indusium griseum, IPAC Interstitial
nucleus of the posterior limb of the anterior commissure,
LOT Nucleus of the lateral olfactory tract/layer 1-3, LPO
Lateral preoptic area, LV Lateral ventricle, M1 Motor cor-
tex/primary area, MCPO Magnocellular preoptic nucleus,
MeA Medial amygdaloid nucleus/anterior part, MPA
Medial preoptic area, MPO Medial preoptic nucleus,
MPOC Medial preoptic nucleus/central part, och Optic
chiasm, PaAP Paraventricular hypothalamic nucleus/ante-
rior parvicellular part, Pe Periventricular hypothalamic
nucleus, Pir 1-3 Piriform cortex/layer 1-3, PT Paratenial
thalamic nucleus, PVA Paraventricular thalamic nucleus/
anterior part, Re Reuniens thalamic nucleus, rf Rhinal fis-
sure, Rt Reticular thalamic nucleus, S1 Somatosensory
cortex/primary area, SChDL Suprachiasmatic nucleus/
dorsolateral part, SChVM Suprachiasmatic nucleus/ven-
tromedial part, SFi Septofimbrial nucleus, SFO
Subfornical organ, SHy Septohypothalamic nucleus, SIB
Substantia innominata/basal part, sm Stria medullaris of
the thalamus, SO Supraoptic nucleus, st Stria terminalis,
STM Bed nucleus of the stria terminalis/medial division,
TS Triangular septal nucleus, VCl Ventral part of claus-
trum, VEn Ventral endopiriform nucleus, vhc Ventral hip-
pocampal commissure, VP Ventral pallidum
54
I: 5.62
Fig. 3.33 
rhinal fissure, Rh Rhomboid thalamic nucleus, RSD
Retrosplenial dysgranular cortex, RSG Retrosplenial
granular cortex, Rt Reticular thalamic nucleus, S1
Somatosensory cortex/primary area, SLu Stratum lucidum
of the hippocampus, sm Stria medullaris of the thalamus,
3  The Degu Brain Atlas in Stereotaxic Coordinates
SO Supraoptic nucleus, TuLH Tuberal region of lateral
hypothalamus, VA Ventral anterior thalamic nucleus, VCl
Ventral part of claustrum, VEn Ventral endopiriform
nucleus, VL Ventrolateral thalamic nucleus, VMH
Ventromedial hypothalamic nucleus
3  The Degu Brain Atlas in Stereotaxic Coordinates 55

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.34  Images for I: 5.62. 3V Third ventricle, Aco
Anterior cortical amygdaloid nucleus, AD Anterodorsal
thalamic nucleus, AHC Anterior hypothalamic area/cen-
tral part, AHP Anterior hypothalamic area/posterior part,
AI Agranular insular cortex, alv Alveus of the hippocam-
pus, AM Anteromedial thalamic nucleus, Arc Arcuate
hypothalamic nucleus, B Basal nucleus (Meynert), BLA
Basolateral amygdaloid nucleus/anterior part, BMA
Basomedial amygdaloid nucleus/anterior part, CA3 Field
CA3 of the hippocampus, cc Corpus callosum, CeC
Central amygdaloid nucleus/capsular part, CeM Central
amygdaloid nucleus/medial part, cg Cingulum, chp
Choroid plexus, CM Central medial thalamic nucleus,
CPu Caudate putamen (striatum), DCl Dorsal part of
claustrum, DEn Dorsal endopiriform nucleus, DI
Dysgranular insular cortex, EA Sublenticular extended
amygdala, ec External capsule, EP Entopedunclar
nucleus, f Fornix, fi Fimbria of the hippocampus, GI
Granular insular cortex, GP Globus pallidus, GrDG
Granule cell layer of the dentate gyrus, IAM
Interanteromedial thalamic nucleus, ic Internal capsule,
LaDL Lateral amygdaloid nucleus/dorsolateral part, LM
Lateral mammillary nucleus, LV Lateral ventricle, M1
Motor cortex/primary area, MeAD Medial amygdaloid
nucleus/anterodorsal part, MeAV Medial amygdaloid
nucleus/anteroventral part, MoDG Molecular layer of the
dentate gyrus, mt Mammillothalamic tract, opt Optic
tract, Or Oriens layer of the hippocampus, Pa
Paraventricular hypothalamic nucleus, PC Paracentral
thalamic nucleus, Pe Periventricular hypothalamic
nucleus, Pir 1-3 Piriform cortex/layer 1-3, PLH
Peduncular part of the lateral hypothalamus, PT Paratenial
thalamic nucleus, PVA Paraventricular thalamic nucleus/
anterior part, Py Pyramidal cell layer of the hippocampus,
Rad Radiatum layer of the hippocampus, RCh
Retrochiasmatic area, Re Reuniens thalamic nucleus, rf
56
I: 4.96
Fig. 3.35 
lateral hypothalamus, PMCo Posteromedial cortical amyg-
daloid nucleus, PoDG Polymorph layer of the dentate
gyrus, PVA Paraventricular thalamic nucleus/anterior part,
Py Pyramidal cell layer of the hippocampus, Rad Radiatum
layer of the hippocampus, Re Reuniens thalamic nucleus,
rf Rhinal fissure, RSD Retrosplenial dysgranular cortex,
RSG Retrosplenial granular cortex, Rt Reticular thalamic
nucleus, S1 Somatosensory cortex/primary area, SLu
Stratum lucidum of the hippocampus, sm Stria medullaris
3  The Degu Brain Atlas in Stereotaxic Coordinates
of the thalamus, st Stria terminalis, TuLH Tuberal region of
lateral hypothalamus, VA Ventral anterior thalamic
nucleus, VCl Ventral part of claustrum, VEn Ventral endop-
iriform nucleus, VL Ventrolateral thalamic nucleus, VM
Ventromedial thalamic nucleus, VMH Ventromedial hypo-
thalamic nucleus, VPL Ventral posterolateral thalamic
nucleus, Xi Xiphoid thalamic nucleus, ZIR Zona incerta/
rostral part
3  The Degu Brain Atlas in Stereotaxic Coordinates 57

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.36  Images for I: 4.96. 3V Third ventricle, AHP
Anterior hypothalamic area/posterior part, AI Agranular
insular cortex, alv Alveus of the hippocampus, AM
Anteromedial thalamic nucleus, AngT Angular thalamic
nucleus, Arc Arcuate hypothalamic nucleus, BLA
Basolateral amygdaloid nucleus/anterior part, BLP
Basolateral amygdaloid nucleus/posterior part, BMP
Basomedial amygdaloid nucleus/posterior part, CA1 Field
CA1 of the hippocampus, CA2 Field CA2 of the hippo-
campus, CA3 Field CA3 of the hippocampus, cc Corpus
callosum, Ce Central amygdaloid nucleus, CeL Central
amygdaloid nucleus/lateral part, CeM Central amygdaloid
nucleus/medial part, cg Cingulum, CL Centrolateral tha-
lamic nucleus, CM Central medial thalamic nucleus, CPu
Caudate putamen (striatum), DCl Dorsal part of claustrum,
DEn Dorsal endopiriform nucleus, ec External capsule, EP
Entopedunclar nucleus, f Fornix, fi Fimbria of the hippo-
campus, GP Globus pallidus, GrDG Granule cell layer of
the dentate gyrus, hif Hippocampal fissure, ic Internal cap-
sule, IMD Intermediodorsal thalamic nucleus, LaDL
Lateral amygdaloid nucleus/dorsolateral part, LaVL
Lateral amygdaloid nucleus/ventrolateral part, LaVM
Lateral amygdaloid nucleus/ventromedial part, LD
Laterodorsal (or lateral dorsal) thalamic nucleus, LMol
Lacunosum moleculare layer of the hippocampus, LV
Lateral ventricle, M1 Motor cortex/primary area, MDL
Mediodorsal thalamic nucleus/lateral part, MDM
Mediodorsal thalamic nucleus/medial part, ME Median
eminence, MePD Medial amygdaloid nucleus/posterodor-
sal part, MePV Medial amygdaloid nucleus/posteroventral
part, MoDG Molecular layer of the dentate gyrus, mt
Mammillothalamic tract, opt Optic tract, Or Oriens layer
of the hippocampus, Pa Paraventricular hypothalamic
nucleus, Pe Periventricular hypothalamic nucleus, Pir 1-3
Piriform cortex/layer 1-3, PLCo 1-3 Posterolateral cortical
amygdaloid nucleus 1-3, PLH Peduncular part of the
58
I: 4.30
Fig. 3.37 
Paraventricular thalamic nucleus, Py Pyramidal cell layer
of the hippocampus, Rad Radiatum layer of the hippo-
campus, Re Reuniens thalamic nucleus, rf Rhinal fissure,
Rh Rhomboid thalamic nucleus, RSD Retrosplenial dys-
granular cortex, RSG Retrosplenial granular cortex, Rt
Reticular thalamic nucleus, S1 Somatosensory cortex/pri-
mary area, SLu Stratum lucidum of the hippocampus, sm
3  The Degu Brain Atlas in Stereotaxic Coordinates
Stria medullaris of the thalamus, st Stria terminalis, TuLH
Tuberal region of lateral hypothalamus, VEn Ventral
endopiriform nucleus, VL Ventrolateral thalamic nucleus,
VM Ventromedial thalamic nucleus, VMH Ventromedial
hypothalamic nucleus, VPL Ventral posterolateral tha-
lamic nucleus, VPM Ventral posteromedial thalamic
nucleus, Xi Xiphoid thalamic nucleus
3  The Degu Brain Atlas in Stereotaxic Coordinates 59

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.38  Images for I: 4.30. 3V Third ventricle, AI
Agranular insular cortex, alv Alveus of the hippocampus,
Arc Arcuate hypothalamic nucleus, BLA Basolateral
amygdaloid nucleus/anterior part, BLP Basolateral amyg-
daloid nucleus/posterior part, BMP Basomedial amygda-
loid nucleus/posterior part, CA1 Field CA1 of the
hippocampus, CA2 Field CA2 of the hippocampus, CA3
Field CA3 of the hippocampus, cc Corpus callosum, Ce
Central amygdaloid nucleus, cg Cingulum, chp Choroid
plexus, CL Centrolateral thalamic nucleus, CM Central
medial thalamic nucleus, CPu Caudate putamen (stria-
tum), DA Dorsal hypothalamic area, DEn Dorsal endop-
iriform nucleus, DI Dysgranular insular cortex, DM
Dorsomedial hypothalamic nucleus, EP Entopeduncular
nucleus, fi Fimbria of the hippocampus, GI Granular insu-
lar cortex, GP Globus pallidus, GrDG Granule cell layer
of the dentate gyrus, ic Internal capsule, IMD
Intermediodorsal thalamic nucleus, LaDL Lateral amyg-
daloid nucleus/dorsolateral part, LaVL Lateral amygda-
loid nucleus/ventrolateral part, LaVM Lateral amygdaloid
nucleus/ventromedial part, LD Laterodorsal (or lateral
dorsal) thalamic nucleus, LHb Lateral habenular nucleus,
LMol Lacunosum moleculare layer of the hippocampus,
LV Lateral ventricle, MDL Mediodorsal thalamic nucleus/
lateral part, MDM Mediodorsal thalamic nucleus/medial
part, ME Median eminence, MePD Medial amygdaloid
nucleus/posterodorsal/part, MePV Medial amygdaloid
nucleus/posteroventral/part, MHb Medial habenular
nucleus, ml Medial lemniscus, opt Optic tract, Or Oriens
layer of the hippocampus, PC Paracentral thalamic
nucleus, Pe Periventricular hypothalamic nucleus, Pir 1-3
Piriform cortex/layer 1-3, PLCo 1-3 Posterolateral corti-
cal amygdaloid nucleus 1-3, PLH Peduncular part of the
lateral hypothalamus, PMCo Posteromedial cortical
amygdaloid nucleus, Po Posterior thalamic nuclear group,
PoDG Polymorph layer of the dentate gyrus, PV
60
I: 3.75
Fig. 3.39 
Perirhinal cortex, PSTh Parasubthalamic nucleus, PVP
Paraventricular thalamic nucleus/posterior part, Py
Pyramidal cell layer of the hippocampus, Rad Radiatum
layer of the hippocampus, rf Rhinal fissure, RRe
Retroreuniens area, RSD Retrosplenial dysgranular cor-
tex, RSG Retrosplenial granular cortex, Rt Reticular tha-
lamic nucleus, S1 Somatosensory cortex/primary area,
scp Superior cerebellar peduncle (brachium conjuncti-
3  The Degu Brain Atlas in Stereotaxic Coordinates
vum), SLu Stratum lucidum of the hippocampus, sm Stria
medullaris of the thalamus, SPF Subparafiscicular tha-
lamic nucleus, STh Subthalamic nucleus, VG Ventral
geniculate nucleus, VPL Ventral posterolateral thalamic
nucleus, VPM Ventral posteromedial thalamic nucleus,
VPPC Ventral posterior nucleus of the thalamus/parvicel-
lular part, ZID Zona incerta/dorsal part, ZIV Zona incerta/
ventral part
3  The Degu Brain Atlas in Stereotaxic Coordinates 61

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.40  Images for I: 3.75.3V Third ventricle, AHiPL
Amygdalohippocam­ pal area/posterolateral part, AHiM
Amygdalohippocampal area/posteromedial part, alv
Alveus of the hippocampus, APir Amygdalopiriform tran-
sition area, Au1 Auditory cortex/primary area, BLP
Basolateral amygdaloid nucleus/posterior part, BMP
Basomedial amygdaloid nucleus/posterior part, CA2 Field
CA2 of the hippocampus, CA3 Field CA3 of the hippo-
campus, cc Corpus callosum, chp Choroid plexus, CL
Centrolateral thalamic nucleus, CM Central medial tha-
lamic nucleus, cp Cerebral peduncle, DEn Dorsal endop-
iriform nucleus, DLG Dorsal lateral geniculate nucleus,
Ect Ectorhinal cortex, f Fornix, FC Fasciola cinereum, fi
Fimbria of the hippocampus, fr Fasciculus retroflexus,
GrDG Granule cell layer of the dentate gyrus, hif
Hippocampal fissure, ic Internal capsule, LaDL Lateral
amygdaloid nucleus/dorsolateral part, LaVM Lateral
amygdaloid nucleus/ventromedial part, LHb Lateral
habenular nucleus, LMol Lacunosum moleculare layer of
the hippocampus, LPL Lateral posterior thalamic nucleus/
lateral part, LPM Lateral posterior thalamic nucleus/
medial part, LV Lateral ventricle, MDL Mediodorsal tha-
lamic nucleus/lateral part, MDM Mediodorsal thalamic
nucleus/medial part, MHb Medial habenular nucleus, ml
Medial lemniscus, MoDG Molecular layer of the dentate
gyrus, MRe/3V Mammillary recess of the 3rd ventricle, mt
Mammillothalamic tract, opt Optic tract, Or Oriens layer
of the hippocampus, PF Parafascicular thalamic nucleus,
PH Posterior hypothalamic nucleus, Pir 1-3 Piriform cor-
tex/layer 1-3, PLCo Posterolateral cortical amygdaloid
nucleus 1-3, PLH Peduncular part of the lateral hypothal-
amus, PMCo Posteromedial cortical amygdaloid nucleus,
PMD Premammillary nucleus/dorsal part, PMV
Premammillary nucleus/ventral part, Po Posterior tha-
lamic nuclear group, PoDG Polymorph layer of the den-
tate gyrus, PoMn Posteromedial thalamic nucleus, PRh
62
I: 2.98
Fig. 3.41 
Perirhinal cortex, PSTh Parasubthalamic nucleus, PVP
Paraventricular thalamic nucleus/posterior part, Py
Pyramidal cell layer of the hippocampus, Rad Radiatum
layer of the hippocampus, rf Rhinal fissure, RRe
Retroreuniens area, RSD Retrosplenial dysgranular cor-
tex, RSG Retrosplenial granular cortex, Rt Reticular tha-
lamic nucleus, S1 Somatosensory cortex/primary area,
scp Superior cerebellar peduncle (brachium conjuncti-
3  The Degu Brain Atlas in Stereotaxic Coordinates
vum), SLu Stratum lucidum of the hippocampus, sm Stria
medullaris of the thalamus, SPF Subparafiscicular tha-
lamic nucleus, STh Subthalamic nucleus, VG Ventral
geniculate nucleus, VPL Ventral posterolateral thalamic
nucleus, VPM Ventral posteromedial thalamic nucleus,
VPPC Ventral posterior nucleus of the thalamus/parvicel-
lular part, ZID Zona incerta/dorsal part, ZIV Zona incerta/
ventral part
3  The Degu Brain Atlas in Stereotaxic Coordinates 63

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.42  Images for I: 2.98. 3V Third ventricle, AHiPL
Amygdalohippocam­pal area/posterolateral part, AHiM
Amygdalohippocampal area/posteromedial part, alv
Alveus of the hippocampus, APir Amygdalopiriform tran-
sition area, Au1 Auditory cortex/primary area, BLP
Basolateral amygdaloid nucleus/posterior part, BMP
Basomedial amygdaloid nucleus/posterior part, CA2 Field
CA2 of the hippocampus, CA3 Field CA3 of the hippocam-
pus, cc Corpus callosum, chp Choroid plexus, CL
Centrolateral thalamic nucleus, CM Central medial tha-
lamic nucleus, cp Cerebral peduncle, DEn Dorsal endop-
iriform nucleus, DLG Dorsal lateral geniculate nucleus,
Ect Ectorhinal cortex, f Fornix, FC Fasciola cinereum, fi
Fimbria of the hippocampus, fr Fasciculus retroflexus,
GrDG Granule cell layer of the dentate gyrus, hif
Hippocampal fissure, ic Internal capsule, LaDL Lateral
amygdaloid nucleus/dorsolateral part, LaVM Lateral
amygdaloid nucleus/ventromedial part, LHb Lateral
habenular nucleus, LMol Lacunosum moleculare layer of
the hippocampus, LPL Lateral posterior thalamic nucleus/
lateral part, LPM Lateral posterior thalamic nucleus/
medial part, LV Lateral ventricle, MDL Mediodorsal tha-
lamic nucleus/lateral part, MDM Mediodorsal thalamic
nucleus/medial part, MHb Medial habenular nucleus, ml
Medial lemniscus, MoDG Molecular layer of the dentate
gyrus, MRe/3V Mammillary recess of the 3rd ventricle, mt
Mammillothalamic tract, opt Optic tract, Or Oriens layer
of the hippocampus, PF Parafascicular thalamic nucleus,
PH Posterior hypothalamic nucleus, Pir 1-3 Piriform cor-
tex/layer 1-3, PLCo Posterolateral cortical amygdaloid
nucleus 1-3, PLH Peduncular part of the lateral hypothal-
amus, PMCo Posteromedial cortical amygdaloid nucleus,
PMD Premammillary nucleus/dorsal part, PMV
Premammillary nucleus/ventral part, Po Posterior tha-
lamic nuclear group, PoDG Polymorph layer of the den-
tate gyrus, PoMn Posteromedial thalamic nucleus, PRh
64
I: 2.32
Fig. 3.43 
nucleus, PRh Perirhinal cortex, Py Pyramidal cell layer of
the hippocampus, Rad Radiatum layer of the hippocam-
pus, SuML Supramammillary nucleus/lateral part, SuMM
Supramammillary nucleus/medial part, RPF Retro­
parafascicular nucleus, RSD Retrosplenial dysgranular
3  The Degu Brain Atlas in Stereotaxic Coordinates
cortex, RSG Retrosplenial granular cortex, SCO Subcom­
missural organ, scp Superior cerebellar peduncle (bra-
chium conjunctivum), SLu Stratum lucidum of the
hippocampus, sm Stria medullaris of the thalamus, STh
Subthalamic nucleus, V1 Visual cortex/primary area, VG
3  The Degu Brain Atlas in Stereotaxic Coordinates 65

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.44  Images for I: 2.32. 3V Third ventricle, AHiPL
Amygdalohippocam­pal area/posterolateral part, AHiM
Amygdalohippocampal area/posteromedial part, alv
Alveus of the hippocampus, APir Amygdalopiriform tran-
sition area, Au1 Auditory cortex/primary area, BLP
Basolateral amygdaloid nucleus/posterior part, bsc
Brachium of the superior colliculus, CA1 Field CA1 of the
hippocampus, CA2 Field CA2 of the hippocampus, CA3
Field CA3 of the hippocampus, cc Corpus callosum, cg
Cingulum, chp Choroid plexus, DEn Dorsal endopiriform
nucleus, DLEnt Dorsolateral entorhinal cortex, DLG
Dorsal lateral geniculate nucleus, Ect Ectorhinal cortex, fr
Fasciculus retroflexus, GrDG Granule cell layer of the
dentate gyrus, hif Hippocampal fissure, ic/cp Internal cap-
sule/cerebral peduncle, LM Lateral mammillary nucleus,
LMol Lacunosum moleculare layer of the hippocampus,
LP Lateral posterior thalamic nucleus, LPM Lateral pos-
terior thalamic nucleus/medial part, LPMR Lateral poste-
rior thalamic nucleus/mediorostral part, Lth Lithoid
nucleus, MCPC Magnocellular nucleus of the posterior
commissure, MGD Medial geniculate nucleus/dorsal part,
MGV Medial geniculate nucleus/ventral part, ml Medial
lemniscus, ML Medial mammillary nucleus/lateral part,
MnA Median accessory nucleus of the medulla, MnM
Medial mammillary nucleus/median part, MoDG
Molecular layer of the dentate gyrus, MPT Medial pretec-
tal nucleus, mtg Mammillotegmental tract, Op Optic
nerve layer of the superior colliculus, opt Optic tract, Or
Oriens layer of the hippocampus, OT Nucleus of the optic
tract, PAG Periaqueductal gray, PC Paracentral thalamic
nucleus, PHA Posterior hypothalamic area, Pir 1-3
Piriform cortex/layer 1-3, PLCo Posterolateral cortical
amygdaloid nucleus, PLH Peduncular part of the lateral
hypothalamus, pm Principal mammillary tract, PMCo
Posteromedial cortical amygdaloid nucleus, PoDG
Polymorph layer of the dentate gyrus, PrC Precommissural
66 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 1.66

