Page 1
Roustem KHAZIPOV, Dilyara ZAYNUTDINOVA, Elena OGIEVETSKY, Olga MITRUKHINA, Jean-Bernard MANENT, Alfonso REPRESA
P1
ATLAS OF THE DEVELOPING RAT BRAIN IN STEREOTAXIC COORDINATES
INMED, INSERM U-901 & Aix-Marseille University, Marseille, FranceLaboratory of Neurobiology, Kazan Federal University, Kazan, Russia
Page 2
Atlas presents a series of microphotographs of coronal 200 micron brain sections of a P1 Wistar rat (weight 8 g). Sections were cut vertical to the horizontal plane extending from bregma to lambda. Therefore using this atlas requires position of the rat head with bregma and lambda adjusted to the same height. Sections at bregma and lambda levels are marked with DiI-trace. Additional DiI trace across the whole brain was used to control slicing vertical to the horizontal plane. Sections were prepared from the paraformaldehyde and glutaraldehyde fixed brains through vibroslicing. No coloration was used. Microphotographs were made from the wet sections in oblique light. Atlas starts with a list of abbreviations and an outline of the brain view from above.For additional information see (reference to the Frontiers in Neuroanatomy data report).
Page 3
List of Structures
3V 3rd Ventricle4V 4th VentricleAcb Accumbens nuAq Aqueduct SylviusAm Ambiguus nuA Amygdalaac anterior commissureArc Arcuate hypothalamic nuAu Auditory cortexBL Basolateral amygdala nuCA1 CA1CA3 CA3CPu Caudate PutamenCC Central Canalcp cerebral peduncleCg Cingulate cortexCl Claustrumcc corpus callossumCnf Cuneiform nuDG Dentate GyrusDB Diagonal BandDR Dorsal Raphe nuDLG Dorso Lateral GeniculateEnd Endopyriform nuEnt Entorhinal cortex7n Facial nerve7 Facial nufi fimbriaf fornix
F Frontal cortexg7 genu of facial nerveHb HabenulaH Hilus12 hypoglosal nucleushypo hypothalamusicp inferior cerebellar peduncleIC Inferior ColliculusIO Inferior Oliveic internal capsuleIPR Interpeduncular nuLa Lateral amygdala nulo lateral olfactory tractLSD Lateral Septal Dorsal nuLSI Lateral Septum IntermediateLT Lateral ThalamusLV Lateral VentricleLC Locus Coeruleusmt mamillothalamic tractMG Medial Geniculate nuMR Medial Raphe nuMS Medial Septal nuMe5 Mesencephalic trigemic numcp middle cerebellar peduncleM Motor cortexM2 Motor cortexm5 motor root trigeminus3 oculomotor nOB Olfactory BulbON Olfactory NuTu olfactory Tubercle
ox optic chiasmaopt optic tractO Orbital cortexPB Parabraquial nuPar Parietal cortexPAG Periaqueductal GrayPir Piriform cortexPn Pontine nuPnR Pontine Raphe nupc posterior commissureM1 primary Motor cortex py pyramidal tractRM Raphe Magnus nuRS Retrosplenial cortexrf rhinal fissures5 sensory root trigeminusSol Solitary nuS1 Somatosensory 1S1BF Somatosensory 1 Barrel FieldS SubiculumSN Substantia NigraSNC Substantia Nigra CompactaSNR Substantia Nigra ReticulataSTh Subthalamic nuscp superior cerebellar peduncleSC Superior ColliculusSCh Suprachiasmatic nuVT Ventral ThalamusVLG Ventro Lateral Geniculate nuVi Visual cortex
Page 4
0 -1123456 -2 -3 -4 -7 -8 -9 mmBregma Lambda
-5 -6
Rat P1weight (g) - 8.00
mm
Page 5
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 7
Bregma 3.20 mmLambda 7.00 mm
Rat P1
OB
Page 6
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 8
Bregma 3.00 mmLambda 6.80 mm
Rat P1
OB
Page 7
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 9
Bregma 2.80 mmLambda 6.60 mm
Rat P1
ON
O
Page 8
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 10
Bregma 2.60 mmLambda 6.40 mm
Rat P1
F
ON
O
Page 9
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 11
Bregma 2.40 mmLambda 6.20 mm
Rat P1
F
ON
O
Cg
Page 10
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 12
Bregma 2.20 mmLambda 6.00 mm
Rat P1
F
loac
Cg
Page 11
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 13
Bregma 2.00 mmLambda 5.80 mm
Rat P1
M1
ac
Cg
lo
Pir
Cl
Acb
Tu
Page 12
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 14
Bregma 1.80 mmLambda 5.60 mm
Rat P1
M1
ac
Cg
loPir
ClAcb
S1
Tu
CPu
Page 13
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 15
Bregma 1.60 mmLambda 5.40 mm
Rat P1
M1
ac
Cg
lo
Pir
Cl
Acb
S1
Tu
CPuLVLSI
Page 14
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 16
Bregma 1.40 mmLambda 5.20 mm
Rat P1
M1
ac
Cg
loPir
Cl
Acb
S1
Tu
CPuLV
LSI
cc
Page 15
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 17
Bregma 1.20 mmLambda 5.00 mm
Rat P1
M1
ac
Cg
lo
Pir
ClAcb
S1
Tu
CPuLV
LSI
cc
DB
Page 16
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 18