Fig. 3.45 

peduncle (brachium conjunctivum), SLu Stratum lucidum colliculus, V1 Visual cortex/primary area, VS Ventral
of the hippocampus, SNC Substantia nigra/compact part, subiculum, VTA Ventral tegmental area, Zo Zonal layer of
SNL Substantia nigra/lateral part, SNR Substantia nigra/ the superior colliculus
reticular part, SuG Superficial gray layer of the superior
3  The Degu Brain Atlas in Stereotaxic Coordinates 67

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.46  Images for I: 1.66. Ahi Amygdalohippocampal
area, alv Alveus of the hippocampus, APir
Amygdalopiriform transition area, APT Anterior pretectal
nucleus, Aq Aqueduct, Au1 Auditory cortex/primary area,
bsc Brachium of the superior colliculus, CA1 Field CA1 of
the hippocampus, CA3 Field CA3 of the hippocampus, cg
Cingulum, cp Cerebral peduncle, csc Commissure of the
superior colliculus, Dk Nucleus of Darkschewitsch, DLEnt
Dorsolateral entorhinal cortex, DLG Dorsal lateral genicu-
late nucleus, DpG Deep gray layer of the superior collicu-
lus, DpWh Deep white layer of the superior colliculus, DS
Dorsal subiculum, Ect Ectorhinal cortex, fr Fasciculus ret-
roflexus, GrDG Granule cell layer of the dentate gyrus, hif
Hippocampal fissure, InC Interstitial nucleus of Cajal, InG
Intermediate gray layer of the superior colliculus, InWh
Intermediate white layer of the superior colliculus, LMol
Lacunosum moleculare layer of the hippocampus, LP
Lateral posterior thalamic nucleus, LV Lateral ventricle,
MeRt Mesencephalic reticular nucleus, MGD Medial
geniculate nucleus/dorsal part, MGV Medial geniculate
nucleus/ventral part, ml Medial lemniscus, ML Medial
mammillary nucleus/lateral part, MoDG Molecular layer
of the dentate gyrus, mp Mammillary peduncle, mtg
Mammillotegmental tract, Op Optic nerve layer of the
superior colliculus, opt Optic tract, Or Oriens layer of the
hippocampus, PAG Periaqueductal gray, pc Posterior com-
missure, PCom Nucleus of the posterior commissure, Pir 1-3
Piriform cortex/layer 1-3, PMCo Posteromedial cortical
amygdaloid nucleus, Po Posterior thalamic nuclear group,
PoDG Polymorph layer of the dentate gyrus, PRh
Perirhinal cortex, Py Pyramidal cell layer of the hippocam-
pus, Rad Radiatum layer of the hippocampus, rf Rhinal
fissure, RLi Rostral linear nucleus of the raphe, SuMM
Supramammillary nucleus/medial part, RSD Retrosplenial
dysgranular cortex, RSG Retrosplenial granular cortex,
SCO Subcommissural organ, scp Superior cerebellar
68 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 1.00

Fig. 3.47 
3  The Degu Brain Atlas in Stereotaxic Coordinates 69

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.48  Images for I: 1.00. 3n Oculomotor nerve, Ahi
Amygdalohippocam­pal area, alv Alveus of the hippocam-
pus, APir Amyg­dalopiriform transition area, APT Anterior
pretectal nucleus, Aq Aqueduct, Au1 Auditory cortex/pri-
mary area, bsc Brachium of the superior colliculus, CA1
Field CA1 of the hippocampus, CA3 Field CA3 of the hip-
pocampus, cp Cerebral peduncle, Dk Nucleus of
Darkschewitsch, DpG Deep gray layer of the superior col-
liculus, DpWh Deep white layer of the superior colliculus,
Ect Ectorhinal cortex, fr Fasciculus retroflexus, GrDG
Granule cell layer of the dentate gyrus, hif Hippocampal
fissure, InC Interstitial nucleus of Cajal, InG Intermediate
gray layer of the superior colliculus, InWh Intermediate
white layer of the superior colliculus, LMol Lacunosum
moleculare layer of the hippocampus, LP Lateral poste-
rior thalamic nucleus, LV Lateral ventricle, MA3 Medial
accessory oculomotor nucleus, MCPC Magnocellular
nucleus of the posterior commissure, MeRt Mesencephalic
reticular nucleus, MGD Medial geniculate nucleus/dorsal
part, MGM Medial geniculate nucleus/medial part, MGV
Medial geniculate nucleus/ventral part, ml Medial lemnis-
cus, mlf Medial longitudinal fasciculus, MoDG Molecular
layer of the dentate gyrus, mp Mammillary peduncle, Op
Optic nerve layer of the superior colliculus, Or Oriens
layer of the hippocampus, PAG Periaqueductal gray,
PMCo Posteromedial cortical amygdaloid nucleus, PPT
Posterior pretectal nucleus, PrEW Pre-Edinger-Westphal
nucleus, PRh Perirhinal cortex, Py Pyramidal cell layer of
the hippocampus, Rad Radiatum layer of the hippocam-
pus, rf Rhinal fissure, RMC Red nucleus/magnocellular
part, RPC Red nucleus/parvicellular part, RSD
Retrosplenial dysgranular cortex, RSG Retrosplenial
granular cortex, scp Superior cerebellar peduncle (bra-
chium conjunctivum), SG Suprageniculate thalamic
nucleus, SLu Stratum lucidum of the hippocampus, SNC
Substantia nigra/compact part, SNL Substantia nigra/lat-
eral part, SNR Substantia nigra/reticular part, SuG
Superficial gray layer of the superior colliculus, V1 Visual
cortex/primary area, VS Ventral subiculum, Zo Zonal
layer of the superior colliculus
70 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: 0.34

Fig. 3.49 
3  The Degu Brain Atlas in Stereotaxic Coordinates 71

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.50 Images for I: 0.34. 3n Oculomotor nerve, 3N
Oculomotor nucleus, alv Alveus of the hippocampus, APir
Amygdalopiriform transition area, APT Anterior pretectal
nucleus, Aq Aqueduct, Au1 Auditory cortex/primary area,
bic Brachium of the inferior colliculus, bsc Brachium of the
superior colliculus, CA1 Field CA1 of the hippocampus, cp
Cerebral peduncle, DLEnt Dorsolateral entorhinal cortex,
DpG Deep gray layer of the superior colliculus, DpWh
Deep white layer of the superior colliculus, DS Dorsal
subiculum, Ect Ectorhinal cortex, EW Edinger-Westphal
nucleus, fmj Forceps major of the corpus callosum,
GrDG Granule cell layer of the dentate gyrus, hif
Hippocampal fissure, IEnt Intermediate entorhinal
cortex, InG Intermediate gray layer of the superior
­colliculus, InWh Intermediate white layer of the
superior colliculus, IPC Interpeduncular nucleus/caudal
subnucleus, IPL Interpeduncular nucleus/lateral subnu-
cleus, IPR, Interpeduncular nucleus/rostral subnucleus,
LMol lacunosum moleculare layer of the h­ ippocampus, LV
Lateral ventricle, me5/Me5 Mesencephalic trigeminal tract/
nucleus, MEnt Medial entorhinal cortex, MeRt
Mesencephalic reticular nucleus, MGD Medial geniculate
nucleus/dorsal part, MGM Medial geniculate nucleus/
medial part, MGV Medial geniculate nucleus/ventral part,
ml Medial lemniscus, mlf Medial longitudinal fasciculus,
MoDG Molecular layer of the dentate gyrus, mp
Mammillary peduncle, Op Optic nerve layer of the superior
colliculus, Or Oriens layer of the hippocampus, PAG
Periaqueductal gray, PoDG Polymorph layer of the dentate
gyrus, Post Postsubiculum, PRh Perirhinal cortex, Py
Pyramidal cell layer of the hippocampus, Rad Radiatum
layer of the hippocampus, rf Rhinal fissure, Rli Rostral lin-
ear nucleus of the raphe, RMC Red nucleus/magnocellular
part, RPC Red nucleus/parvicellular part, RSD Retrosplenial
dysgranular cortex, RSG Retrosplenial granular cortex, scp
Superior cerebellar peduncle (brachium conjunctivum), SG
Suprageniculate thalamic nucleus, SNC Substantia nigra/
compact part, SNL Substantia nigra/lateral part, SNR
Substantia nigra/reticular part, Su3 Supraoculomotor peri-
aqueductal gray, SuG Superficial gray layer of the superior
colliculus, V1 Visual cortex/primary area, VS Ventral subic-
ulum, Zo Zonal layer of the superior colliculus
72 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –0.32

Fig. 3.51 
3  The Degu Brain Atlas in Stereotaxic Coordinates 73

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.52  Images for I:−0.32. 3PC Oculomotor nucleus/
parvicellular part, alv Alveus of the hippocampus, Aq
Aqueduct, BIC Nucleus of the brachium of the inferior
colliculus, bic Brachium of the inferior colliculus, CEnt
Caudomedial entorhinal cortex, CLi Caudal linear nucleus
of the raphe, cp Cerebral peduncle, DLEnt Dorsolateral
entorhinal cortex, DpG Deep gray layer of the
superior colliculus, DpWh Deep white layer of the
­superior ­colliculus, ECIC External cortex of the inferior
colliculus, Ect Ectorhinal cortex, IEnt Intermediate ento-
rhinal cortex, InG Intermediate gray layer of the superior
­colliculus, InWh Intermediate white layer of the superior col-
liculus, IPC Interpeduncular nucleus/caudal subnucleus,
IPI Interpeduncular nucleus/intermediate subnucleus,
IPL Interpeduncular nucleus/lateral subnucleus, IPR
Interpeduncular nucleus/rostral subnucleus, LV Lateral ven-
tricle, me5/Me5 Mesencephalic trigeminal tract/nucleus,
MEnt Medial entorhinal cortex, ml Medial lemniscus, mlf
Medial longitudinal fasciculus, Op Optic nerve layer of
the superior colliculus, PAG Periaqueductal gray, PaS
Parasubiculum, Post Postsubiculum, PRh Perirhinal cor-
tex, Prs Presubiculum, rf Rhinal fissure, rs Rubrospinal
tract, RSD Retrosplenial dysgranular cortex, RSG
Retrosplenial granular cortex, s5/m5 Sensory/motor root
of the trigeminal nerve, scp Superior cerebellar peduncle
(brachium conjunctivum), SNC Substantia nigra/compact
part, SNR Substantia nigra/reticular part, Su3
Supraoculomotor periaqueductal gray, SuG Superficial
gray layer of the superior colliculus, ts Tectospinal tract,
V1 Visual cortex/primary area, xscp Decussation of supe-
rior cerebellar peduncle, Zo Zonal layer of the superior
colliculus
74 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –0.98

Fig. 3.53 
3  The Degu Brain Atlas in Stereotaxic Coordinates 75

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.54  Images for I:−0.98. 4n Trochlear nerve, 4N
Trochlear nucleus, Aq Aqueduct, BIC Nucleus of the bra-
chium of the inferior colliculus, bic Brachium of the infe-
rior colliculus, CEnt Caudomedial entorhinal cortex, CIC
Central nucleus of the inferior colliculus, CnF Cuneiform
nucleus, DLEnt Dorsolateral entorhinal cortex, DpG Deep
gray layer of the superior colliculus, DpWh Deep white
layer of the superior colliculus, DRD Dorsal raphe
nucleus/dorsal part, DRL Dorsal raphe nucleus/lateral
part, DRV Dorsal raphe nucleus/ventral part, ECIC
External cortex of the inferior colliculus, Ect Ectorhinal
cortex, IEnt Intermediate entorhinal cortex, InWh
Intermediate white layer of the superior colliculus, lfp
Longitudinal fasciculus of the pons, mcp Middle cerebel-
lar peduncle, me5/Me5 Mesencephalic trigeminal tract/
nucleus, MEnt Medial entorhinal cortex, ml Medial lem-
niscus, mlf Medial longitudinal fasciculus, MnR Median
raphe nucleus, Op Optic nerve layer of the superior col-
liculus, PAG Periaqueductal gray, PaS Parasubiculum,
PBG Parabigeminal nucleus, Pn Pontine nuclei, PnO
Pontine reticular nucleus/oral part, Post Postsubiculum,
PRh Perirhinal cortex, rf Rhinal fissure, rs Rubrospinal
tract, RSD Retrosplenial dysgranular cortex, RSG
Retrosplenial granular cortex, RtTg Reticulotegmental
nucleus of the pons, s5/m5 Sensory/motor root of the tri-
geminal nerve, scp Superior cerebellar peduncle (bra-
chium conjunctivum), SuG Superficial gray layer of the
superior colliculus, tfp Transverse fibers of the pons, ts
Tectospinal tract, V1 Visual cortex/primary area, VLL
Ventral nucleus of the lateral lemniscus, xscp Decussation
of superior cerebellar peduncle, Zo Zonal layer of the
superior colliculus
76 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –1.64

Fig. 3.55 
3  The Degu Brain Atlas in Stereotaxic Coordinates 77

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.56  Images for I:−1.64. 4Cb Lobule 4 of cerebellar
vermis, 4n Trochlear nerve, 5Cb Lobule 5 of cerebellar
vermis, Aq Aqueduct, bic Brachium of the inferior collic-
ulus, CEnt Caudomedial entorhinal cortex, CIC Central
nucleus of the inferior colliculus, cic Commissure of the
inferior colliculus, CnF Cuneiform nucleus, DCIC Dorsal
cortex of the inferior colliculus, DLEnt Dorsolateral ento-
rhinal cortex, DLL Dorsal nucleus of the lateral lemnis-
cus, DRD Dorsal raphe nucleus/dorsal part, DRL Dorsal
raphe nucleus/lateral part, DRV Dorsal raphe nucleus/
ventral part, ECIC External cortex of the inferior collicu-
lus, Ect Ectorhinal cortex, ILL Intermediate nucleus of the
lateral lemniscus, lfp Longitudinal fasciculus of the pons,
ll Lateral lemniscus, mcp Middle cerebellar peduncle,
me5/Me5 Mesencephalic trigeminal tract/nucleus, MEnt
Medial entorhinal cortex, ml Medial lemniscus, mlf
Medial longitudinal fasciculus, MnR Median raphe
nucleus, PAG Periaqueductal gray, PaS Parasubiculum,
Pn Pontine nuclei, PnO Pontine reticular nucleus/oral
part, Post Postsubiculum, PRh Perirhinal cortex, rf Rhinal
fissure, rs Rubrospinal tract, RSD Retrosplenial dysgranu-
lar cortex, RSG Retrosplenial granular cortex, RtTg
Reticulotegmental nucleus of the pons, s5/m5 Sensory/
motor root of the trigeminal nerve, scp Superior cerebellar
peduncle (brachium conjunctivum), tfp Transverse fibers
of the pons, ts Tectospinal tract, V1 Visual cortex/primary
area, VLL Ventral nucleus of the lateral lemniscus, VTg
Ventral tegmental nucleus
78 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –2.3

Fig. 3.57 
3  The Degu Brain Atlas in Stereotaxic Coordinates 79

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.58  Images for I:−2.3. 2Cb Lobule 2 of cerebellar
vermis, 4Cb Lobule 4 of cerebellar vermis, 4V Fourth
ventricle, 5Cb Lobule 5 of cerebellar vermis, bic Brachium
of the inferior colliculus, CEnt Caudomedial entorhinal
cortex, CG Central gray, CIC Central nucleus of the infe-
rior colliculus, CnF Cuneiform nucleus, DCIC Dorsal
cortex of the inferior colliculus, DLL Dorsal nucleus of
the lateral lemniscus, DMTg Dorsomedial tegmental area,
DRC Dorsal raphe nucleus/caudal part, DTg Dorsal teg-
mental nucleus, ECIC External cortex of the inferior col-
liculus, Ect Ectorhinal cortex, ILL Intermediate nucleus of
the lateral lemniscus, LDTg Laterodorsal tegmental
nucleus, lfp Longitudinal fasciculus of the pons, ll Lateral
lemniscus, LPB Lateral parabrachial nucleus, m5 Motor
root of the trigeminal nerve, mcp Middle cerebellar
peduncle, me5/Me5 Mesencephalic trigeminal tract/
nucleus, mlf Medial longitudinal fasciculus, MnR Median
raphe nucleus, MPB Medial parabrachial nucleus, PaS
Parasubiculum, PnO Pontine reticular nucleus/oral part,
PRh Perirhinal cortex, rf Rhinal fissure, rs Rubrospinal
tract, RSD Retrosplenial dysgranular cortex, RtTg
Reticulotegmental nucleus of the pons, s5 Sensory root of
the trigeminal nerve, Sag Sagulum nucleus, scp Superior
cerebellar peduncle (brachium conjunctivum), tfp
Transverse fibers of the pons, ts Tectospinal tract, V1
Visual cortex/primary area, VLL Ventral nucleus of the
lateral lemniscus, vsc Ventral spinocerebellar tract
80 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –2.96

Fig. 3.59 
3  The Degu Brain Atlas in Stereotaxic Coordinates 81

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.60  Images for I:−2.96. 1Cb Lobule 1 of cerebellar
vermis (lingula), 2Cb Lobule 2 of cerebellar vermis, 3Cb
Lobule 3 of cerebellar vermis, 4Cb Lobule 4 of cerebellar
vermis, 4n Trochlear nerve, 4V Fourth ventricle, 5Cb
Lobule 5 of cerebellar vermis, CG Central gray, DMTg
Dorsomedial tegmental area, DRC Dorsal raphe nucleus/
caudal part, Fl Flocculus, IC Inferior colliculus, KF
Kölliker-Fuse nucleus, LDTg Laterodorsal tegmental
nucleus, lfp Longitudinal fasciculus of the pons, ll Lateral
lemniscus, LPB Lateral parabrachial nucleus, m5 Motor
root of the trigeminal nerve, mcp Middle cerebellar
peduncle, me5/Me5 Mesencephalic trigeminal tract/
nucleus, mlf Medial longitudinal fasciculus, MnR Median
raphe nucleus, MPB Medial parabrachial nucleus, MVPO
Medioventral periolivary nucleus, pcuf Preculminate fis-
sure, PnO Pontine reticular nucleus/oral part, prf Primary
fissure, psf Posterior superior fissure, rs Rubrospinal tract,
RtTg Reticulotegmental nucleus of the pons, s5 Sensory
root of the trigeminal nerve, scp Superior cerebellar
peduncle (brachium conjunctivum), Sim Simple lobule,
Su5 Supratrigeminal nucleus, tfp Transverse fibers of the
pons, ts Tectospinal tract, tz Trapezoid body, Tz Nucleus
of the trapezoid body, VLL Ventral nucleus of the lateral
lemniscus, vsc Ventral spinocerebellar tract
82 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –3.62

Fig. 3.61 
3  The Degu Brain Atlas in Stereotaxic Coordinates 83

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.62  Images for I:−3.62. 1Cb Lobule 1 of cerebellar
vermis (lingula), 2Cb Lobule 2 of cerebellar vermis, 3Cb
Lobule 3 of cerebellar vermis, 4Cb Lobule 4 of cerebellar
vermis, 4V Fourth ventricle, 5Cb Lobule 5 of cerebellar
vermis, 8cn Cochlear root of the vestibulocochlear nerve,
8vn Vestibular root of the vestibulocochlear nerve, CG
Central gray, Fl Flocculus, GrC Granule cell layer of the
cochlear nuclei, II Intermediate interstitial nucleus of the
medial longitudinal fasciculus, KF Kolliker-Fuse nucleus,
LC Locus coeruleus, LVPO Lateroventral periolivary
nucleus, M5 Nucleus of motor root of the trigeminal
nerve, m5 Motor root of the trigeminal nerve, mcp Middle
cerebellar peduncle, me5/Me5 Mesencephalic trigeminal
tract/nucleus, ml Medial lemniscus, mlf Medial longitudi-
nal fasciculus, MPB Medial parabrachial nucleus, MPBE
Medial parabrachial nucleus/external part, MSO Medial
superior olive, MVPO Medioventral periolivary nucleus,
PnC Pontine reticular nucleus/caudal part, Pr5 Principal
sensory trigeminal nucleus, pcuf Preculminate fissure, py
Pyramidal tract, RMg Raphe magnus nucleus, rs
Rubrospinal tract, RtTg Reticulotegmental nucleus of the
pons, s5 Sensory root of the trigeminal nerve, scp Superior
cerebellar peduncle (brachium conjunctivum), Sim Simple
lobule, sp5 Spinal trigeminal tract, ts Tectospinal tract, tz
Trapezoid body, Tz Nucleus of the trapezoid body, VCA
Ventral cochlear nucleus/anterior part, vsc Ventral spino-
cerebellar tract
84 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –4.28

Fig. 3.63 
3  The Degu Brain Atlas in Stereotaxic Coordinates 85

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.64  Images for I:−4.28. 1Cb Lobule 1 of cerebellar
vermis (lingula), 2Cb Lobule 2 of cerebellar vermis, 3Cb
Lobule 3 of cerebellar vermis, 4Cb Lobule 4 of cerebellar
vermis, 4V Fourth ventricle, 5Cb Lobule 5 of cerebellar
vermis, 5Tr Trigeminal transition zone, 6n Abducens
nerve, 7n Facial nerve, 8cn Cochlear root of the vestibulo-
cochlear nerve, 8vn Vestibular root of the vestibuloco-
chlear nerve, Fl Flocculus, g7 Genu of the facial nerve,
GrC Granule cell layer of the cochlear nuclei, icp Inferior
cerebellar peduncle (restiform body), LC Locus coeru-
leus, LPO Lateral preoptic area, LSO Lateral superior
olive, M5 Nucleus of motor root of the trigeminal nerve,
mcp Middle cerebellar peduncle, ml Medial lemniscus,
mlf Medial longitudinal fasciculus, MPB Medial parabra-
chial nucleus, MPO Medial preoptic nucleus, MSO
Medial superior olive, MVeMC Medial vestibular nucleus/
magnocellular part, P5 Peritrigeminal zone, PCRt
Parvicellular reticular nucleus, pcuf Preculminate fissure,
PFl Paraflocculus, plf Posterolateral fissure, PnC Pontine
reticular nucleus/caudal part, Pr Prepositus nucleus, Pr5
Principal sensory trigeminal nucleus, prf Primary fissure,
psf Posterior superior fissure, py Pyramidal tract, RIP
Raphe interpositus nucleus, RMg Raphe magnus nucleus,
RPa Raphe pallidus nucleus, rs Rubrospinal tract, scp
Superior cerebellar peduncle (brachium conjunctivum),
Sim Simple lobule, Pr5 Principal sensory trigeminal
nucleus, SuVe Superior vestibular nucleus, ts Tectospinal
tract, tz Trapezoid body, Tz Nucleus of the trapezoid body,
un Uncinate fasciculus of the cerebellum, VCA Ventral
cochlear nucleus/anterior part, vsc Ventral spinocerebellar
tract
86 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –4.94

Fig. 3.65 
3  The Degu Brain Atlas in Stereotaxic Coordinates 87

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.66  Images for I:−4.94. 1Cb Lobule 1 of cerebellar
vermis (lingula), 2Cb Lobule 2 of cerebellar vermis, 3Cb
Lobule 3 of cerebellar vermis, 4Cb Lobule 4 of cerebellar
vermis, 4V Fourth ventricle, 5Cb Lobule 5 of cerebellar
vermis, 6Cb Lobule 6 of cerebellar vermis, 6N Abducens
nucleus, 7N Facial nucleus, 8vn Vestibular root of the ves-
tibulocochlear nerve, Crus1 Crus1 of the ansiform lobule,
DCDp Dorsal cochlear nucleus/deep core, DCFu Dorsal
cochlear nucleus/fusiform layer, DCMo Dorsal cochlear
nucleus/molecular layer, DMSp5 Dorsomedial spinal tri-
geminal nucleus, DPGi Dorsal paragigantocellular
nucleus, Fl Flocculus, g7 Genu of the facial nerve, Gi
Gigantocellular reticular nucleus, icp Inferior cerebellar
peduncle (restiform body), IntA Anterior interposed cere-
bellar nucleus, IRt Intermediate reticular nucleus, Lat
Lateral (dentate) cerebellar nucleus, LPGi Lateral paragi-
gantocellular nucleus, LPO Lateral preoptic area, LR4V
Lateral recess of the 4th ventricle, LSO Lateral superior
olive, LVe Lateral vestibular nucleus, ml Medial lemnis-
cus, MPO Medial preoptic nucleus, MSO Medial superior
olive, MVeMC Medial vestibular nucleus/magnocellular
part, MVePC Medial vestibular nucleus/parvicellular part,
PCRt Parvicellular reticular nucleus, pcuf Preculminate
fissure, PFl Paraflocculus, pfs Parafloccular sulcus, plf
Posterolateral fissure, Pr Prepositus nucleus, prf Primary
fissure, psf Posterior superior fissure, py Pyramidal tract,
RIP Raphe interpositus nucleus, RMg Raphe magnus
nucleus, RPa Raphe pallidus nucleus, rs Rubrospinal
tract, scp Superior cerebellar peduncle (brachium con-
junctivum), Sim Simple lobule, RMg Raphe magnus
nucleus, RPa Raphe pallidus nucleus, SuS Superior saliva-
tory nucleus, SuVe Superior vestibular nucleus, tz
Trapezoid body, Tz Nucleus of the trapezoid body, VCP
Ventral cochlear nucleus/posterior part, VeCb
Vestibulocerebellar nucleus, vsc Ventral spinocerebellar
tract
88 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –5.60

Fig. 3.67 
3  The Degu Brain Atlas in Stereotaxic Coordinates 89

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.68  Images for I:−5.60. 3Cb Lobule 3 of cerebellar
vermis, 4Cb Lobule 4 of cerebellar vermis, 4V Fourth
ventricle, 5Cb Lobule 5 of cerebellar vermis, 5Sol trigem-
inal-solitary transition zone, 6Cb Lobule 6 of cerebellar
vermis, 7N Facial nucleus, Crus1 Crus1 of the ansiform
lobule, das Dorsal acoustic stria, DCDp Dorsal cochlear
nucleus/deep core, DCFu Dorsal cochlear nucleus/fusi-
form layer, DCMo Dorsal cochlear nucleus/molecular
layer, DMSp5 Dorsomedial spinal trigeminal nucleus,
DPGi Dorsal paragigantocellular nucleus, Gi
Gigantocellular reticular nucleus, GiA Gigantocellular
reticular nucleus/alpha part, icp Inferior cerebellar pedun-
cle (restiform body), IntA Anterior interposed cerebellar
nucleus, IRt Intermediate reticular nucleus, IS Inferior
salivatory nucleus, Lat Lateral (dentate) cerebellar
nucleus, LatPC lateral cerebellar nucleus, parvicellular
part, LR4V Lateral recess of the 4th ventricle, LVe Lateral
vestibular nucleus, Med Medial (fastigial) cerebellar
nucleus, ml Medial lemniscus, mlf Medial longitudinal
fasciculus, MVeMC Medial vestibular nucleus/magnocel-
lular part, MVePC Medial vestibular nucleus/parvicellular
part, PFl Paraflocculus, pfs Parafloccular sulcus, prf
Primary fissure, psf Posterior superior fissure, py
Pyramidal tract, PCRt Parvicellular reticular nucleus,
RMg Raphe magnus nucleus, RPa Raphe pallidus nucleus,
rs Rubrospinal tract, Sim Simple lobule, simf Simplex fis-
sure, SMV Superior medullary velum, sp5 Spinal trigemi-
nal tract, Sp5O Spinal trigeminal nucleus/oral part, SpVe
Spinal vestibular nucleus, ts Tectospinal tract, tz Trapezoid
body, VCP Ventral cochlear nucleus/posterior part, VeCb
Vestibulocerebellar nucleus, Y Nucleus Y of the vestibular
complex
90 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –6.26

Fig. 3.69 
3  The Degu Brain Atlas in Stereotaxic Coordinates 91

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.70  Images for I:−6.26. 10Cb Lobule 10 of cere-
bellar vermis (nodule), 4V Fourth ventricle, 5Sol trigemi-
nal-solitary transition zone, 6Cb Lobule 6 of cerebellar
vermis, 7N Facial nucleus, 8cn Cochlear root of the ves-
tibulocochlear nerve, chp Choroid plexus, Crus1 Crus1 of
the ansiform lobule, Crus2 Crus2 of the ansiform lobule,
das Dorsal acoustic stria, DCDp Dorsal cochlear nucleus/
deep core, DCFu Dorsal cochlear nucleus/fusiform layer,
DCMo Dorsal cochlear nucleus/molecular layer, DMSp5
Dorsomedial spinal trigeminal nucleus, DPGi Dorsal
paragigantocellular nucleus, Gi Gigantocellular reticular
nucleus, icf Intercrural fissure, icp Inferior cerebellar
peduncle (restiform body), IntP Posterior interposed cer-
ebellar nucleus, IRt Intermediate reticular nucleus, LPGi
Lateral paragigantocellular nucleus, LR4V Lateral recess
of the 4th ventricle, Med Medial (fastigial) cerebellar
nucleus, ml Medial lemniscus, mlf Medial longitudinal
fasciculus, MVe Medial vestibular nucleus, PCRt
Parvicellular reticular nucleus, PFl Paraflocculus, pfs
Parafloccular sulcus, Pr Prepositus nucleus, py Pyramidal
tract, RMg Raphe magnus nucleus, RPa Raphe pallidus
nucleus, rs Rubrospinal tract, Sol Nucleus of the solitary
tract, SolM Nucleus of the solitary tract/medial part, sp5
Spinal trigeminal tract, Sp5O Spinal trigeminal nucleus/
oral part, SpVe Spinal vestibular nucleus, ts Tectospinal
tract, VCP Ventral cochlear nucleus/posterior part, X
Nucleus X
92 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –6.92

Fig. 3.71 
3  The Degu Brain Atlas in Stereotaxic Coordinates 93

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.72  Images for I:−6.92. 10Cb Lobule 10 of cere-
bellar vermis (nodule), 10N Dorsal motor nucleus of
vagus, 4V Fourth ventricle, 5Sol trigeminal-solitary tran-
sition zone, 6Cb Lobule 6 of cerebellar vermis, 7Cb
Lobule 7 of cerebellar vermis, 8Cb Lobule 8 of cerebellar
vermis, 9Cb Lobule 9 of cerebellar vermis (uvula), Amb
Ambiguus nucleus, ampf Ansoparamedian fissure, chp
Choroid plexus, Cop Copula of the pyramis, Crus1 Crus1
of the ansiform lobule, DMSp5 Dorsomedial spinal tri-
geminal nucleus, ECu External cuneate nucleus, Gi
Gigantocellular reticular nucleus, GiV Gigantocellular
reticular nucleus/ventral part, icf Intercrural fissure, icp
Inferior cerebellar peduncle (restiform body), IOD
Inferior olive/dorsal nucleus, IOM Inferior olive/medial
nucleus, IOPr Inferior olive/principal nucleus, IRt
Intermediate reticular nucleus, LPGi Lateral paragiganto-
cellular nucleus, LR4V Lateral recess of the 4th ventricle,
ml Medial lemniscus, mlf Medial longitudinal fasciculus,
MVe Medial vestibular nucleus, PCRt Parvicellular reticu-
lar nucleus, PFl Paraflocculus, plf Posterolateral fissure,
PM Paramedian lobule, ppf Prepyramidal fissure, Pr
Prepositus nucleus, psf Posterior superior fissure, py
Pyramidal tract, Rob Raphe obscurus nucleus, RPa Raphe
pallidus nucleus, rs Rubrospinal tract, sf Secondary fis-
sure, Sol Nucleus of the solitary tract, SolM Nucleus of
the solitary tract/medial part, SolV Nucleus of the solitary
tract/ventral part, SolVL Nucleus of the solitary tract/ven-
trolateral part, sp5 Spinal trigeminal tract, Sp5I Spinal
trigeminal nucleus/interpolar part, SpVe Spinal vestibular
nucleus, ts Tectospinal tract
94 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –7.58

Fig. 3.73 
3  The Degu Brain Atlas in Stereotaxic Coordinates 95

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.74  Images for I:−7.58. 10Cb Lobule 10 of cere-
bellar vermis (nodule), 10N Dorsal motor nucleus of
vagus, 12N Hypoglossal nucleus, 5Sol Trigeminal-solitary
transition zone, 6Cb Lobule 6 of cerebellar vermis, 7Cb
Lobule 7 of cerebellar vermis, 8Cb Lobule 8 of cerebellar
vermis, 9Cb Lobule 9 of cerebellar vermis (uvula), Amb
Ambiguus nucleus, ampf Ansoparamedian fissure, Cop
Copula of the pyramis, Crus1 Crus1 of the ansiform lob-
ule, Crus2 Crus2 of the ansiform lobule, Cu Cuneate
nucleus, DMSp5 Dorsomedial spinal trigeminal nucleus,
ECu External cuneate nucleus, Gi Gigantocellular reticu-
lar nucleus, GiV Gigantocellular reticular nucleus/ventral
part, icf Intercrural fissure, icp Inferior cerebellar peduncle
(restiform body), IOD Inferior olive/dorsal nucleus, IOM
Inferior olive/medial nucleus, IOPr Inferior olive/principal
nucleus, IRt Intermediate reticular nucleus, Li Linear
nucleus of the medulla, LPGi Lateral paragigantocellular
nucleus, ml Medial lemniscus, mlf Medial longitudinal fas-
ciculus, MVe Medial vestibular nucleus, Mx Matrix region
of the medulla, PCRt Parvicellular reticular nucleus, PFl
Paraflocculus, plf Posterolateral fissure, ppf Prepyramidal
fissure, psf Posterior superior fissure, Ro Nucleus of Roller,
ROb Raphe obscurus nucleus, RPa Raphe pallidus nucleus,
rs Rubrospinal tract, sf Secondary fissure, Sol Nucleus of
the solitary tract, SolL Nucleus of the solitary tract/lateral
part, SolM Nucleus of the solitary tract/medial part, SolV
Nucleus of the solitary tract/ventral part, sp5 Spinal tri-
geminal tract, Sp5I Spinal trigeminal nucleus/interpolar
part, SpVe Spinal vestibular nucleus, ts Tectospinal tract,
vsc Ventral spinocerebellar tract
96 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –8.24

Fig. 3.75 
3  The Degu Brain Atlas in Stereotaxic Coordinates 97

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.76  Images for I:−8.24. 10Cb Lobule 10 of cere-
bellar vermis (nodule), 10N Dorsal motor nucleus of
vagus, 12N Hypoglossal nucleus, 7Cb Lobule 7 of cere-
bellar vermis, 8Cb Lobule 8 of cerebellar vermis, 9Cb
Lobule 9 of cerebellar vermis (uvula), Amb Ambiguus
nucleus, AP Area postrema, ampf Ansoparamedian fis-
sure, cc Corpus callosum, CeCv Central cervical nucleus,
Cop Copula of the pyramis, Crus2 Crus2 of the ansiform
lobule, cu Cuneate fasciculus, Cu Cuneate nucleus, dcs
Dorsal corticospinal tract, ECu External cuneate nucleus,
gr Gracile fasciculus, Gr Gracile nucleus, IOD Inferior
olive/dorsal nucleus, IOM Inferior olive/medial nucleus,
IRt Intermediate reticular nucleus, LRt Lateral reticular
nucleus, LRtPC Lateral reticular nucleus/parvicellular
part, MdD Medullary reticular nucleus/dorsal part, MdV
Medullary reticular nucleus/ventral part, ml Medial lem-
niscus, mlf Medial longitudinal fasciculus, PM Paramedian
lobule, PMn Paramedian reticular nucleus, py Pyramidal
tract, rs Rubrospinal tract, Sol Nucleus of the solitary
tract, SolC Nucleus of the solitary tract/commissural part,
SolL Nucleus of the solitary tract/lateral part, SolM
Nucleus of the solitary tract/medial part, SolV Nucleus of
the solitary tract/ventral part, sp5 Spinal trigeminal tract,
Sp5C Spinal trigeminal nucleus/caudal part, Sp5I Spinal
trigeminal nucleus/interpolar part, ts Tectospinal tract, vsc
Ventral spinocerebellar tract
98 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –8.90

Fig. 3.77 
3  The Degu Brain Atlas in Stereotaxic Coordinates 99

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.78  Images for I:−8.90.10N Dorsal motor nucleus
of vagus, 12N Hypoglossal nucleus, 8Cb Lobule 8 of cer-
ebellar vermis, 9Cb Lobule 9 of cerebellar vermis (uvula),
CC Central canal, cu Cuneate fasciculus, Cu Cuneate
nucleus, dcs Dorsal corticospinal tract, gr Gracile fascicu-
lus, Gr Gracile nucleus, IOM Inferior olive/medial
nucleus, IRt Intermediate reticular nucleus, LRt Lateral
reticular nucleus, LRtPC Lateral reticular nucleus/parvi-
cellular part, MdD Medullary reticular nucleus/dorsal
part, MdV Medullary reticular nucleus/ventral part, mlf
Medial longitudinal fasciculus, mlx Decussation of the
medial lemniscus, Mx Matrix region of the medulla, py
Pyramidal tract, pyx Pyramidal decussation, RAmb
Retroambiguus nucleus, rs Rubrospinal tract, Sol Nucleus
of the solitary tract, SolC Nucleus of the solitary tract/
commissural part, SolL Nucleus of the solitary tract/lat-
eral part, SolM Nucleus of the solitary tract/medial part,
SolV Nucleus of the solitary tract/ventral part, sp5 Spinal
trigeminal tract, Sp5C Spinal trigeminal nucleus/caudal
part, ts Tectospinal tract, vsc Ventral spinocerebellar tract
100 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –9.56

Fig. 3.79 
3  The Degu Brain Atlas in Stereotaxic Coordinates 101

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.80  Images for I:−9.56. 10N Dorsal motor nucleus
of vagus, 9Cb Lobule 9 of cerebellar vermis (uvula), CC
Central canal, CeCv Central cervical nucleus, cu Cuneate
fasciculus, Cu Cuneate nucleus, dcs Dorsal corticospinal
tract, dsc Dorsal spinocerebellar tract, gr Gracile fascicu-
lus, Gr Gracile nucleus, IRt Intermediate reticular nucleus,
MdD Medullary reticular nucleus/dorsal part, MdV
Medullary reticular nucleus/ventral part, mlf Medial lon-
gitudinal fasciculus, pyx Pyramidal decussation, rs
Rubrospinal tract, SolC Nucleus of the solitary tract/com-
missural part, SolM Nucleus of the solitary tract/medial
part, sp5 Spinal trigeminal tract, Sp5C Spinal trigeminal
nucleus/caudal part, ts Tectospinal tract, vsc Ventral spi-
nocerebellar tract
102 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –10.22

Fig. 3.81 
3  The Degu Brain Atlas in Stereotaxic Coordinates 103

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.82  Images for I:−10.22. 11N Accessory nerve
nucleus, 9Cb Lobule 9 of cerebellar vermis (uvula), CC
Central canal, CeCv Central cervical nucleus, cu Cuneate
fasciculus, Cu Cuneate nucleus, dcs Dorsal corticospinal
tract, dsc Dorsal spinocerebellar tract, gr Gracile fascicu-
lus, Gr Gracile nucleus, IRt Intermediate reticular nucleus,
MdD Medullary reticular nucleus/dorsal part, MdV
Medullary reticular nucleus/ventral part, mlf Medial lon-
gitudinal fasciculus, pyx Pyramidal decussation, rs
Rubrospinal tract, mlf Medial longitudinal fasciculus, pyx
Pyramidal decussation, rs Rubrospinal tract, vsc Ventral
spinocerebellar tract
104 3  The Degu Brain Atlas in Stereotaxic Coordinates

I: –10.88

Fig. 3.83 
3  The Degu Brain Atlas in Stereotaxic Coordinates 105

10 9 8 7 6 5 4 3 2 1 0 1

5 5

0 0

5 5

10 9 8 7 6 5 4 3 2 1 0 1

Fig. 3.84  Images for I:−10.88. 11N Accessory nerve
nucleus, CC Central canal, CeCv Central cervical nucleus,
cu Cuneate fasciculus, dcs Dorsal corticospinal tract, dsc
Dorsal spinocerebellar tract, gr Gracile fasciculus, IRt
Intermediate reticular nucleus, MdD Medullary reticular
nucleus/dorsal part, MdV Medullary reticular nucleus/
ventral part, mlf Medial longitudinal fasciculus, pyx
Pyramidal decussation, rs Rubrospinal tract, sp5 Spinal
trigeminal tract, Sp5C Spinal trigeminal nucleus/caudal
part, ts Tectospinal tract, vsc Ventral spinocerebellar tract
106 3  The Degu Brain Atlas in Stereotaxic Coordinates

Interaural: +17.0 mm Interaural: +13.0 mm

14 14
12 12
10 10
8 8
6 6
4 4
2 2
0 0
2 2
4 4
6 6
8 8
10 10
12 12
14 14
12 10 8 6 4 2 0 2 4 6 8 10 12 12 10 8 6 4 2 0 2 4 6 8 10 12

Interaural: +9.0 mm Interaural: +5.0 mm

14 14
12 12
10 10
8 8
6 6
4 4
2 2
0 0
2 2
4 4
6 6
8 8
10 10
12 12
14 14
12 10 8 6 4 2 0 2 4 6 8 10 12 12 10 8 6 4 2 0 2 4 6 8 10 12
Interaural: +1.0 mm (Marker) Interaural: –3.0 mm
14 14
12 12
10 10
8 8
6 6
4 4
2 2
0 0
2 2
4 4
6 6
8 8
10 10
12 12
14 14
12 10 8 6 4 2 0 2 4 6 8 10 12 12 10 8 6 4 2 0 2 4 6 8 10 12

Fig. 3.85  Coronal images, reconstructed from volume rendered brain model, in “conventional” plane with an AC-PC
line as a horizontal zero axis. Annotations are in common with Figs. 3.2 through 3.84
3  The Degu Brain Atlas in Stereotaxic Coordinates 107

a
10
8
6
4
2
0
2
4
6
8
10
18 16 14 12 10 8 6 4 2 0 2 4 6 8 10
10
8
6
4
2
0
2
4
6
8
10
18 16 14 12 10 8 6 4 2 0 2 4 6 8 10
b
6
4
2
0
2
4
6

18 16 14 12 10 8 6 4 2 0 2 4 6 8 10

6
4
2
0
2
4
6

18 16 14 12 10 8 6 4 2 0 2 4 6 8 10

Fig. 3.86  Horizontal (a) and parasagittal (b) images, reconstructed from volume rendered brain model, in “conven-
tional” plane with an AC-PC line as a horizontal zero axis. Annotations are in common with Figs. 3.2 through 3.84
 Operation of Web-Accessible
Volume-Rendering Model
of the Degu Brain
Introduction
Overview
SG-eye Atlas is a software used for viewing the
brain atlas database created by SG-eye Studio,
and consists of the following two applications:
• SG-eye Atlas
• SG-eye 3D Atlas
SG-eye Atlas displays various images such as
staining images of brain sections and MRI images
that also contain structure information. It also
displays 3D models created from images that
also contain structure information and 3D shapes
with color coding for all types of structures.
Other features include defining cutting planes
and displaying sections.
SG-eye Atlas and SG-eye 3D Atlas use the
same data files. In other words, one data file
contains both image data and 3D models. The
application has a link feature, but its capabili-
ties include the ability to display, with just one
© Springer Japan KK, part of Springer Nature 2018
N. Kumazawa-Manita et al., The 3D Stereotaxic Brain Atlas of the Degu, Brain Science,
https://doi.org/10.1007/978-4-431-56615-1_4
4
click, staining images in SG-eye Atlas that cor-
respond to sections displayed in SG-eye 3D
Atlas.
Installing SG-Eye Atlas (Windows)
SG-eye Atlas can be installed using the following
commands:
[DRIVE LETTER]\SGeyeAtlas\setup.exe 32 bit
[DRIVE LETTER]\SGeyeAtlas.x64\setup.exe 64 bit
on the installation disk. When performing a
64-bit OS installation, the use of the “x64” file is
recommended. During the installation, only the
installation destination can be configured.
Installing SG-Eye Atlas (Mac OS X)
SG-eye Atlas can be installed using
「SGeyeAtlas\AGeyeAtlas.pkg」
on the installation disk. Please enter the
administrator password when asked.
109
110 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain
Launching SG-Eye Atlas (Windows)
Launch the application by clicking on Start > All
programs  >  SG-eye v 3.7  >  SG-eye Atlas or
SG-eye 3D Atlas.
As there are no data immediately after launch-
ing the application, nothing is displayed. The
loading of data and other operations are explained
below.
Launching SG-Eye Atlas (Mac OS X)
The application is launched by double-clicking
on SG-eye Atlas or SG-eye 3D Atlas in the
Applications/SG-eye/SG-eye Atlas v 3.7 folder
in the Finder.
When using Mac OS X 10.7, the application
can also be launched by clicking on SG-eye
Atlas or SG-eye 3D Atlas in SG-eye (others) in
Launchpad.
Operating Environment
The software requires one of the following oper-
ating system environments:
OS Windows XP (32 bit / 64 bit)
Windows Vista (32 bit / 64 bit)
Windows 7 (32 bit / 64 bit)
Mac OS X 10.5 or higher
CPU Intel x86 CPU or equivalent CPU, Pentium
4 or higher essential (Core2Duo 2.0 GHz,
equivalent, or higher recommended)
Memory 1 GB or more (2 GB or more
recommended)
Hard 200 MB or more free space (excluding
disk data storage domain)
Graphics OpenGL compatible GPU (For the
acceleration for volume rendering, support
of OpenGL 2.0 or higher, Shader Model
3.0 or higher, and Frame Buffer Object is
essential)
SG-eye 3D Atlas provides a 3D shape display
feature using volume rendering. The volume ren-
dering speed varies greatly depending on the
computer’s graphics performance. To obtain the
optimum speed, the conditions given in parenthe-
ses above are required. Conversely, if the condi-
tions above are not met, calculations and
rendering are automatically performed by the
CPU (low speed). In addition, even if the condi-
tions outlined above are met, calculations and
rendering are performed by the CPU if the graph-
ics memory is insufficient. To display the optional
high-resolution volume rendering, hardware
acceleration is essential.
The required hard disk capacity indicates the
memory required to install all SG-eye Atlas
applications. Please note that higher capacity is
required for data storage.
Using SG-Eye Atlas 111

Using SG-Eye Atlas Loading Data

In this section, the actual use of the application is When SG-eye Atlas is launched, the data are first
explained, starting with SG-eye Atlas, which is loaded. To load data, use the File > Open menu.
an application for viewing 2D images. When the data have been loaded, the screen
changes as follows.

Displaying Images thumbnail images in the Thumbnail. By clicking

on any of the images, the image in that position is
When the data have been loaded, the 3D models displayed in the main window.
in the Position window are displayed as complete
112 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

The image displayed in the main window can Switch to line drawing layer display
be panned and zoomed.
Pan Move the image by clicking the
left mouse button and dragging Switch to structure display

Zoom Zoom in or zoom out the image

by clicking the left mouse button Switch to coordinate axes display
and dragging

Fit Display image to fill the whole Switch to grid display

window

Switch to dimensions display

10% Display at a magnification of 10%
20% Display at a magnification of 20%
50% Display at a magnification of 50%
100% Display at a magnification of Switch to bounding box display
100%
200% Display at a magnification of
200% Switch to information display

The Navigator window shows the scope of the

Switch to label display
image currently displayed in the main window.
When clicking the left mouse button in the
Navigator window, the image displayed in the
Switch to annotation display
main window shifts such that its new center posi-
tion is the location that was clicked.

Switch to markers display

Grid and dimension properties can be set in

the dialog box displayed under Image  >  Set
Options.

It is also possible to switch to the following

display modes:
Switch to image display

Switch to MRI layer display

Switch to MRI layer display (top right

corner of screen)
Using SG-Eye Atlas 113

Scale Solid Line Sets the interval for a solid line on the grid
Dot Line Sets the interval for a dotted line on the grid
Scale Sets the interval for the dimensions displayed on the screen
Unit Sets the dimension units at either mm or μm
Decimal Sets the number of decimal points for the dimensions displayed
Font Sets the font for the displayed dimensions
Color Sets the color for the grid lines and the displayed dimensions
Line Sets the line width for the grid (solid lines)
Width–Solid
Line Width–Dot Sets the line width for the grid (dotted lines)

Selecting Structures The selected structure can also be selected in

the Structures tree view. In addition, the structure
Structures can be selected by clicking on the selected in the main window is highlighted and
structure displayed in the main window with the the hierarchical brain structure is displayed at the
right mouse button or by clicking on the structure top left corner.
with the left mouse button, after switching to the
structure select mode by clicking on the
button
­ in the Image toolbar.
114 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

Searching Structures Display Properties for Groups

Structures can also be searched and selected by
entering the name or abbreviation in the search
box in the toolbar. The option to allow searches
by either name or abbreviation can be set using
the Name radio button or Abbreviation radio
button.
When structures have been grouped, display prop-
erties can be set for each group. They can be set in
the menu displayed by clicking on the Group tab
in the Structure window, by right-­clicking on the
group name, or from the tool button at the top of
the list. The properties that can be set are the same
as the individual structure display properties.

Structure Display Properties

Adding Labels or Annotations
Display properties for the selected structure can
be set using the menu displayed by right-clicking
Labels can be added to both images and structures.
on the Structure window or from the tool button
at the top of the structure tree.
1. Display the image to which you want to add
Show Switches to structure a label. If you want to add a label to a struc-
display
ture, first select that structure.
2. When adding a label to an image, switch to
Transparent Switches to Background using the button in the Label
semitransparent
display
window. When adding a label to a structure,
use the same method to switch to Structures.
Fill Switched to fill display
mode

Line Switched to line

display mode
Using SG-Eye Atlas 115

3. By clicking on the Label  >  Append menu, 4. Enter a subject. The subject text will be dis-
the Add label window opens. played with the image.

5. The display color of the subject is entered as

RGB values.

6. Enter the font for the subject. Select the font

from the dialog box displayed when clicking
on the […] button.

7. Select the marker shape. Markers are the

symbols placed at both sides of the ticks.
116 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

8. Enter the marker color as RGB values.

9. Enter the numbers, that is, numbers or letters

placed at both sides of the ticks. Leave this
space blank if you do not want to add these.

10. Enter the number color in RGB values.

11. Enter the number font.

12. Select the number of joints for the ticks.

Entering 0 signifies the absence of ticks.
Using SG-Eye Atlas 117

13. Enter the color of the ticks in RGB values.

14. Enter a memo. This can be omitted.

This is how labels are added. The default dis-

play position for labels is randomized. Please
refer to the description below on how to move a
label to its intended location.

4. After the label is moved, click the Commit

button in the Label toolbar.

Adding Annotations

It is possible to add annotations to images or

structures.

1. Display the image to which you want to add

an annotation. If you want to add an annota-
Moving Labels
tion to a structure, first select the structure.
2. When adding an annotation to an image,

1. Select the label that you want to move in the
switch to Background using the Annotation
Label window.
window button. If you want to add an annota-
2. Click the Translate button in the Label tool-
tion to a structure, use the same method to
bar. The joints of the ticks are displayed with
switch to Structures.
X signs.

3. Labels can be moved by clicking the left

mouse button on the joints and dragging
them.
118 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

3. When you click on the Annotation > Append

menu, the Add annotation wizard opens.
4. Select a marker. You can choose from 10

colors.

5. Enter the subject. A speech balloon will be

displayed for the subject and a note (which is
to be set next) when the annotation is clicked.

6. Enter a note. This is optional. A speech bal-

loon will be displayed for the subject and a
note when the annotation is clicked.

This is how annotations are added. The default The speech balloon will disappear if the anno-
display position of annotations is random. Refer tation is clicked again.
to the description below on how to move an
annotation to its intended location.
Moving Annotations

1. Select the annotation that you want to move in

the Annotation window.
2. Click the Translate button in the Annotation
toolbar.
Using SG-Eye Atlas 119

3. Move the annotation by clicking on the left
mouse button and dragging it.
4. After the annotation is moved, click the
Commit button in the Annotation toolbar.
2. When adding a marker to an image, switch to
Background using the button in the Marker
window. When adding a marker to a struc-
ture, use the same method to switch to
Structures.

Adding Markers

It is possible to add markers to images and struc-

tures. Markers are very similar to labels, but they
do not have ticks. Also, they do not have a subject
displayed. They are simply used as markers.

1. Display the image to which you want to add a

marker. If you want to add a marker to a struc- 3. By clicking on the Marker > Append menu,
ture, first select that structure. the Add marker wizard opens.
4. Enter a subject. The subject text will be dis-
played with the image.

5. Select the shape of the marker.

6. Select the size of the marker. When selecting

Small, the marker is displayed as an 8-pixel
image, and when selecting Large, it is dis-
played as a 16-pixel image.
120 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain
This is how a marker is added. The default dis-
play position of markers is random. Refer to the
description below on how to move a marker to its
intended location.
Moving Markers
1. Select the marker that you want to move in the
Marker window.
2. Click the Translate button in the Marker
­toolbar.
3. Markers can be moved by clicking the left
mouse button on the joints and dragging them.
4. After the marker is moved, click the Commit
button in the Marker toolbar.
Links
If 3D model data are contained in the data file, an
M icon is displayed at the top right corner of the
SG-eye Atlas main window.
Using SG-Eye Atlas 121

By clicking on the M icon, SG-eye 3D Atlas is

launched; the same file opens automatically and
the 3D shape is displayed.
122 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

Using SG-Eye 3D Atlas Moves viewpoint to show any free

section
This section explains the use of SG-eye 3D
Atlas, which is an application for viewing 3D Switches to model display
models.
Switches to structure contour display (in
clipping view)
Loading Data
Switches to label display
When launching SG-eye 3D Atlas, data are first
loaded. To load data, use the File > Open menu.
When data have been loaded, the screen Switches to annotation display
changes as follows.
The 3D model displayed in the main window
can be panned, rotated, and zoomed. Switches to marker display
Pan Move the model by clicking the
left mouse button and dragging
Switches to coordinates display
Rotate Rotate the model by clicking the
left mouse button and dragging
Switches to bounding box display

Zoom Expand or shrink the model by

clicking the left mouse button
and dragging Switches to dimensions display

Fit Display the model to fill the

whole window
Switches to information display

It is possible to change to the following dis- Switches to volume rendering display

play modes:
Switches to perspective or parallel
projection display of the model

Switches to high resolution volume

Moves viewpoint to show sagittal rendering display
section. When pressed repeatedly, the
model is rotated by 90° on its sagittal
(X) axis Switches to MRI layer display
Moves viewpoint to show coronal
section. When pressed repeatedly, the
model is rotated by 90° on its coronal
Switches to bregma/lambda position
(Y) axis
display
Moves viewpoint to show horizontal (Z)
section. When pressed repeatedly, the
model is rotated by 90° on its horizontal Other display properties can be set in the dialog
axis
box displayed under Volume Model > Set options.
Using SG-Eye 3D Atlas 123
124 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

Rendering Surface Specular Switches specular reflection On/Off

Rendering
Volume Type Selects the type of volume rendering. Select from the following:
Rendering  • No Shading
 • Shading
 • Shading With Specular
Quality Sets the display quality. Select from 0 (most coarse) to 6 (highest
resolution)
Quality when Sets display quality when moving, rotating, and zooming with
Moving mouse
Select from 0 (most coarse) to 4 (same as when at standstill)
Scale Interval–Long Sets dimension display interval (long)
Interval–Short Sets dimension display interval (short)
Interval–Number Sets dimension interval display (numbers)
Direction Sets the side dimensions displayed on
C (+h/+s) which signifies that dimensions are displayed on the
+h side (+z side, +s side, +x side) in the direction of the C axis
(Y axis) of the bounding box
Unit Sets the dimensions units at either mm or μm
Decimal Sets the number of decimal points for the dimensions displayed
Font Sets the font of the displayed dimensions
Color Sets the color of the displayed dimensions
Line Width Sets the line width of the displayed dimensions

Selecting Structures The selected structure can also be selected in

the Structures tree view. In addition, the structure
Structures can be selected by clicking the right selected in the main window is highlighted and
mouse button on the structure displayed in the the hierarchical brain structure is displayed at the
main window or by double-clicking the left top left corner.
mouse button on the structure after switching to
the structure select mode using the button in
the Volume > Model toolbar.
Using SG-Eye 3D Atlas 125

Wireframe Switches to line display (in

By clicking on the button, the structure surface view)
can be rotated, expanded, or shrunk, as it was
selected.
Dot Switches to dots display
(in surface view)

Searching Structures
Show Switches structure contour
Contour display On/Off (in clipping
Structures can also be searched and selected by view)
entering a name or abbreviation in the search box
Transparent Switches semitransparent
in the toolbar. The option enabling you to search display of contours On/Off
by either name or abbreviation can be set using (in clipping view)
the Name radio button or Abbreviation radio
button. Fill Fill display mode (in
clipping view)

Line Line display mode (in

clipping view)

Display Properties for Groups

When structures have been grouped, display prop-

erties can be set for each group. They can be set in
the menu displayed by clicking on the Group tab
in the Structure window, by right-­clicking on the
group name, or from the tool button at the top of
the list. The properties that can be set are the same
as the individual structure display properties.

Structure Display Properties

Display properties for the selected structure can

be set using the menu displayed by right-clicking
on the Structure window or from the tool button
at the top of the structure tree.

Show Switches structure display

On/Off

Transparent Switches semitransparent

display On/Off (in surface
view)

Surface Switches to surface display

(in surface view)
126 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

Displaying Clippings and Sections Axial Clipping S/C/H Switches the clipping’s

checkboxes axial direction
Display settings for 3D shape clippings and cut- S/C/H slider Sets the clipping
position
ting planes (sections) can be set in the Clipping
S/C/H Rev Reverses the clipping
window. checkboxes direction
Plane S/C/H Switches the section’s
checkboxes axial direction
S/C/H sliders, Switches the section’s
edit display position
Free Clipping C checkbox Switches clippings
S/C/H sliders Sets the clipping
position and angle. S
signifies the angles
around the X axis (red)
and H signifies the
angles around the Z
axis (green)
C Rev Reverses the clipping
checkbox direction
Plane C checkbox Switches sections
S/C/H sliders Sets the section
position and angle. S
signifies the angles
around the X axis (red)
and H signifies the
angles around the Z
axis (green)
Using SG-Eye 3D Atlas 127

 dding Labels, Annotation,

A Adds labels, etc., to sagittal sections
and Markers to Sections (X axis sections)

It is possible to add labels, annotations, and
markers to clippings of 3D shapes. When click-
ing on the next button on the Axial page in the
Clipping window, a special tool, for example,
label settings, is launched.
Adds labels, etc., to coronal sections
(Y axis sections)
Adds labels, etc., to horizontal
sections (Z axis sections)
128 4  Operation of Web-Accessible Volume-Rendering Model of the Degu Brain

Labels, etc., are added and edited in the same Links

way as in SG-eye Atlas. Labels, etc., that are
added using the tool are also displayed on the 3D
When image data are contained in the data file, a
models.
C/H/S icon is displayed at the top right corner of
the SG-eye 3D Atlas main window.

By clicking on the icon, SG-eye Atlas is

launched; the same file opens automatically and
the images corresponding to the cutting plane
position are displayed.
 Index of Structures
A Anterior olfactory nucleus/medial part (AOM), 31, 33
A1 noradrenaline cells (A1), 15
A2 noradrenaline cells (A2), 15
A5 noradrenaline cells (A5), 15
Abducens nerve (6n), 19, 85
Abducens nucleus (6N), 14, 87
Accessory nerve nucleus (11N), 15, 103, 105
Accessory olfactory bulb (AOB), 10, 27, 29
Accumbens nucleus (Acb), 11
Accumbens nucleus/core (AcbC), 11, 41, 43, 45, 47
Accumbens nucleus/shell (AcbSh), 11, 41, 43, 45, 47
Agranular insular cortex, (AI), 10, 35, 37, 39, 41, 43, 45,
47, 49, 51, 53, 55, 57, 59
Alveus of the hippocampus (alv), 18, 55, 57, 59, 61, 63,
65, 67, 69, 71, 73
Ambiguus nucleus (Amb), 15, 93, 95, 97
Ambiguus nucleus/compact part (AmbC), 15
Ambiguus nucleus/loose part (AmbL), 15
Amygdala (AMG), 11
Amygdalohippocampal area (AHi), 11, 67
Amygdalohippocampal area/posterolateral part (AHiPL),
61, 63, 65
Amygdalohippocampal area/posteromedial part (AHiM),
61, 63, 65
Amygdalopiriform transition (APir), 61, 63, 65, 67, 71
Angular thalamic nucleus (AngT), 12, 57
Ansoparamedian fissure (ampf), 19, 93, 95, 97
Anterior amygdaloid area (AA), 11, 51, 53
Anterior commissure (ac), 18, 51
Anterior commissure/anterior part (aca), 18, 37, 39, 41,
43, 45, 47, 49
Anterior commissure/intrabulbar part (aci), 18, 25, 27,
29, 33, 35
Anterior commissure/posterior limb (acp), 18, 51
Anterior hypothalamic area (AH), 13
Anterior hypothalamic area/central part (AHC), 55
Anterior hypothalamic area/posterior part (AHP), 55, 57
Anterior interposed cerebellar nucleus (IntA),
17, 87, 89
Anterior nuclei (ANN), 12
Anterior olfactory nucleus (AON), 10, 27
Anterior olfactory nucleus/dorsal part (AOD), 31, 33, 35
Anterior olfactory nucleus/external part (AOE), 29, 31
Anterior olfactory nucleus/lateral part (AOL), 29, 35
© Springer Japan KK, part of Springer Nature 2018
N. Kumazawa-Manita et al., The 3D Stereotaxic Brain Atlas of the Degu, Brain Science,
https://doi.org/10.1007/978-4-431-56615-1
Anterior olfactory nucleus/posterior part (AOP), 37, 39
Anterior olfactory nucleus/ventroposterior part (AOVP),
33, 35, 37, 39
Anterior pretectal nucleus (APT), 13, 67, 69, 71
Anterodorsal thalamic nucleus (AD), 12, 55
Anteromedial thalamic nucleus (AM), 12, 53, 55, 57
Anteroventral thalamic nucleus (AV), 12, 53
Antrior cortical amygdaloid nucleus (Aco), 11
Aqueduct (Aq), 19, 67, 69, 71, 73, 75, 77
Arcuate hypothalamic nucleus (Arc), 13, 55, 57, 59
Area postrema (AP), 19, 97
Ascending fibers of the facial nerve (asc7), 18
Association nuclei (ASN), 12
Auditory cortex/primary area (Au1), 10, 61, 63, 65,
67, 69, 71
Auditory thalamus (AuT), 12
B
BASAL GANGLIA (BG), 11
Basal nucleus (Meynert) (B), 11, 53, 55
Basolateral amygdaloid nucleus (BL), 11
Basolateral amygdaloid nucleus/anterior part (BLA), 11,
55, 57, 59
Basolateral amygdaloid nucleus/posterior part (BLP), 11,
57, 59, 61, 63, 65
Basolateral amygdaloid nucleus/ventral part (BLV), 11
Basomedial amygdaloid nucleus (BM), 11
Basomedial amygdaloid nucleus/anterior part (BMA),
11, 55
Basomedial amygdaloid nucleus/posterior part (BMP),
11, 57, 59, 61, 63
Bed nucleus of the stria terminalis (ST), 11
Bed nucleus of the stria terminalis/lateral division (STL),
11, 49, 51
Bed nucleus of the stria terminalis/medial division
(STM), 11, 49, 51, 53
Brachium of the inferior colliculus (bic), 18, 71, 73,
75, 77, 79
Brachium of the superior colliculus (bsc), 18, 65, 67,
69, 71
BRAIN STEM (MIDBRAIN+PONS+MEDULLA
OBLONGATA) (STEM), 14, 15
129
130
C Deep gray layer of the superior colliculus (DpG), 14, 67,
C1 adrenaline cells (C1), 15
C2 adrenaline cells (C2), 15
C3 adrenaline cells (C3), 15
Caudal linear nucleus of the raphe (CLi), 15, 73
Caudate putamen (striatum) (CPu), 11, 41, 43, 45,
47, 49, 51, 53, 55, 57, 59
Caudomedial entorhinal cortex (CEnt), 73, 75, 77, 79
Central amygdaloid nucleus (Ce), 11, 59
Central amygdaloid nucleus/capular part (CeC), 11, 55
Central amygdaloid nucleus/lateral part (CeL), 11, 57
Central amygdaloid nucleus/medial part (CeM), 11, 55,
58
Central canal (CC), 19, 99, 101, 103, 105
Central cervical nucleus (CeCv), 15, 97, 101, 103, 105
Central gray (CG), 14, 79, 81, 83
Central medial thalamic nucleus (CM), 12, 55, 57,
59, 61, 63
Central nucleus of the inferior colliculus (CIC), 14, 75,
77, 79
Centrolateral thalamic nucleus (CL), 12, 57, 59, 61, 63
Cerebellar cortex (Cb), 17
CEREBELLUM (METENCEPHALON) (CB), 17
Cerebral peduncle (cp), 18, 61, 63, 67, 69, 71, 73
CEREBRUM/CEREBRAL CORTEX (CER), 10
Choroid plexus (chp), 53, 55, 59, 61, 63, 65, 91, 93
Cingulate cortex (Cg), 10, 35, 37, 39, 41, 43, 45, 47, 49,
51, 53
Cingulum (cg), 18, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59,
65, 67
CIRCUMVENTRICULAR ORGAN (CvO), 19
Claustrum (Cl), 11, 37, 39, 41
Cochlear nuclei (C), 14, 53
Cochlear root of the vestibulocochlear nerve (8cn), 19,
83, 85, 91
Commissural nucleus of the inferior colliculus (Com), 14
Commissure of the inferior colliculus (cic), 18, 77
Commissure of the superior colliculus (csc), 18, 67
Conterminal nucleus (Ct), 15
Copula of the pyramis (Cop), 17, 93, 95, 97
Corpus callosum (cc), 18, 49, 51, 53, 55, 57, 59, 61, 63,
65, 93
Cortex-amygdala transition zone, layer 1 (CxA1), 51, 53
Cortical amygdaloid group (corticomedial group)
(CoAG), 11
Cortical amygdaloid nucleus (Co), 11
Cortical areas (CorA), 10
CRANIAL NERVE (CN), 19
Crus1 of the ansiform lobule (Crus1), 17, 87, 89, 91,
93, 95
Crus2 of the ansiform lobule (Crus2), 17, 91, 95, 97
Cuneate fasciculus (cu), 18, 97, 99, 101, 103, 105
Cuneate nucleus (Cu), 15, 95, 97, 99, 101, 103
Cuneinform nucleus (CnF), 14
D E
Decussation of the medial lemniscus (mlx), 18, 99
Decussation of the superior cerebellar peduncle (scpx), 18
Deep cerebellar nuclei (Dc), 17
Index of Structures
69, 71, 73, 75
Deep white layer of the superior colliculus (DpWh), 14,
67, 69, 71, 73, 75
Dentate gyrus (DG), 10
DIENCEPHALON (DIEN), 12, 13
Dorsal cochlear nucleus (DC), 14, 17
Dorsal cochlear nucleus/deep core (DCDp), 14, 87, 89, 91
Dorsal cochlear nucleus/fusiform layer (DCFu), 14, 87,
89, 97
Dorsal cochlear nucleus/molecular layer (DCMo), 14,
87, 89, 91
Dorsal cortex of the inferior colliculus (DCIC), 14, 77, 79
Dorsal corticospinal tract (dcs), 18, 97, 99, 101, 103, 105
Dorsal endopiriform nucleus (DEn), 11, 39, 41, 43, 45,
47, 49, 51, 53, 55, 57, 59, 61, 63, 65
Dorsal hypothalamic area (DA), 59
Dorsal lateral geniculate nucleus (DLG), 12, 61, 63, 65, 67
Dorsal motor nucleus of vagus (10N), 15, 93, 95, 97,
99, 101
Dorsal nucleus of the lateral lemniscus (DLL), 14, 77, 79
Dorsal olfactory tract (dlo), 27, 29
Dorsal paragigantocellular nucleus (DPGi), 87, 89, 91
Dorsal part of claustrum (DCl), 45, 47, 49, 51, 53, 55, 57
Dorsal peduncular cortex (DP), 36, 39, 41, 43, 45
Dorsal periolivary region (DPO), 15
Dorsal raphe nucleus (DR), 14
Dorsal raphe nucleus/caudal part (DRC), 14, 15, 79, 81
Dorsal raphe nucleus/dorsal part (DRD), 14, 75, 77
Dorsal raphe nucleus/lateral part (DRL), 14, 75, 77
Dorsal raphe nucleus/ventral part (DRV), 14, 75, 77
Dorsal spinocerebellar tract (dsc), 18, 101, 103, 105
Dorsal subiculum (DS), 10, 67, 71
Dorsal tegmental decussation (dtgx), 18
Dorsal tegmental nucleus (DTg), 79
Dorsal tegmental nucleus (DTgm), 15
Dorsal tegmental nucleus/central part (DTgC), 15
Dorsal tegmental nucleus/medial part (DTgm), 15
Dorsal tegmental nucleus/pericentral part (DTgP), 15
Dorsal tenia tecta (DTT 1-2), 41, 43
Dorsal transition zone (DTr), 37, 39
Dorsolateral entorhinal cortex (DLEnt), 65, 67, 71, 73,
75, 77
Dorsomedial hypothalamic nucleus (DM), 13, 59
Dorsomedial hypothalamic nucleus/compact part
(DMC), 13
Dorsomedial hypothalamic nucleus/dorsal
part (DMD), 13
Dorsomedial spinal trigeminal nucleus (DMSp5), 87, 89,
91, 93, 95
Dorsomedial tegmental area (DMTg), 15, 79, 81
Dosal acoustic atria (das), 18
Dysgranular insular cortex (DI), 10, 37, 39, 41, 43, 45,
47, 49, 51, 53, 55, 59
Ectorhinal cortex (Ect), 61, 63, 65, 67, 69, 71, 73,
75, 77, 79
Edinger-Westphal nucleus (EW), 14, 71
Index of Structures
Endopiriform nucleus, 11, 39, 41, 43, 45, 47, 49, 51,
53-59, 61, 63, 65
Entorhinal cortex (Ent), 10, 65, 67, 71, 73, 75, 77, 79
Ependyma & subependymal layer (E), 10, 37, 43, 4343
Ependyma & subependymal layer/lateral
ventricle (E/LV), 37, 41
Ependyma & subependymal layer/olfactory
ventricle (E/OV), 23, 25, 27, 29, 31, 33, 35, 37, 39
Epifacicular nucleus (EF), 15
EPITHALAMUS (EPI), 12
Extended amygdala (EXA), 11, 53, 55
External capsule (ec), 18, 45, 49, 51, 53, 55, 57
External cortex of the inferior colliculus (ECIC), 14, 73,
75, 77, 79
External cuneate nucleus (ECu), 15, 93, 95, 97
External globus pallidus (globus pallidus) (EGP), 11
External medullary lamina (eml), 18
External plexiform layer of the accessory olfactory
bulb (EPlA), 10, 27, 29, 31
External plexiform layer of the olfactory bulb (EPl),
10, 23, 25, 27, 29, 31
F Indusium griseum (IG), 10, 41, 43, 45, 47, 49, 51, 53
Facial nerve (7n), 19, 85, 87
Facial nucleus (7N), 14, 87, 89, 91
Faciola cinereum (FC), 10, 61, 63
Fasciculus retroflexus (fr), 61, 63, 65, 67, 69
Fiber bundle (FB), 18
Field CA1 of the hippocampus (CA1), 10, 57, 59, 65, 67,
69, 71
Field CA2 of the hippocampus (CA2), 10, 57, 59, 63, 65
Field CA3 of the hippocampus (CA3), 55–57, 59, 61, 63,
65, 67, 69
Fimbria of the hippocampus (fi), 49, 51, 53, 55, 57, 59,
61, 63
Flocculus (Fl), 81, 83, 85, 87
Forceps major of the corpus callosum (Fmj), 71
Forceps minor of the corpus callosum (Fmi), 35, 37, 39
Forebrain (Telencephalon and diencephalon) (FORE),
10–13
Fornix (F), 53, 55, 61, 63
Fourth ventricle (4V), 19, 79, 81, 83, 85, 87, 89, 91, 93
Frontal associational cortex (FrA), 27, 29, 31
G Intermediate gray layer of the superior colliculus (InG),
Genu of the corpus callosum (gcc), 18, 41
Genu of the facial nerve (g7), 18, 85, 87
Gigantocellular reticular nucleus (Gi), 16, 87, 89, 91,
93, 95
Gigantocellular reticular nucleus/alpha part (GiA), 89
Gigantocellular reticular nucleus/ventral part (GiV),
93, 95
Globus pallidus (GP), 11, 51, 53, 55, 57, 59
Glomerular layer of the accessory olfactory bulb (GlA),
10, 27, 29
Glomerular layer of the olfactory bulb (Gl), 10
Gracile fasciculus (gr), 18, 97, 99, 101, 103, 105
Gracile nucleus (Gr), 15, 97, 99, 101, 103
131
Granular insular cortex (GI), 10, 23, 25, 27, 29, 31, 37,
39, 41, 43, 45, 47, 49, 51, 53, 55, 59
Granule cell layer of the accessory olfactory bulb (GrA),
10, 25, 27, 29
Granule cell layer of the cochlear nuclei (GrC), 14, 83, 85
Granule cell layer of the dentate gyrus (GrDG), 10, 55,
57, 59, 61, 63, 65, 67, 69, 71
Granule cell layer of the olfactory bulb (GrO), 10, 23, 25,
27, 29, 31
H
Habenular commissure (hbc), 18
Habenular nucleus (Hb), 12, 61, 63
Hippocampal fissure (hif), 57, 61, 63, 65, 67, 69, 71
Hippocampal formation (HipF), 10
Hippocampus (Hip), 3, 49, 51, 53–67, 69, 71, 73
Hypoglossal nerve (12n), 19
Hypoglossal nucleus (12N), 95, 97, 99
Hypothalamus (HYPO), 13, 54–57, 59, 61, 63, 65
I
Inferior cerebellar peduncle (restiform body) (icp),
18, 85, 86, 89, 91, 93, 95
Inferior colliculus (IC), 73, 75, 77, 79, 81
Inferior olive (IO), 15
Inferior olive/beta subnucleus of the medial nucleus
(IOBe), 16
Inferior olive/cap of Kooy of the medial nucleus (IOK), 16
Inferior olive/dorsal nucleus (IOD), 16, 93, 95, 97
Inferior olive/dorsomedial cell group (IODM), 16
Inferior olive/medial nucleus (IOM), 16, 93, 95, 97, 99
Inferior olive/principal nucleus (IOPr), 16, 93, 95
Inferior olive/subnucleus A of medial nucleus (IOA), 16
Inferior olive/subnucleus B of medial nucleus (IOB), 16
Inferior olive/subnucleus C of medial nucleus (IOC), 16
Inferior olive/ventrolateral prorusion (IOVL), 16
Inferior salivatory nucleus (IS), 16, 59
Infralimbic cortex (IL), 37, 39, 41
Interanterodorsal thalamic nucleus (IAD), 12
Interanteromedial thalamic nucleus (IAM), 12, 55
Intercalated nuclei of the amygdala (I), 11
Intercalated nucleus of the medulla (In), 15
Intercrural fissure (icf), 19, 91, 93, 95
14, 67, 69, 71, 73
Intermediate nucleus of the lateral lemniscus (ILL),
14, 77
Intermediate interstitial nucleus of the medial
longitudinal fasciculus (II), 83
Intermediate reticular nucleus (IRt), 16, 87, 89, 91, 93,
95, 97, 99, 101, 103, 105
Intermediate white layer of the superior colliculus
(InWh), 14, 67, 69, 71, 73, 75
Intermediodorsal thalamic nucleus (IMD), 12, 57, 59
Internal capsule (ic), 18, 49, 51, 53, 55, 57, 59, 61, 65
Internal globus pallidus (ento-/ intrapeduncular nucleus)
(IGP), 11
132
Internal plexiform layer of the olfactory bulb (IPl),
10, 23, 25, 27, 29, 31
Interpeduncular nucleus (IP), 71, 73
Interpeduncular nucleus/caudal subnucleus (IPC),
14, 71, 73
Interpeduncular nucleus/intermediate
subnucleus (IPI), 14, 73
Interpeduncular nucleus/lateral subnucleus (IPL),
14, 71, 73
Interpeduncular nucleus/rostrall subnucleus (IPR),
14, 71, 73
Interstitial nucleus of Cajal (InC), 14, 67, 69
Interstitial nucleus of the posterior limb of the anterior
commissure (IPAC), 11, 49, 51, 53
Interstitial nucleus of the posterior limb of the anterior
commissure, lateral part (IPACL), 11, 51
Interstitial nucleus of the vestibular part of the
8th nerve (I8), 15
Interventricular foramen (IVF), 19
Islands of Calleja (ICj), 10, 41, 43, 45, 47, 49
Islands of Calleja/major island (ICjM), 10, 41, 43, 45,
47, 49
K Lateroventral periolivary nucleus (LVPO), 15, 83
Kolliker-Fuse nucleus (KF), 16, 81, 83
L 85, 87
Lacunosum moleculare layer of the hippocampus
(LMol), 10, 57, 59, 61, 63, 65, 67, 69
Lamina terminalis (Lter), 13, 19, 49
Lateral amygdaloid nucleus (La), 11
Lateral amygdaloid nucleus/dorsolateral part (LaDL),
11, 55, 57, 59, 61, 63
Lateral amygdaloid nucleus/ventrolateral part (LaVL),
11, 57, 59
Lateral amygdaloid nucleus/ventromedial part (LaVM),
11, 57, 59, 61, 63
Lateral (dentate) derebellar nucleus (Lat), 16, 87, 89
Lateral habenular nucleus (LHb), 12, 59, 61, 63
Lateral hypothalamic area (LH), 13
Lateral lemniscus (ll), 14, 15, 18, 75, 77, 79, 81
Lateral mammillary nucleus (LM), 13, 55, 65
Lateral nuclei (LTN), 12
Lateral olfactory tract (lo), 18, 27, 29, 31, 33, 35, 37,
39, 43, 45, 47, 49, 51, 53
Lateral orbital cortex (LO), 31, 33, 35, 37, 39, 41
Lateral parabrachial nucleus (LPB), 14, 79, 81
Lateral paragigantocellular nucleus (LPGi), 16, 87,
91, 93, 95
Lateral posterior thalamic nucleus (LP), 12, 65, 69
Lateral posterior thalamic nucleus/lateral part (LPL),
61, 63
Lateral posterior thalamic nucleus/medial part (LPM),
61, 63, 65
Lateral posterior thalamic nucleus/mediorostral part
(LPMR), 65
Lateral preoptic area (LPO), 13, 49, 51, 53, 85, 87
Index of Structures
Lateral recess of the 4th ventricle (LR4V), 19, 87,
89, 91, 93
Lateral reticular nucleus (LRt), 16, 97, 99
Lateral reticular nucleus/parvicellular part (LRtPC),
16, 97, 99
Lateral septal nucleus (LS), 11
Lateral septal nucleus/dorsal part (LSD), 11, 45, 47,
49, 51
Lateral septal nucleus/intermediate part (LSI), 11, 43,
45, 47, 49
Lateral septal nucleus/ventral part (LSV), 11, 45, 47,
49, 51
Lateral stripe of the striatum (LSS), 47, 49
Lateral superior olive (LSO), 15, 85, 87
Lateral terminal nucleus of the accessory
optic tract (LT), 16
Lateral ventricle (LV), 19, 43, 45, 47, 49, 51, 53, 55, 57,
59, 61, 63, 67, 69, 71, 73
Lateral vestibular nucleus (LVe), 16, 87, 89
Latero-basal nuclear complex (bassolateral group)
(Lbn), 11
Laterodorsal tegmental nucleus (LDTg), 14, 79, 81
Laterodorsal/lateral dorsal thalamic nucleus (LD),
12, 57, 59
Linear nucleus of the medulla (Li), 16, lfp
Lithoid nucleus (Lth), 65
Lobule 1 of cerebellar vermis (lingula) (1Cb), 17, 81, 83,
Lobule 2 of cerebellar vermis (2Cb), 17, 79, 81, 83, 85, 87
Lobule 3 of cerebellar vermis (3Cb), 17, 81, 83, 85, 87, 89
Lobule 4 of cerebellar vermis (4Cb), 17, 77, 79, 81, 83,
85, 87, 89
Lobule 5 of cerebellar vermis (5Cb), 17, 77, 79, 81, 83,
85, 87, 89
Lobule 6 of cerebellar vermis (6Cb), 17, 87, 89, 91, 93, 95
Lobule 7 of cerebellar vermis (7Cb), 17, 93, 95, 97
Lobule 8 of cerebellar vermis (8Cb), 17, 93, 95, 97, 99
Lobule 9 of cerebellar vermis (uvula) (9Cb), 17, 93, 95,
97, 99, 101, 103
Lobule 10 of cerebellar vermis (nodule) (10Cb), 17, 91,
93, 95, 97
Locus coeruleus (LC), 14, 83, 85
Longitudinal fasciculs of the pons (lfp), 18, 75, 77,
79, 81
M
Magnocellular nucleus of the posterior commissure
(MCPC), 13, 65, 69
Magnocellular preoptic nucleus (MCPO), 49, 51, 53
Mamillary peduncle (mp), 18
Mamillary recess of the 3rd ventricle (MRe), 19
Mammillary body (MB), 13
Mammillotegmental tract (mtg), 65, 67
Mammillothalamic tract (mt), 55, 57, 61, 63
Matrix region of the medulla (Mx), 16, 95, 99
Medial accessory oculomotor nucleus (MA3), 69
Medial amygdaloid nucleus (Me), 11
Index of Structures
Medial amygdaloid nucleus, anterodorsal
part (MeAD), 55
Medial amygdaloid nucleus, anteroventral
part (MeAV), 55
Medial amygdaloid nucleus, posterodorsal
part (MePD), 57, 59
Medial amygdaloid nucleus, posteroventral
part (MePV), 57, 59
Medial (fastigal) cerebellar nucleus (Med), 16
Medial entorhinal cortex (MEnt), 71, 73, 75, 77
Medial geniculate nucleus (MG), 12
Medial geniculate nucleus/dorsal part (MGD), 12, 65,
67, 69, 71
Medial geniculate nucleus/medial part (MGM), 12, 69, 71
Medial geniculate nucleus/ventral part (MGV), 12, 65,
67, 69, 71
Medial habenular nucleus (MHb), 12, 59, 61, 63
Medial lemniscus (ml), 18, 59, 61, 63, 65, 67, 69, 71, 73,
75, 77, 83, 85, 87, 89, 91, 93, 95, 97, 99
Medial longitudinal faciculcus (mlf), 18
Medial mamillary nucleus/lateral part (ML), 13
Medial mamillary nucleus/medial part (MM), 13
Medial mamillary nucleus/median part (MnM), 13
Medial orbital cortex (MO), 31, 33, 35
Medial parabrachial nucleus (MPB), 14, 79, 81, 83, 85
Medial parabrachial nucleus/external part (MPBE), 83
Medial preoptic area (MPA), 13, 51, 53
Medial preoptic nucleus (MPO), 13, 51, 53, 85, 87
Medial preoptic nucleus/central part (MPOC), 53
Medial pretectal nucleus (MPT), 13, 65
Medial septal nucleus (MS), 11, 45, 47, 49
Medial superior olive (MSO), 15, 83, 85, 87
Medial tuberal nucleus (MTu), 13
Medial vestibular nucleus (MVe), 16, 91, 93, 95
Medial vestibular nucleus/magnocellular part (MVeMC),
16, 85, 87, 89
Medial vestibular nucleus/parvicellular part (MVePC),
16, 87, 89
Median accessory nucleus of the medulla (MnA), 16, 65
Median eminence (ME), 19, 57, 59
Median preoptic nucleus (MnPO), 13, 49, 51
Median raphe nucleus (MnR), 15, 75, 77, 79, 81
Mediodorsal thalamic nucleus (MD), 12, 57, 59, 61, 63
Mediodorsal thalamic nucleus/lateral part (MDL), 12, 57,
59, 61, 63
Mediodorsal thalamic nucleus/medial part (MDM),
12, 57, 59, 61, 63
Medioventral periolivary nucleus (MVPO), 15, 81, 83
MEDULLA OBLONGATA (MYELENCEPHALON)
(MED), 15–16
Medullary reticular nucleus (MeRt) (MRt), 16
Medullary reticular nucleus/dorsal part (MdD), 97, 99,
101, 103, 105
Medullary reticular nucleus/ventral part (MdV), 97, 99,
101, 105
Mesencephalic trigeminal nucleus (Me5), 14, 71, 73, 75,
77, 79, 81, 83
Mesencephalic trigeminal tract (me5), 18, 71, 73, 75, 77,
79, 81, 83
133
MIDBRAIN (MESENCEPHALON) (MID), 14, 15
Middle cerebellar peduncle (mcp), 18, 75, 77, 79, 81, 83, 85
Midline and intralaminar nuclei (MIN), 12
Mitral cell layer of the accessory olfactory bulb (MiA),
10, 27, 29, 31
Mitral cell layer of the olfactory bulb (Mi), 10, 23, 25,
27, 29, 31
Molecular layer of the dentate gyrus (MoDG), 10, 55, 57,
61, 63, 65, 67, 69, 71
Motor cortex/primary area (M1), 10, 37, 39, 41, 43, 45,
47, 49, 51, 53, 55, 57
Motor root of the trigeminal nerve (m5), 14, 73, 75, 77,
79, 81, 83, 85
Motor thalamus (MTT), 12
Motor trigeminal nucleus (5N), 14
N
Navicular nucleus of the basal forebrain (Nv), 10, 43
Nucleus of Darkschewitsch (Dk), 14, 67, 69
Nucleus of Roller (Ro), 16, 95
Nucleus of the horizontal limb of the diagonal band
(HDB), 11, 49, 53
Nucleus of the lateral olfactory tract, layer 1-3
(LOT 1-3), 53
Nucleus of the lateral olfactry tract (LOT), 11
Nucleus of the optic tract (OT), 13, 65
Nucleus of the posterior commissure (PCom), 13, 14,
65, 67, 69
Nucleus of the solitary tract (Sol), 16
Nucleus of the solitary tract/central part (SolCe), 16
Nucleus of the solitary tract/commissural part (SolC),
16, 99
Nucleus of the solitary tract/dorsolateral part (SolDL), 16
Nucleus of the solitary tract/dorsomedial
part (SolDM), 16
Nucleus of the solitary tract/gelatinous part (SolG), 16
Nucleus of the solitary tract/intermediate
part (SolIM), 16
Nucleus of the solitary tract/interstitial part (SolI), 16
Nucleus of the solitary tract/lateral part (SolL), 16, 95,
97, 99
Nucleus of the solitary tract/medial part (SolM), 16, 91,
93, 95, 97, 99, 101
Nucleus of the solitary tract/rostrolateral
part (SolRL), 16
Nucleus of the solitary tract/ventral part (SolV), 16, 93,
95, 97, 99
Nucleus of the solitary tract/ventrolateral part (SolVL),
16, 93
Nucleus of the spinal trigeminal tract (Sp5MED), 16
Nucleus of the spinal trigeminal tract (SP5PONS), 14
Nucleus of the stria medullaris (SM), 13
Nucleus of the trapezoid body (Tz), 14, 81, 83, 85, 87
Nucleus of the vertical limb of the diagonal band (VDB),
11, 45, 47
Nucleus X (X), 16, 91
Nucleus Y of the vestibular complex (Y), 17, 89
Nuclus of the brachium of the inferior colliculus (BIC), 14
134
O PONS (METENCEPHALON) (PONS), 14, 15
Occulomotor nerve (3n), 19
Oculomotor nucleus (3N), 14, 69, 71
Oculomotor nucleus/parvicellular part (3PC), 14, 73
Olfactory bulb (OB), 10
OLFACTORY BULB (OLB), 10
Olfactory cortex (OlfC), 10
Olfactory nerve (olf), 23, 25
Olfactory nerve layer (ON), 10
Olfactory ventricle (olfactory part of lateral
ventricle) (OV), 19
Olfactry tubercle (Tu), 10
Olivary pretectal nucleus (OPT), 13
Optic chiasm (och), 18, 49, 51, 53
Optic tract (opt), 13, 18, 36
Orbital cortex (Orb), 10, 31, 33
Oriens layer of the hippocampus (Or), 10, 57
Oval paracentral thalamic nucleus (OPC), 12
P Preculminate fissure (pcuf), 19, 81, 83, 85, 87
Parabigeminal nucleus (PBG), 14, 75
Paracentral thalamic nucleus (PC), 12, 55, 59, 65
Parafascicular thalamic nucleus (PaF), 12
Parafascicular thalamic nucleus (PF), 61, 63
Parafloccular sulcus (pfs), 19, 87, 89, 91
Paraflocculus (PFl), 17, 85, 87, 89, 91, 93, 95
Paramedian lobule (PM), 17, 93, 97
Paramedian raphe nucleus (PMnR), 15
Paramedian reticular nucleus (PMn), 16, 97
Parasolitary nucleus (PSol), 16
Parasubiculum (PaS), 10, 73, 75, 77, 79
Parasubthalamic nucleus (PSTh), 12, 60, 62
Paratenial thalamic nucleus (PT), 12, 53, 55
Paraventricular hypothalamic nucleus (Pa), 13, 53, 55, 57
Paraventricular hypothalamic nucleus/anterior
parvicellular part (PaAP), 53
Paraventricular hypothalamic nucleus/dorsal cap (PaDC),
13, 53, 55, 57
Paraventricular thalamic nucleus (PV), 12, 58
Paraventricular thalamic nucleus/anterior part (PVA),
12, 53, 55, 56
Paraventricular thalamic nucleus/posterior part (PVP),
12, 60, 62
Parvicellular reticular nucleus (PCRt), 16, 85, 87, 89, 91,
93, 95
Peduncular part of the lateral hypothalamus (PLH),
55, 59, 61, 63, 65
Periaqueductal gray (PAG), 14, 65, 67, 69, 71, 73, 75, 77
Perirhinal corex (PRh), 61, 63, 64, 67, 69, 71, 73, 75,
77, 79
Periventricular hypothalamic nucleus (Pe), 13, 51,
53, 55, 57, 59
Pineal gland (Pi), 19
Piriform cortex (Pir), 10
Piriform cortex/layer 1 (Pir1), 10
Piriform cortex/layer 2 (Pir 2), 10
Piriform cortex/layer 3 (Pir 3), 10
Polymorph layer of the dentate gyrus (PoDG), 10, 56, 59,
61, 63, 65, 67, 71
Index of Structures
Pontine nuclei (Pn), 14, 75, 77
Pontine reticular nucleus/caudal part (PnC), 15, 83, 85
Pontine reticular nucleus/oral part (PnO), 15, 75, 77, 79, 81
Pontine reticular nucleus/ventral part (PnV), 15
Posterior commissure (pc), 18, 65, 67, 69
Posterior hypothalamic area (PHA), 13, 65
Posterior hypothalamic nucleus (PH), 13, 61, 63
Posterior interposed cerebellar nucleus (IntP), 17, 91
Posterior pretectal nucleus (PPT), 13, 69
Posterior superior fissure (psf), 19, 81, 85, 87, 89, 93, 95
Posterior thalamic nuclear group (Po), 12, 59, 61, 63, 67
Posterolateral cortical amygdaloid nucleus (PLCo), 11,
57, 59, 61, 63, 65
Posterolateral fissure (plf), 19, 85, 87, 93, 95
Posteromedial cortical amygdaloid nucleus (PMCo), 11,
56, 59, 61, 63, 65, 67, 69
Posteromedial thalamic nucleus (PoMn), 61, 63
Postsubiculum (Post), 10, 71, 73, 75, 77
Precommissural nucleus (PrC), 65–66
Pre-Edinger-Westphal nucleus (PrEW), 69
Prelimbic cortex (PrL), 33, 35, 37, 39, 41
Premamillary nucleus (PrM), 13
Premammillary nucleus, dorsal part (PMD), 61, 63
Premammillary nucleus, ventral part (PMV), 61, 63
Preoptic area (PO), 13
Prepositus nucleus (Pr), 16, 85, 87, 91, 93
Prepyramidal fissure (ppf), 19, 93, 95
PRETECTUM (Pt), 13
Primary fissure (prf), 19, 81, 85, 87, 89
Principal sensory trigeminal nucleus (Pr5), 14, 83, 85
Pyramidal cell layer of the hippocampus (Py), 10, 55, 56,
58, 60, 62, 64, 67, 69, 71
Pyramidal decussation (pyx), 18, 99, 101, 103, 105
Pyramidal tract (py), 18, 83, 85, 87, 89, 91, 93, 97, 99
R
Radiatum layer of the hippocampus (Rad), 10, 55,
56, 58, 60, 62, 64, 67, 69, 71
Raphe interpositus (RIP) nucleus, 15, 85, 87
Raphe magnus (RMg) nucleus, 15, 83, 85, 87, 89, 91
Raphe nuclei (RaMEDRaMIDRaPONS), 14–16
Raphe obscurus nucleus (ROb), 16, 93, 95
Raphe pallidus nucleus (RPa), 16, 85, 87, 89, 91, 93, 95
Red nucleus (R), 14, 69, 71
Red nucleus/magnocellular part (RMC), 14, 69, 71
Red nucleus/parvicellular part (RPC), 14, 69, 71
Reticular formation (RtMED/RtMID/RtPONS), 14–16
Reticular thalamic nucleus (Rt), 12, 53, 54, 56, 58, 60, 62
Reticulotegmental nucleus of the pons (RtTg), 15, 75,
77, 79, 81, 83
Reticulotegmental nucleus of the pons/lateral
part (RtTgL), 15
Retroambiguus nucleus (RAmb), 16, 99
Retrochiasmatic area (RCh), 55
Retroisthmic nucleus (RIs), 15
Retrolemniscal nucleus (RL), 15
Retroparafacicular nucleus (RPF), 64
Index of Structures
Retroreuniens area (RRe), 12, 60, 62
Retrosplenial dysgranular cortex (RSD), 10, 54, 56, 58,
60, 62, 64, 67, 69, 71, 73, 75, 77, 79
Retrosplenial granular cortex (RSG), 10, 54, 56, 58, 60,
62, 64, 67, 69, 71, 73, 75, 77
Reuniens thalamic nucleus (Re), 12, 53, 55, 56, 58
Rhabdoid nucleus (Rbd), 15
Rhinal fissure (rf), 19, 27, 29, 31, 33, 35, 37, 39, 41, 43,
45, 47, 49, 51, 53, 54, 58, 60, 62, 67, 69, 71, 73, 75,
77, 79
Rhinal incisures (ri), 27, 29, 31, 33, 35
Rhomboid thalamic nucleus (Rh), 12, 54, 60
Rostral linear nucleusof the raphe (RLi), 14, 67, 71
Rostrum of the corpus callosum (rcc), 18
Rubrospinal tract (rs), 18, 73, 75, 77, 79, 81, 83, 85, 87,
89, 91, 93, 95, 97, 99, 101, 103, 105
S Superior medullary velum (SMV), 89
Sagulum nucleus (Sag), 15, 79
Sensory/motor root of the trigeminal nerve (s5/m5),
73, 75, 77
Sensory root of the trigeminal nerve (s5), 18, 79, 81, 83
Septofimbrial nucleus (SFi), 11, 49, 51, 53
Septohippocampal nucleus (SHi), 11
Septohypothalamic nucleus (SHy), 49, 51, 53
SEPTUM (SEP), 11
Simple lobule (Sim), 17, 81, 83, 85, 87, 89
Simplex fissure (simf), 19, 89
Solitary tract (sol), 18
Somatosensory cortex/primary area (S1), 10, 37, 39, 41,
43, 45, 47, 49, 51, 53, 54, 56, 58, 60, 62
Somatosensory thalamus (SST), 12
Spinal trigeminal nucleus/caudal part (Sp5C), 16, 97, 99,
101, 105
Spinal trigeminal nucleus/interpolar part (Sp5I), 16, 93,
95, 97
Spinal trigeminal nucleus/oral part (Sp5O), 16, 89, 91
Spinal trigeminal tract (sp5), 18, 83, 89, 91, 93, 95, 97,
99, 101, 105
Spinal vestibular nucleus (SpVe), 16, 89, 91, 93, 95
Splenium of the corpus callosum (scc), 18
Stratum lucidum of the hippocampus (SLu), 10, 54, 56,
58, 60, 62, 64, 66, 69
Stria medullaris of the thalamus (sm), 18, 53, 54, 56, 58,
60, 62, 64
Stria terminalis (st), 18, 51, 53, 56, 58
Striatum (St), 11
Subcoeruleus nucleus (SubC), 15
Subcoeruleus nucleus/alpha part (SubCA), 15
Subcoeruleus nucleus/dorsal part (SubCD), 15
Subcoeruleus nucleus/ventral part (SubCV), 15
Subcommissural organ (SCO), 19, 64, 67
Subfornical organ (SFO), 19, 53
Subiculum (S), 10
Sublenticular extended amygdala (EA), 11, 55
Subparafiscicular thalamic nucleus (SPF), 12, 60, 62
Subpeduncular tegmental nucleus (SPTg), 15
Subpostrema area (SubP), 16
Substantia innominata (SI), 11
135
Substantia innominata/basal part (SIB), 11, 49, 51, 53
Substantia innominata/dorsal part (SID), 11
Substantia nigra (SN), 11
Substantia nigra (SNMID), 14
Substantia nigra/compact part (SNC), 11, 66, 69, 71, 73
Substantia nigra/compact part/dorsal tier (SNCD), 11
Substantia nigra/compact part/medial tier (SNCM), 11
Substantia nigra/compact part/ventral tier (SNCV), 11
Substantia nigra/lateral part (SNL), 11, 66, 69, 71
Substantia nigra/reticular part (SNR), 11, 66, 69, 71, 73
Subthalamic nucleus (STh), 11, 60, 62, 64
SULCUS (SUL), 19
Superficial gray layer of the superior colliculcus (SuG),
14, 66, 69, 71, 73, 75
Superior cerebellar peduncle (brachium conjunctivum)
(scp), 18, 60, 62, 64, 67, 69, 71, 73, 75, 77, 79, 81,
83, 85, 87
Superior colliculus (SC), 14
Superior olive (SOl), 15
Superior paraolivary nucleus (SPO), 15
Superior salivatory nucleus (SuS), 16, 87
Superior vestibular nucleus (SuVe), 16, 85, 87
Suprachiasmatic nucleus (SCh), 13
Suprachiasmatic nucleus/dorsolateral part (SChDL),
13, 53
Suprachiasmatic nucleus/ventromedial part (SChVM),
13, 53
Suprageniculate thalamic nucleus (SG), 12, 69, 71
Supramammillary nucleus, lateral part (SuML), 64
Supramammillary nucleus, medial part (SuMM), 64, 67
Supraoculomotor cap (Su3C), 14
Supraoculomotor periaqueductal gray (Su3),
14, 71, 73
Supraoptic nucleus (SO), 13, 49, 51, 53, 54
Supratrigeminal nucleus (Su5), 15, 81
SURFACE (GH), 2–4, 21, 124, 125
Susbtantia innominata/ventral part (SIV), 11
T
Tectospinal tract (ts), 18, 73, 75, 77, 79, 81, 83, 85, 89,
91, 93, 95, 97, 99, 101, 105
TELENCEPHALON (TEL), 10–13
Tenia tecta (TT), 10, 33, 35, 37, 39, 41, 43
Terete hypothalamic nucleus (Te), 13
THALAMUS (THAL), 12
Third ventricle (3V), 19, 53, 55, 57, 59, 61, 63, 65
Transverse fibers of the pons (tfp), 18, 75, 77, 79, 81
Trapezoid body (tz), 14, 18, 81, 83, 85, 87, 89
Triangular nucleus of the lateral lemniscus (Tr), 15
Triangular septal nucleus (TS), 11, 51, 53
Trigeminal nerve (5n), 19
Trigeminal transition zone (5Tr), 85
Trochlear nerve (4n), 19, 75, 77, 81
Trochlear nucleus (4N), 14, 75
U
Uncinate fasciculus of the cerebellum (un), 18, 85
136
V Ventral tuberomamillary nucleus (VTM), 13
Vagus nerve (10n), 19
Vascular organ of the lamina terminalis (VOLT), 19, 49
Ventoromedial hypothalamic nucleus (VMH), 13, 54,
56, 58
Ventral anterior thalamic nucleus (VA), 12, 54, 56
Ventral cochlear nucleus (VC), 14
Ventral cochlear nucleus/anterior part (VCA), 14, 83, 85
Ventral cochlear nucleus/posterior part (VCP), 14, 87,
89, 91
Ventral endopiriform nucleus (VEn), 11, 39, 41, 43, 45,
47, 49, 51, 53, 54, 56, 58
Ventral geniculate nucleus (VG), 60, 62, 64
Ventral hippocampal commissure (vhc), 18, 53
Ventral nucleus of the lateral lemniscus (VLL), 15, 75,
77, 79, 81
Ventral orbital cortex (VO), 31, 33, 35, 37, 39
Ventral pallidum (VP), 11, 43, 45, 47, 49, 51, 53
Ventral part of claustrum (VCl), 43, 45, 47, 49, 51,
53, 54, 56
Ventral posterior nucleus of the thalamus/parvicellular
part (VPPC), 60, 62
Ventral posterolateral thalamic nucleus (VPL), 12, 56,
58, 60, 62
Ventral posteromedial thalamic nucleus (VPM), 12, 58,
60, 62
Ventral spinocerebellar tract (vsc), 18, 79, 81, 83, 85,
87, 95, 97, 99, 101, 103, 105
Ventral subiculum (VS), 10, 66, 69, 71
Ventral tegmental area (VTA), 14, 66
Ventral tegmental decussation (vtgx), 18
Ventral tegmental nucleus (VTg), 15, 77
Ventral tenia tecta, layer 1-2 (VTT 1-2), 33, 35
Ventral thalamus (VNT), 12
Index of Structures
VENTRICLE (V), 4, 5, 19
Ventrolateral preoptic nucleus (VLPO), 13
Ventrolateral thalamic nucleus (VL), 12, 54, 56, 58
Ventromedial preoptic nucleus (VMPO), 13
Ventromedial thalamic nucleus (VM), 12, 56, 58
Vestibular nuclei (VeMED), 16
Vestibular nuclei (VePONS), 15
Vestibular root of the vestibulocochlear nerve (8vn),
19, 83, 85, 87
Vestibulocerebellar nucleus (VeCb), 17, 87, 89
Vestibulocochlear nerve (8n), 19
Visual cortex/primary area (V1), 10, 64, 66, 69, 71,
73, 75, 77, 79
Visual thalamus (VST), 12
W
WHOLE BRAIN (WHOLE), 3, 10–16
X
Xiphoid thalamic nucleus (Xi), 12, 56, 58
Z
Zona incerta (ZI), 12, 56, 60–62
Zona incerta/caudal part (ZIC), 12
Zona incerta/dorsal part (ZID), 12, 60, 62
Zona incerta/rostral part (ZIR), 12, 56
Zona incerta/ventral part (ZIV), 12, 60, 62
Zonal layer of the superior colliculus (Zo), 14, 66, 69,
71, 73, 75
 Index of Abbreviations
A Anterior olfactory nucleus, medial part (AOM), 31, 33
A1 noradrenaline cells (A1), 15
A2 noradrenaline cells (A2), 15
A5 noradrenaline cells (A5), 15
6n (Abducens nerve), 19, 85
Abducens nerve (6n), 19, 85
Abducens nucleus (6N), 14, 87
Accessory nerve nucleus (11N), 15, 103, 105
Accessory olfactory bulb (AOB), 10
Accumbens nucleus (Acb), 11
Accumbens nucleus/core (AcbC), 11, 41, 43, 45, 47
Accumbens nucleus/shell (AcbSh), 11, 41, 43, 45, 47
Agranular insular cortex (AI), 10, 35, 37, 39, 41, 43,
45, 47, 49, 51, 53, 55, 57, 59
Alveus of the hippocampus (alv), 18, 55, 57, 59, 61,
63, 65, 67, 69, 71, 73
Ambiguus nucleus (Amb), 15, 93, 95, 97
Ambiguus nucleus/compact part (AmbC), 15
Ambiguus nucleus/loose part (AmbL), 15
Amygdala (AMG), 11
Amygdalohippocampal area (AHi), 11, 67, 69
Amygdalohippocampal area/posterolateral part (AHiPL),
61, 63, 65
Amygdalohippocampal area/posteromedial part (AHiM),
61, 63, 65
Amygdalopiriform transition (APir), 61, 63, 65, 67, 69, 71
Angular thalamic nucleus (AngT), 57
Ansoparamedian fissure (ampf), 19, 93, 95, 97
Anterior amygdaloid area (AA), 11, 51, 53
Anterior commissure (ac), 18, 51
Anterior commissure/anterior part (aca), 18, 37, 39, 41,
43, 45, 47, 49
Anterior commissure/intrabulbar part (aci), 18, 25, 27,
29, 33, 35
Anterior commissure/posterior limb (acp), 18, 51
Anterior hypothalamic area (AH), 13
Anterior hypothalamic area/central part (AHC), 55
Anterior hypothalamic area/posterior part (AHP), 55, 57
Anterior interposed cerebellar nucleus (IntA), 17, 87, 89
Anterior nuclei (ANN), 12
Anterior olfactory nucleus (AON), 10
Anterior olfactory nucleus, dorsal part (AOD), 31, 33, 35
Anterior olfactory nucleus, external part (AOE), 29, 31
Anterior olfactory nucleus, lateral part (AOL), 29, 31, 33, 35
© Springer Japan KK, part of Springer Nature 2018
N. Kumazawa-Manita et al., The 3D Stereotaxic Brain Atlas of the Degu, Brain Science,
https://doi.org/10.1007/978-4-431-56615-1
Anterior olfactory nucleus, posterior part (AOP),
37, 39
Anterior olfactory nucleus, ventroposterior part (AOVP),
33, 35, 37, 39
Anterior pretectal nucleus (APT), 13, 67, 69, 71
Anterodorsal thalamic nucleus (AD), 12, 55
Anteromedial thalamic nucleus (AM), 12, 53, 55, 57
Anteroventral thalamic nucleus (AV), 12, 53
Antrior cortical amygdaloid nucleus (Aco), 11, 55
Aqueduct (Aq), 19, 67, 69, 71, 73, 75, 77
Arcuate hypothalamic nucleus (Arc), 13, 55, 57, 59
Area postrema (AP), 19, 97
Ascending fibers of the facial nerve (asc7), 18
Association nuclei (ASN), 12
Auditory cortex/primary area (Au1), 10, 61, 63, 65,
67, 69, 71
Auditory thalamus (AuT), 12
B
BASAL GANGLIA (BG), 11
Basal nucleus (Meynert) (B), 53, 55
Basolateral amygdaloid nucleus (BL), 11
Basolateral amygdaloid nucleus/anterior part (BLA),
11, 55, 57, 59
Basolateral amygdaloid nucleus/posterior part (BLP),
11, 57, 59, 61, 63, 65
Basolateral amygdaloid nucleus/ventral part (BLV), 11
Basomedial amygdaloid nucleus (BM), 11
Basomedial amygdaloid nucleus/anterior part (BMA),
11, 55
Basomedial amygdaloid nucleus/posterior part (BMP),
11, 57, 59, 61, 63
Bed nucleus of the stria terminalis (ST), 11
Bed nucleus of the stria terminalis/lateral division (STL),
11, 49, 51
Bed nucleus of the stria terminalis/medial division
(STM), 11, 49, 51, 53
Brachium of the inferior colliculus (bic), 18, 71, 73, 75,
77, 79
Brachium of the superior colliculus (bsc), 18, 65, 67, 69, 71
BRAIN STEM (MIDBRAIN+PONS+MEDULLA
OBLONGATA) (STEM), 14, 15
137
138
C Deep white layer of the superior colliculus (DpWh),
C1 adrenaline cells (C1), 15
C2 adrenaline cells (C2), 15
C3 adrenaline cells (C3), 15
Caudal linear nucleus of the raphe (CLi), 15, 73
Caudate putamen (striatum) (CPu), 11, 41, 43, 45,
47, 49, 51, 53, 55, 57, 59
Caudomedial entorhinal cortex (CEnt), 73, 75, 77, 79
Central amygdaloid nucleus (Ce), 11, 57, 59
Central amygdaloid nucleus/capular part (CeC), 11, 55
Central amygdaloid nucleus/lateral part (CeL), 11, 57
Central amygdaloid nucleus/medial part (CeM),
11, 55, 57
Central canal (CC), 19, 99, 101, 103, 105
Central cervical nucleus (CeCv), 15, 97, 101, 103, 105
Central gray (CG), 14, 79, 81, 83
Central medial thalamic nucleus (CM), 12, 55, 57,
59, 61, 63
Central nucleus of the inferior colliculus (CIC),
14, 75, 77, 79
Centrolateral thalamic nucleus (CL), 12, 57, 59, 61, 63
Cerebellar cortex (Cb), 17
CEREBELLUM (METENCEPHALON) (CB), 17
Cerebral peduncle (cp), 18, 61, 63, 67, 69, 71, 73
CEREBRUM/CEREBRAL CORTEX (CER), 10
Choroid plexus (chp), 53, 55, 59, 61, 63, 65, 91, 93
Cingulate cortex (Cg), 10, 35, 37, 41, 43, 45, 47, 49, 51
Cingulum (cg), 18, 41, 43, 45, 47, 49, 51, 53, 55, 57,
59, 65, 67
CIRCUMVENTRICULAR ORGAN (CvO), 19
Claustrum (Cl), 11, 37, 39, 41
Cochlear nuclei (C), 14, 53
Cochlear root of the vestibulocochlear nerve (8cn),
19, 83, 85, 91
Commissural nucleus of the inferior colliculus (Com), 14
Commissure of the inferior colliculus (cic), 18, 77
Commissure of the superior colliculus (csc), 18, 67
Conterminal nucleus (Ct), 15
Copula of the pyramis (Cop), 17, 93, 95, 97
Corpus callosum (cc), 18, 43, 45, 47, 49, 51, 53, 55, 57,
59, 61, 63, 65, 97
Cortex-amygdala transition zone, layer 1 (CxA1), 51, 53
Cortical amygdaloid group (corticomedial group)
(CoAG), 11
Cortical amygdaloid nucleus (Co), 11
Cortical areas (CorA), 10
CRANIAL NERVE (CN), 19
Crus1 of the ansiform lobule (Crus1), 17, 87, 89, 91, 93, 95
Crus2 of the ansiform lobule (Crus2), 17, 91, 95, 97
Cuneate fasciculus (cu), 18, 97, 99, 101, 103, 105
Cuneate nucleus (Cu), 15, 95, 97, 99, 101, 103
Cuneinform nucleus (CnF), 14, 75, 77, 79
D Ectorhinal cortex (Ect), 61, 63, 65, 67, 69, 71, 73,
Decussation of the medial lemniscus (mlx), 18, 99
Decussation of the superior cerebellar peduncle (scpx), 18
Deep cerebellar nuclei (Dc), 17
Deep gray layer of the superior colliculus (DpG), 14, 67,
69, 71, 73, 75
Index of Abbreviations
14, 67, 69, 71, 73, 75
Dentate gyrus (DG), 10
DIENCEPHALON (DIEN), 12, 13
Dorsal cochlear nucleus (DC), 14
Dorsal cochlear nucleus/deep core (DCDp), 14, 87, 89, 91
Dorsal cochlear nucleus/fusiform layer (DCFu), 14, 87,
89, 91
Dorsal cochlear nucleus/molecular layer (DCMo),
14, 87, 89, 91
Dorsal cortex of the inferior colliculus (DCIC),
14, 77, 79
Dorsal corticospinal tract (dcs), 18, 97, 99, 101, 103, 105
Dorsal endopiriform nucleus (DEn), 11, 39, 41, 43, 45,
47, 49, 51, 53, 55, 57, 59, 61, 63, 65
Dorsal hypothalamic area (DA), 59
Dorsal lateral geniculate nucleus (DLG), 12, 61, 63, 65, 67
Dorsal motor nucleus of vagus (10N), 15, 93, 95, 97, 101
Dorsal nucleus of the lateral lemniscus (DLL), 14, 77, 79
Dorsal olfactory tract (dlo), 27, 29
Dorsal paragigantocellular nucleus (DPGi), 87, 89, 91
Dorsal part of claustrum (DCl), 45, 47, 49, 51, 53, 55, 57
Dorsal peduncular cortex (DP), 37, 39, 41, 43, 45
Dorsal periolivary region (DPO), 15
Dorsal raphe nucleus (DR), 14
Dorsal raphe nucleus/caudal part (DRC), 14, 15, 79, 81
Dorsal raphe nucleus/dorsal part (DRD), 14, 75, 77
Dorsal raphe nucleus/lateral part (DRL), 14, 75, 77
Dorsal raphe nucleus/ventral part (DRV), 14, 75, 77
Dorsal spinocerebellar tract (dsc), 18, 101, 103, 105
Dorsal subiculum (DS), 10, 67, 71
Dorsal tegmental decussation (dtgx), 18
Dorsal tegmental nucleus (DTg), 79
Dorsal tegmental nucleus (DTgm), 15
Dorsal tegmental nucleus/central part (DTgC), 15
Dorsal tegmental nucleus/pericentral part (DTgP), 14, 15
Dorsal tenia tecta (DTT 1-2), 41, 43
Dorsal transition zone (DTr), 37, 39
Dorsolateral entorhinal cortex (DLEnt), 65, 67, 71,
73, 75, 77
Dorsomedial hypothalamic nucleus (DM), 13, 59
Dorsomedial hypothalamic nucleus/compact part
(DMC), 13
Dorsomedial hypothalamic nucleus/dorsal
part (DMD), 13
Dorsomedial spinal trigeminal nucleus (DMSp5), 87, 89,
91, 93, 95
Dorsomedial tegmental area (DMTg), 15, 79, 81
Dosal acoustic atria (das), 18, 89, 91
Dysgranular insular cortex (DI), 10, 37, 39, 41, 43, 45,
47, 49, 51, 53, 55, 59
E
75, 77, 79
Edinger-Westphal nucleus (EW), 14, 71
Endopiriform nucleus, 11, 39, 41, 43, 45, 47, 49, 51,
53-59, 61, 63, 65
Entorhinal cortex (Ent), 10
Index of Abbreviations
Ependyma & subependymal layer (E), 10, 43, 45
Ependyma & subependymal layer/lateral
ventricle (E/LV), 41
Ependyma & subependymal layer/olfactory ventricle (E/
OV), 23, 25, 27, 29, 31, 33, 35, 37, 39
Epifacicular nucleus (EF), 15
EPITHALAMUS (EPI), 12
Extended amygdala (EXA), 11
External capsule (ec), 18, 45, 49, 51, 53, 55, 57
External cortex of the inferior colliculus (ECIC),
14, 73, 75, 77, 79
External cuneate nucleus (ECu), 15, 93, 95, 97
External globus pallidus (globus pallidus) (EGP), 11
External medullary lamina (eml), 18
External plexiform layer of the accessory olfactory bulb
(EPlA), 10, 27, 29, 31
External plexiform layer of the olfactory bulb (EPl),
10, 23, 25, 27, 29, 31
F I
Facial nerve (7n), 19, 85
Facial nucleus (7N), 14, 87, 89, 91
Faciola cinereum (FC), 10, 61, 63
Fasciculus retroflexus (fr), 18, 61, 63, 65, 67, 69
FIBER BUNDLE (FB), 18
Field CA1 of the hippocampus (CA1), 10, 57, 59, 65,
67, 69, 71
Field CA2 of the hippocampus (CA2), 10, 57, 59, 61,
63, 65
Field CA3 of the hippocampus (CA3), 10, 55, 57, 59, 61,
63, 65, 67, 69
Fimbria of the hippocampus (fi), 18, 49, 51, 53, 55, 57,
59, 61, 63
Flocculus (Fl), 17, 81, 83, 85, 87
Forceps major of the corpus callosum (fmj), 18, 71
Forceps minor of the corpus callosum (fmi), 18, 35, 37, 39
FOREBRAIN (TELENCEPHALON and
DIENCEPHALON) (FORE), 10–13
Fornix (f), 18, 55, 57, 61, 63
Fourth ventricle (4V), 19, 79, 81, 83, 85, 87, 89, 91, 93
Frontal associational cortex (FrA), 27, 29, 31
G Intercalated nucleus of the medulla (In), 15
Genu of the corpus callosum (gcc), 18, 41
Genu of the facial nerve (g7), 18, 85, 87
Gigantocellular reticular nucleus (Gi), 16, 87, 89, 91,
93, 95
Gigantocellular reticular nucleus/alpha part (GiA), 89
Gigantocellular reticular nucleus/ventral part (GiV),
93, 95
Globus pallidus (GP), 11, 51, 53, 55, 57, 59
Glomerular layer of the accessory olfactory bulb (GlA),
10, 27, 29
Glomerular layer of the olfactory bulb (Gl), 10
Gracile fasciculus (gr), 18, 97, 99, 101, 103, 105
Gracile nucleus (Gr), 15, 97, 99, 101, 103
Granular insular cortex (GI), 10, 23, 25, 27, 29, 31,
37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 59
139
Granule cell layer of the accessory olfactory bulb (GrA),
10, 25, 27, 29
Granule cell layer of the cochlear nuclei (GrC), 14, 83, 85
Granule cell layer of the dentate gyrus (GrDG),
10, 55, 57, 59, 61, 63, 65, 67, 69, 71
Granule cell layer of the olfactory bulb (GrO), 10, 23, 25,
27, 29, 31
H
Habenular commissure (hbc), 18
Habenular nucleus (Hb), 12, 59, 61, 63
Hippocampal fissure (hif), 19, 57, 63, 65, 67, 69, 71
Hippocampal formation (HipF), 10
Hippocampus (Hip), 3, 10, 18
Hypoglossal nerve (12n), 19
Hypoglossal nucleus (12N), 15, 95, 97, 99
HYPOTHALAMUS (HYPO), 13, 54–56, 59, 61, 63, 65
Indusium griseum (IG), 10, 41, 43, 45, 47, 49, 51, 53
Inferior cerebellar peduncle (restiform body) (ICP),
18, 85, 87, 89, 91, 93, 95
Inferior colliculus (IC), 14, 18, 71, 73, 75, 77, 79, 81
Inferior olive (IO), 15, 93, 95, 97, 99
Inferior olive/beta subnucleus of the medial nucleus
(IOBe), 16
Inferior olive/cap of Kooy of the medial
nucleus (IOK), 16
Inferior olive/dorsal nucleus (IOD), 16, 93, 95, 97
Inferior olive/dorsomedial cell group (IODM), 16
Inferior olive/medial nucleus (IOM), 16, 93, 95, 97, 99
Inferior olive/principal nucleus (IOPr), 16, 93, 95
Inferior olive/subnucleus A of medial nucleus (IOA), 16
Inferior olive/subnucleus B of medial nucleusInferior
olive/subnucleus B of medial nucleus (IOB), 16
Inferior olive/subnucleus C of medial nucleus (IOC), 16
Inferior olive/ventrolateral prorusion (IOVL), 16
Inferior salivatory nucleus (IS), 16, 89
Infralimbic cortex (IL), 37, 39, 41
Interanterodorsal thalamic nucleus (IAD), 12
Interanteromedial thalamic nucleus (IAM), 12, 55
Intercalated nuclei of the amygdala, 11
Intercrural fissure (ICF), 19, 91, 93, 95
Intermediate gray layer of the superior colliculus (InG),
14, 67, 69, 71, 73
Intermediate interstitial nucleus of the medial
longitudinal fasciculus (II), 83
Intermediate nucleus of the lateral lemniscus (ILL),
14, 77, 79
Intermediate reticular nucleus (IRt), 16, 87, 89, 91, 93,
95, 97, 99, 101, 103, 105
Intermediate white layer of the superior colliculus
(InWh), 14, 67, 69, 71, 73, 75
Intermediodorsal thalamic nucleus (IMD), 12, 57, 59
Internal capsule (IC), 18, 49, 51, 53, 55, 59, 61, 63, 65
Internal globus pallidus (ento-/or intrapeduncular
nucleus) (IGP), 11
140
Internal medullary lamina (IML), 18
Internal plexiform layer of the olfactory bulb (IPl),
10, 23, 25, 27, 29, 31
Interpeduncular nucleus (IP), 14, 71, 73
Interpeduncular nucleus/caudal subnucleus (IPC),
14, 71, 73
Interpeduncular nucleus/intermediate subnucleus (IPI),
14, 73
Interpeduncular nucleus/lateral subnucleus (IPL),
14, 71, 73
Interpeduncular nucleus/rostrall subnucleus (IPR), 14
Interstitial nucleus of Cajal (InC), 14, 67, 69
Interstitial nucleus of the posterior limb of the anterior
commissure (IPAC), 11, 49, 51
Interstitial nucleus of the posterior limb of the anterior
commissure, lateral part (IPACL), 51
Interstitial nucleus of the posterior limb of the anterior
commissure, medial part (IPACM), 51
Interstitial nucleus of the vestibular part of the
8th nerve (I8), 15
Interventricular foramen (IVF), 19
Islands of Calleja (ICj), 10, 41, 43, 45, 47, 49
Islands of Calleja/major island (ICjM), 10, 45, 47
K Laterodorsal (or lateral dorsal) thalamic nucleus (LD),
Kolliker-Fuse nucleus (KF), 16, 81, 83
L Lithoid nucleus (Lth), 65
Lacunosum moleculare layer of the hippocampus
(LMol), 10, 57, 59, 60, 63, 65, 67, 69
Lambdoid septal zone (Ld), 12, 57, 59
Lamina terminalis (Lter), 13, 19, 49
Lateral amygdaloid nucleus (La), 11, 55, 57, 59,
61, 63, 65
Lateral amygdaloid nucleus/dorsolateral part (LaDL),
11, 55, 57, 59, 61, 63
Lateral amygdaloid nucleus/ventrolateral part (LaVL),
11, 57, 59
Lateral amygdaloid nucleus/ventromedial part (LaVM),
11, 57, 59, 61, 63
Lateral (dentate) derebellar nucleus (Lat), 17
Lateral derebellar nucleus/parvicelllar part (LatPC), 89
Lateral habenular nucleus (LHb), 12, 59, 61, 63
Lateral hypothalamic area (LH), 13
Lateral lemniscus (LL), 18, 77, 79, 81
Lateral mammillary nucleus (LM), 13, 55, 65, 67
Lateral nuclei (LTN), 12
Lateral olfactory tract (LO), 18, 27, 29, 31, 33, 35,
37, 39, 43, 45, 47, 49, 51, 53
Lateral orbital cortex (LO), 31, 33, 35, 37, 39, 41
Lateral parabrachial nucleus (LPB), 14, 79, 81
Lateral paragigantocellular nucleus (LPGi), 16, 87, 91,
93, 95
Lateral posterior thalamic nucleus (LP), 12, 61, 63,
65, 67, 69
Lateral posterior thalamic nucleus/lateral part (LPL),
61, 63
Lateral posterior thalamic nucleus/medial part (LPM),
61, 63, 65
Index of Abbreviations
Lateral posterior thalamic nucleus/mediorostral
part (LPMR), 65
Lateral preoptic area (LPO), 13, 49, 51, 53, 85, 87
Lateral recess of the 4th ventricle (LR4V), 19, 87, 89,
91, 93
Lateral reticular nucleus (LRt), 16, 87, 97, 99
Lateral reticular nucleus/parvicellular part (LRtPC),
16, 97, 99
Lateral septal nucleus (LS), 11, 43, 45, 47, 49, 51
Lateral septal nucleus/dorsal part (LSD), 11, 45, 47,
49, 51
Lateral septal nucleus/intermediate part (LSI), 11, 43, 45,
47, 49
Lateral septal nucleus/ventral part (LSV), 11, 45, 47,
49, 51
Lateral stripe of the striatum (LSS), 47, 49
Lateral superior olive (LSO), 15, 85, 87
Lateral terminal nucleus of the accessory
optic tract (LT), 16
Lateral ventricle (LV), 19, 41, 43, 45, 47, 49, 51, 53, 55,
57, 59, 61, 63, 67, 69, 71, 73, 89
Lateral vestibular nucleus (LVe), 16, 87, 89
Latero-basal nuclear complex (bassolateral group)
(Lbn), 11
Laterodorsal tegmental nucleus (LDTg), 14, 79, 81
12, 57, 59
Lateroventral periolivary nucleus (LVPO), 15, 83
Linear nucleus of the medulla (Li), 16, 95
Lobule 1 of cerebellar vermis (lingula) (1Cb), 17, 81, 83,
85, 87
Lobule 2 of cerebellar vermis (2Cb), 17, 79, 81, 83, 85, 87
Lobule 3 of cerebellar vermis (3Cb), 17, 81, 83, 85, 87, 89
Lobule 4 of cerebellar vermis (4Cb), 17, 77, 79, 81, 83,
85, 87, 89
Lobule 5 of cerebellar vermis (5Cb), 17, 77, 79, 81, 83,
85, 87, 89
Lobule 6 of cerebellar vermis (6Cb), 17, 87, 89, 91,
93, 95
Lobule 7 of cerebellar vermis (7Cb), 17, 93, 95, 97
Lobule 8 of cerebellar vermis (8Cb), 17, 93, 95, 97, 99
Lobule 9 of cerebellar vermis (uvula) (9Cb), 17, 93, 95,
97, 99, 101, 103
Lobule 10 of cerebellar vermis (nodule) (10Cb),
17, 91, 93, 95, 97
Locus coeruleus (LC), 14, 83, 85
Longitudinal fasciculs of the pons (lfp), 18, 75, 77, 79, 81
M
Magnocellular nucleus of the posterior commissure
(MCPC), 13, 65, 69
Magnocellular preoptic nucleus (MCPO), 49, 51, 53
Mamillary peduncle (mp), 18
Mamillary recess of the 3rd ventricle (MRe), 19
Mammillary body (MB), 13, 109
Mammillotegmental tract (mtg), 65, 67
Mammillothalamic tract (mt), 55, 57, 61, 63
Matrix region of the medulla (Mx), 16, 95, 99
Medial accessory oculomotor nucleus (MA3), 69
Index of Abbreviations
Medial amygdaloid nucleus (Me), 11
Medial amygdaloid nucleus, anterodorsal
part (MeAD), 55
Medial amygdaloid nucleus, anteroventral
part (MeAV), 55
Medial amygdaloid nucleus, posterodorsal
part (MePD), 57, 59
Medial amygdaloid nucleus, posteroventral
part (MePV), 57, 59
Medial (fastigal) cerebellar nucleus (Med), 16
Medial entorhinal cortex (MEnt), 71, 73, 75, 77
Medial geniculate nucleus (MG), 12, 65, 67, 69, 71
Medial geniculate nucleus/dorsal part (MGD),
12, 65, 67, 69, 71
Medial geniculate nucleus/medial part (MGM), 12, 69, 71
Medial geniculate nucleus/ventral part (MGV),
12, 65, 67, 69, 71
Medial habenular nucleus (MHb), 12, 59, 61, 63
Medial lemniscus (ml), 18, 59, 61, 63, 65, 67, 69, 71, 73,
75, 77, 83, 85, 87, 89, 91, 93, 95, 97, 99
Medial longitudinal faciculcus (mlf), 18, 69, 71, 73, 75,
77, 79, 81, 83, 85, 89, 91, 93, 95, 97, 99, 101, 103, 105
Medial mamillary nucleus/lateral part (ML), 13
Medial mamillary nucleus/medial part (MM), 13
Medial mamillary nucleus/median part (MnM), 13, 65
Medial orbital cortex (MO), 31, 33, 35
Medial parabrachial nucleus (MPB), 14, 79, 81, 83, 85
Medial parabrachial nucleus/external part (MPBE), 83
Medial preoptic area (MPA), 13, 51, 53
Medial preoptic nucleus (MPO), 13, 51, 53, 85, 87
Medial preoptic nucleus/central part (MPOC), 53
Medial pretectal nucleus (MPT), 13, 65
Medial septal nucleus (MS), 11, 45, 47, 49
Medial superior olive (MSO), 15, 83, 85, 87
Medial tuberal nucleus (MTu), 13
Medial vestibular nucleus (MVe), 16, 85, 87, 91, 93, 95
Medial vestibular nucleus/magnocellular part (MVeMC),
16, 85, 87, 89
Medial vestibular nucleus/parvicellular part (MVePC),
16, 87, 89
Median accessory nucleus of the medulla (MnA), 16, 65
Median eminence (ME), 19, 57, 59
Median preoptic nucleus (MnPO), 13, 49, 51
Median raphe nucleus (MnR), 15, 75, 77, 79, 81
Mediodorsal thalamic nucleus (MD), 12, 57, 59, 61, 63
Mediodorsal thalamic nucleus/lateral part (MDL),
12, 57, 59, 61, 63
Mediodorsal thalamic nucleus/medial part (MDM),
12, 57, 59, 61, 63
Medioventral periolivary nucleus (MVPO), 15, 81, 83
MEDULLA OBLONGATA (MYELENCEPHALON)
(MED), 15, 16
Medullary reticular nucleus (or MeRt) (MRt), 14, 67,
69, 71
Medullary reticular nucleus/dorsal part (MdD), 97, 99,
101, 103, 105
Medullary reticular nucleus/ventral part (MdV), 97, 99,
101, 103, 105
Mesencephalic trigeminal nucleus (me5), 14
Mesencephalic trigeminal tract (Me5), 18, 71, 73, 75, 77,
79, 81, 83
141
MIDBRAIN (MESENCEPHALON) (MID), 14, 15
Middle cerebellar peduncle (MCP), 18, 75, 77, 79, 81,
83, 85
Midline and intralaminar nuclei (MIN), 12
Mitral cell layer of the accessory olfactory bulb (MiA),
10, 27, 29, 31
Mitral cell layer of the olfactory bulb (Mi), 10, 23, 25,
27, 29, 31
Molecular layer of the dentate gyrus (MoDG), 10, 55, 57,
61, 63, 65, 67, 69, 71
Motor cortex/primary area (M1), 10, 37, 39, 41, 43, 45,
47, 49, 51, 53, 55, 57
Motor root of the trigeminal nerve (M5), 18, 73, 75, 77,
79, 81, 83, 85
Motor thalamus (MTT), 12
Motor trigeminal nucleus (5N), 14
N
Navicular nucleus of the basal forebrain (Nv), 10, 43
Nucleus of Darkschewitsch (Dk), 14, 67, 69
Nucleus of Roller (Ro), 16, 95
Nucleus of the horizontal limb of the diagonal band
(HDB), 11, 49, 53
Nucleus of the lateral olfactory tract,
layer 1-3 (LOT 1-3), 53
Nucleus of the lateral olfactry tract (LOT), 11
Nucleus of the optic tract (OT), 13, 65
Nucleus of the posterior commissure (PCom), 14, 67
Nucleus of the solitary tract (Sol), 16, 91, 93, 95, 97, 99
Nucleus of the solitary tract/central part (SolCe), 16
Nucleus of the solitary tract/commissural part (SolC),
16, 97, 99, 101
Nucleus of the solitary tract/dorsolateral
part (SolDL), 16
Nucleus of the solitary tract/dorsomedial
part (SolDM), 16
Nucleus of the solitary tract/gelatinous part (SolG), 16
Nucleus of the solitary tract/intermediate
part (SolIM), 16
Nucleus of the solitary tract/interstitial part (SolI), 16
Nucleus of the solitary tract/lateral part (SolL), 16, 95,
97, 99
Nucleus of the solitary tract/medial part (SolM),
16, 91, 93, 95, 97, 99, 101
Nucleus of the solitary tract/rostrolateral
part (SolRL), 16
Nucleus of the solitary tract/ventral part (SolV),
16, 93, 95, 97, 99
Nucleus of the solitary tract/ventrolateral
part (SolVL), 16, 93
Nucleus of the spinal trigeminal tract (Sp5MED), 16
Nucleus of the spinal trigeminal tract (Sp5PONS), 14
Nucleus of the stria medullaris (SM), 13
Nucleus of the trapezoid body (Tz), 14, 81, 83, 85, 87
Nucleus of the vertical limb of the diagonal band (VDB),
11, 45, 47
Nucleus X (X), 16, 91
Nucleus Y of the vestibular complex (Y), 17, 89
Nuclus of the brachium of the inferior colliculus (BIC),
14, 73, 75
142
O Piriform cortex/layer 2 (Pir 2), 10, 37, 39, 41, 43, 45, 47,
Occulomotor nerve (3n), 19, 69, 71
Oculomotor nucleus (3N), 14, 71
Oculomotor nucleus/parvicellular part (3PC), 14, 73
Olfactory bulb (OB), 10
OLFACTORY BULB (OLB), 3, 10, 23, 27, 29, 31
Olfactory cortex (OlfC), 10
Olfactory nerve (OLF), 23, 25
Olfactory nerve layer (ON), 10
Olfactory ventricle (olfactory part of lateral ventricle)
(OV), 19
Olfactry tubercle (Tu), 10, 41, 43, 45, 47, 49
Olivary pretectal nucleus (OPT), 13
Optic chiasm (OCH), 18, 49, 51, 53
Optic nerve layer of the superior colliculus (Op), 14, 65,
67, 69, 71, 73, 75
Optic tract (OPT), 13, 16, 18, 55, 57, 59, 61, 63, 65, 67
Orbital cortex (Orb), 10, 31, 33, 35, 37, 39, 41
Oriens layer of the hippocampus (Or), 10, 55, 57, 59, 61,
63, 65, 67, 69, 71
Oval paracentral thalamic nucleus (OPC), 12
P 56, 58, 61, 63, 65, 67, 69
Parabigeminal nucleus (PBG), 14, 75
Paracentral thalamic nucleus (PC), 12, 55, 59, 65
Parafascicular thalamic nucleus (PaF), 12, 61, 63
Parafascicular thalamic nucleus (PF), 12, 61, 63
Parafloccular sulcus (pfs), 19, 87, 89, 91
Paraflocculus (PFl), 17, 85, 87, 89, 91, 93, 95
Paramedian lobule (PM), 17, 93, 97
Paramedian raphe nucleus (PMnR), 15
Paramedian reticular nucleus (PMn), 16, 97
Paranigral nucleus of the VTA (PN), 14, 75, 77
Parasolitary nucleus (PSol), 16
Parasubiculum (PaS), 10, 73, 75, 77, 79
Parasubthalamic nucleus (PSTh), 12, 60, 62
Paratenial thalamic nucleus (PT), 12, 53, 55
Paraventricular hypothalamic nucleus (Pa), 13, 53, 55, 57
Paraventricular hypothalamic nucleus/anterior
parvicellular part (PaAP), 53
Paraventricular thalamic nucleus (PV), 12
Paraventricular thalamic nucleus/anterior part (PVA),
12, 53, 55, 56
Paraventricular thalamic nucleus/posterior part (PVP),
12, 60, 62
Parvicellular reticular nucleus (PCRt), 85, 87, 89, 91,
93, 95, 163
Peduncular part of the lateral hypothalamus (PLH),
55, 59, 61, 63, 65
Periaqueductal gray (PAG), 14, 65, 67, 69, 71, 73, 75, 77
Perirhinal cortex (PRh), 64, 67, 69, 71, 73, 75, 77, 79
Periventricular hypothalamic nucleus (Pe), 13, 51, 53,
55, 57, 59
Periventricular hypothalamic nucleus/anterior
parvicellular part (PeAP), 53
Pineal gland (Pi), 19
Piriform cortex (Pir), 10
Piriform cortex/layer 1 (Pir 1), 10, 37, 39, 41, 43, 45,
47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67
Index of Abbreviations
49, 51, 53, 55, 57, 59, 61, 63, 65, 67
Piriform cortex/layer 3 (Pir 3), 10, 37, 39, 41, 43, 45, 47,
49, 51, 53, 55, 57, 59, 61, 63, 65, 67
Polymorph layer of the dentate gyrus (PoDG), 10, 56, 59,
61, 63, 65, 67, 71
PONS (METENCEPHALON) (PONS), 14, 15
Pontine nuclei (Pn), 14, 75, 77
Pontine reticular nucleus/caudal part (PnC), 15, 83, 85
Pontine reticular nucleus/oral part (PnO), 15, 75, 77,
79, 81
Pontine reticular nucleus/ventral part (PnV), 15
Posterior commissure (PC), 18, 67
Posterior hypothalamic area (PHA), 13, 65
Posterior hypothalamic nucleus (PH), 13, 61, 63
Posterior interposed cerebellar nucleus (IntP), 17, 91
Posterior pretectal nucleus (PPT), 13, 69
Posterior superior fissure (psf), 19, 81, 85, 87, 89, 93, 95
Posterior thalamic nuclear group (Po), 12, 59, 61, 63, 67
Posterolateral cortical amygdaloid nucleus (PLCo), 11,
57, 59, 61, 63, 65
Posterolateral fissure (plf), 19, 85, 87, 93, 95
Posteromedial cortical amygdaloid nucleus (PMCo), 11,
Posteromedial thalamic nucleus (PoMn), 61, 63
Postsubiculum (Post), 10, 71, 73, 75, 77
Precommissural nucleus (PrC), 65
Preculminate fissure (PCUF), 19, 81, 83, 85, 87
Pre-Edinger-Westphal nucleus (PrEW), 69
Prelimbic cortex (PrL), 33, 35, 37, 39, 41
Premamillary nucleus (PrM), 13
Premammillary nucleus, dorsal part (PMD), 61, 63
Premammillary nucleus, ventral part (PMV), 61, 63
Preoptic area (PO), 13
Prepositus nucleus (Pr), 16, 85, 87, 91, 93
Prepyramidal fissure (ppf), 19, 93, 95
Presubiculum (PrS), 10, 73
PRETECTUM (Pt), 13
Primary fissure (prf), 19, 81, 85, 87, 89
Principal sensory trigeminal nucleus (Pr5), 14, 83, 85
Pyramidal cell layer of the hippocampus (Py), 10, 55, 56,
58, 60, 62, 64, 67, 69, 71
Pyramidal decussation (pyx), 18, 99, 101, 103, 105
Pyramidal tract (py), 18, 83, 85, 87, 89, 91, 93, 97, 99
R
Radiatum layer of the hippocampus (Rad), 10, 55, 56,
58, 60, 62, 64, 67, 69, 71
Raphe interpositus nucleus (RIP), 15, 85, 87
Raphe magnus nucleus (RMg), 15, 83, 85, 87, 89, 91
Raphe nuclei (RaMED), 16
Raphe nuclei (RaMID), 14
Raphe nuclei (RaPONS), 15
Raphe obscurus nucleus (ROb), 16, 93, 95
Raphe pallidus nucleus (RPa), 16, 85, 87, 89, 91, 93, 95
Red nucleus (R), 14
Red nucleus/magnocellular part (RMC), 14, 69, 71
Red nucleus/parvicellular part (RPC), 14, 69, 71
Reticular formation (RtMED), 16
Index of Abbreviations
Reticular formation (RtMID), 14
Reticular formation (RtPONS), 15
Reticular thalamic nucleus (Rt), 12, 53, 54, 56,
58, 60, 62
Reticulotegmental nucleus of the pons (RtTg),
15, 75, 77, 79, 81, 83
Reticulotegmental nucleus of the pons/lateral
part (RtTgL), 15
Retroambiguus nucleus (RAmb), 16, 99
Retrochiasmatic area (RCh), 55
Retroisthmic nucleus (RIs), 15
Retrolemniscal nucleus (RL), 15
Retroparafacicular nucleus (RPF), 64
Retroreuniens area (RRe), 12, 60, 62
Retrosplenial dysgranular cortex (RSD), 10, 54, 56, 58,
60, 62, 64, 67, 69, 71, 73, 75, 77, 79
Retrosplenial granular cortex (RSG), 10, 54, 56, 58, 60,
62, 64, 67, 69, 71, 73, 75, 77
Reuniens thalamic nucleus (Re), 12, 53, 55, 56, 58
Rhabdoid nucleus (Rbd), 15
Rhinal fissure (rf), 6, 7, 19, 27, 29, 31, 33, 35, 37, 39, 41,
43, 45, 47, 49, 51, 53, 55, 56, 58, 60, 62, 67, 71, 73,
75, 77, 79
Rhinal incisures (ri), 27, 29, 31, 33, 35
Rhomboid thalamic nucleus (Rh), 12, 54, 58
Rostral linear nucleusof the raphe (RLi), 14, 67, 71
Rostrum of the corpus callosum (rcc), 18
Rubrospinal tract (rs), 18, 73, 75, 77, 79, 81, 83, 85, 87,
89, 91, 93, 95, 97, 99, 101, 103, 105
S Superior salivatory nucleus (SuS), 16, 87
Sagulum nucleus (Sag), 15, 79
Sensory/motor root of the trigeminal nerve (s5/m5), 73,
75, 77
Sensory root of the trigeminal nerve (s5), 18, 79, 81, 83
Septofimbrial nucleus (SFi), 11, 49, 51, 53
Septohippocampal nucleus (SHi), 11
Septohypothalamic nucleus (SHy), 49, 51, 53
SEPTUM (SEP), 11
Simple lobule (Sim), 17, 81, 83, 85, 87, 89
Simplex fissure (simf), 19, 89
Solitary tract (sol), 18
Somatosensory cortex/primary area (S1), 10, 37, 39,
41, 43, 45, 47, 49, 51, 53, 54, 56, 58, 60, 62
Somatosensory thalamus (SST), 12
Spinal trigeminal nucleus/caudal part (Sp5C), 16, 97,
99, 101, 105
Spinal trigeminal nucleus/interpolar part (Sp5I),
16, 93, 95, 97
Spinal trigeminal nucleus/oral part (Sp5O), 16, 89, 91
Spinal trigeminal tract (sp5), 18, 83, 89, 91, 93, 95, 97,
99, 101, 105
Spinal vestibular nucleus (SpVe), 16, 89, 91, 93, 95
Splenium of the corpus callosum (scc), 18
Stratum lucidum of the hippocampus (SLu), 10, 54, 56,
58, 60, 62, 64, 66, 69
Stria medullaris of the thalamus (sm), 18, 53, 54, 56, 58,
60, 62, 64
Stria terminalis (st), 18, 51, 53, 56, 58
143
Striatum (St), 11
Subcoeruleus nucleus (SubC), 15
Subcoeruleus nucleus/alpha part (SubCA), 15
Subcoeruleus nucleus/dorsal part (SubCD), 15
Subcoeruleus nucleus/ventral part (SubCV), 15
Subcommissural organ (SCO), 19, 64, 67
Subfornical organ (SFO), 19, 53
Subiculum (S), 10
Sublenticular extended amygdala (EA), 11, 55
Subparafiscicular thalamic nucleus (SPF), 12, 60, 62
Subpeduncular tegmental nucleus (SPTg), 15
Subpostrema area (SubP), 16
Substantia innominata (SI), 11
Substantia innominata/basal part (SIB), 11, 49, 51, 53
Substantia innominata/dorsal part (SID), 11
Substantia nigra (SN), 11
Substantia nigra (SNMID), 14
Substantia nigra/compact part (SNC), 11, 66, 69, 71, 73
Substantia nigra/lateral part (SNL), 11, 66, 69, 71
Substantia nigra/reticular part (SNR), 11, 66, 69, 71, 73
Subthalamic nucleus (STh), 11, 60, 62, 64
SULCUS (SUL), 19
Superficial gray layer of the superior colliculcus (SuG),
14, 66, 69, 71, 73, 75
Superior cerebellar peduncle (brachium conjunctivum)
(scp), 18, 60, 62, 64, 67, 69, 71, 73, 75, 77, 79, 81,
83, 85, 87
Superior colliculus (SC), 14
Superior medullary velum (SMV), 17, 89
Superior olive (SOl), 15
Superior paraolivary nucleus (SPO), 15
Superior vestibular nucleus (SuVe), 16, 85, 87
Suprachiasmatic nucleus (SCh), 13
Suprachiasmatic nucleus/dorsolateral
part (SChDL), 13, 53
Suprachiasmatic nucleus/ventromedial part (SChVM),
13, 53
Suprageniculate thalamic nucleus (SG), 12, 69, 71
Supramammillary nucleus, lateral part (SuML), 64
Supramammillary nucleus, medial part (SuMM), 64, 67
Supraoculomotor cap (Su3C), 14
Supraoculomotor periaqueductal gray (Su3), 14, 71, 73
Supraoptic nucleus (SO), 13, 49, 51, 53, 54
Supratrigeminal nucleus (Su5), 15, 81
Susbtantia innominata/ventral part (SIV), 11
T
Tectospinal tract (ts), 18, 73, 75, 77, 79, 81, 83, 85, 89,
91, 93, 95, 97, 99, 101, 105
TELENCEPHALON (TEL), 10, 11
Tenia tecta (TT), 10
Terete hypothalamic nucleus (Te), 13
THALAMUS (THAL), 12
Third ventricle (3V), 19, 53, 55, 57, 59, 61, 63, 65
Transverse fibers of the pons (tfp), 18, 75, 77, 79, 81
Trapezoid body (tz), 18, 81, 83, 85, 87, 89
Triangular nucleus of the lateral lemniscus (Tr), 15
Triangular septal nucleus (TS), 11, 51, 53
144
Trigeminal nerve (5n), 19
Trigeminal transition zone (5Tr), 85
Trochlear nerve (4n), 19, 75, 77, 81
Trochlear nucleus (4N), 14, 75
U Ventral tuberomamillary nucleus (VTM), 13
Uncinate fasciculus of the cerebellum (un), 18, 85
V Ventromedial preoptic nucleus (VMPO), 13
Vagus nerve (10n), 19
Vascular organ of the lamina terminalis (VOLT), 19, 49
Ventoromedial hypothalamic nucleus (VMH),
13, 54, 56, 58
Ventral anterior thalamic nucleus (VA), 12, 54, 56
Ventral cochlear nucleus (VC), 14
Ventral cochlear nucleus/anterior part (VCA), 14, 83, 85
Ventral cochlear nucleus/posterior part (VCP),
14, 87, 89, 91
Ventral endopiriform nucleus (VEn), 11, 39, 41, 43, 45,
47, 49, 51, 53, 54, 56, 58
Ventral geniculate nucleus (VG), 60, 62
Ventral hippocampal commissure (vhc), 18, 53
Ventral lateral geniculate nucleus (VLG), 12
Ventral nucleus of the lateral lemniscus (VLL),
15, 75, 77, 79, 81
Ventral orbital cortex (VO), 31, 33, 35, 37, 39
Ventral pallidum (VP), 11, 43, 45, 47, 49, 51, 53
Ventral part of claustrum (VCl), 43, 45, 47, 49, 51,
53, 54, 56
Ventral posterior nucleus of the thalamus/parvicellular
part (VPPC), 60, 62
Ventral posterolateral thalamic nucleus (VPL), 12, 56,
58, 60, 62
Ventral posteromedial thalamic nucleus (VPM),
12, 58, 60, 62
Ventral spinocerebellar tract (vsc), 18, 79, 81, 83, 85, 87,
95, 97, 99, 101, 103, 105
Index of Abbreviations
Ventral subiculum (VS), 10, 66, 69, 71
Ventral tegmental area (VTA), 14, 66
Ventral tegmental decussation (vtgx), 18
Ventral tegmental nucleus (VTg), 15, 77
Ventral tenia tecta, layer 1-2 (VTT 1-2), 33, 35
Ventral thalamus (VNT), 12
VENTRICLE (V), 19
Ventrolateral preoptic nucleus (VLPO), 13
Ventrolateral thalamic nucleus (VL), 12, 54, 56, 58
Ventromedial thalamic nucleus (VM), 12, 56, 58
Vestibular nuclei (VeMED), 16
Vestibular nuclei (VePONS), 15
Vestibular root of the vestibulocochlear nerve (8vn),
19, 83, 85, 87
Vestibulocerebellar nucleus (VeCb), 17, 87, 89
Vestibulocochlear nerve (8n), 19
Visual cortex/primary area (V1), 10, 64, 66, 69, 71, 73,
75, 77, 79
Visual thalamus (VST), 12
W
WHOLE BRAIN (WHOLE), 10–17
X
Xiphoid thalamic nucleus (Xi), 12, 56, 58
Z
Zona incerta (ZI), 12
Zona incerta/caudal part (ZIC), 12
Zona incerta/dorsal part (ZID), 12, 60, 62
Zona incerta/rostral part (ZIR), 12, 56
Zona incerta/ventral part (ZIV), 12, 60, 62
Zonal layer of the superior colliculus (Zo), 14, 66, 69,
71, 73, 75