Bregma 1.00 mmLambda 4.80 mm
Rat P1
M1
ac
Cg
loPir
Cl
Acb
S1
Tu
CPu
LV
LSI
cc
MS
DB
Page 17
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 19
Bregma 0.80 mmLambda 4.60 mm
Rat P1
M1
ac
Cg
lo
Pir
Cl
S1
Tu
CPuLV
LSI
cc
MS
DB
Acb
Page 18
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 20
Bregma 0.60 mmLambda 4.40 mm
Rat P1
M1
ac
Cg
loPir
Cl
S1
CPu
LVcc
DB
LSD
MS
Tu
Page 19
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 21
Bregma 0.40 mmLambda 4.20 mm
Rat P1
ac
Cg
lo
Pir
Cl
CPu
LV
cc
MS
LSD
DB
Tu
M1
S1
Page 20
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 22
Bregma 0.20 mmLambda 4.00 mm
Rat P1
ac
Cg
lo
Pir
Cl
S1BF
CPu
LV
cc
hypo
LSD
3V
ic
Page 21
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 23
Bregma 0.00 mmLambda 3.80 mm
Rat P1
Cg
Pir
Cl
CPu
LVcc
hypo
f ic
rf
S1BF
3V
fi
Page 22
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 24
Bregma -0.20 mmLambda 3.60 mm
Rat P1
Cg
Pir
Cl
CPu
LVcc
f
ic
hypo
fi
rf
S1BF
3V
Page 23
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 25
Bregma -0.40 mmLambda 3.40 mm
Rat P1
Cg
Pir
End
CPu
LVcc
DG
f
CA1
ic
hypo
fi
rf
S1BF
3VH
Page 24
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 26
Bregma -0.60 mmLambda 3.20 mm
Rat P1
Cg
Pir
La
CPu
LVcc
f
CA3
ic
hypo
fi3V
LT
DG
CA1
End
VTrf
S1BF
BL
H
Page 25
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 27
Bregma -0.80 mmLambda 3.00 mm
Rat P1
Cg
PirBL
CPu
LV
cc
f
CA3
hypo
3V
S1BF
rf ic
fiLT
DG
CA1
End
VT
H
La
Page 26
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 28
Bregma -1.00 mmLambda 2.80 mm
Rat P1
RS
Pir
CPu
LV
f
CA3
ic
hypo
fi
3V
Par
rfLT
DG
CA1
H
VT
BL
La
Page 27
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 29
Bregma -1.20 mmLambda 2.60 mm
Rat P1
RS
Pir
CPu
LV
f
CA3
ic
hypo
fi
3V
Par
rf
LT
DGCA1
VT
H
BL
La
Page 28
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 30
Bregma -1.40 mmLambda 2.40 mm
Rat P1
Pir
CPu
LV
f
CA3
hypo
fi
Hb
rf
LT
DG CA1
VT
H
BLLa
RSPar
Page 29
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 31
Bregma -1.60 mmLambda 2.20 mm
Rat P1
Pirf
CA3
hypo
fi
Hb
Arc
rf
LT
DG CA1
VT
H
BL
La
RSPar
Page 30
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 32
Bregma -1.80 mmLambda 2.00 mm
Rat P1
Pirf
CA3
DLG
hypo
fi
Hb
rf
DGCA1H
BL
La
RS Par
STh
mt
VLG
Page 31
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 33
Bregma -2.00 mmLambda 1.80 mm
Rat P1
RS
Pir
Par
f
DG
CA3
hypo
Arc
rfCA1
BL
H DLG
mt
VLG
Page 32
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 34
Bregma -2.20 mmLambda 1.60 mm
Rat P1
RS
Pir
Par
DG
CA3
hypo
rfCA1
H
DLG
VLG
mtSTh
Page 33
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 35
Bregma -2.40 mmLambda 1.40 mm
Rat P1
RS
Au
DG
hypoEnt
CA1
Arc
DLG
VLG
STh
Page 34
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 36
Bregma -2.60 mmLambda 1.20 mm
Rat P1
RSVi
LVDG
hypo Arc
Ent
CA1
SC
STh
Page 35
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 37
Bregma -2.80 mmLambda 1.00 mm
Rat P1
RS
Ent
SC
CA1
S
Vi
Au
SN
MG
Page 36
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 38
Bregma -3.00 mmLambda 0.80 mm
Rat P1
RS
Ent
SC
S
Vi
MG
Page 37
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 39
Bregma -3.20 mmLambda 0.60 mm
Rat P1
Ent
MG
SN
SC
Page 38
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 40Rat P1
Ent
Aq
SN
SC
MG
Page 39
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 41
Bregma -3.60 mmLambda 0.20 mm
Rat P1
Aq
SC
MG
Page 40
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 42
Bregma -3.80 mmLambda 0.00 mm
Rat P1
Aq
SC
Pn
Page 41
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 43
Bregma -4.00 mmLambda -0.20 mm
Rat P1
Aq
SC
s5
Page 42
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 44
Bregma -4.20 mmLambda -0.40 mm
Rat P1
Aq
SC
Page 43
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 45
Bregma -4.40 mmLambda -0.60 mm
Rat P1
Aq
py
m5
SC
Page 44
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 46
Bregma -4.60 mmLambda -0.80 mm
Rat P1
Aq
py
m5
SC
Page 45
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 47
Bregma -4.80 mmLambda -1.00 mm
Rat P1
Aq
py
m5
IC
s5
Page 46
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 48
Bregma -5.00 mmLambda -1.20 mm
Rat P1
Aq
py
mcp
PB
7
IC
Page 47
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 49
Bregma -5.20 mmLambda -1.40 mm
Rat P1
py
scp
IC
Aq
Page 48
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 50
Bregma -5.40 mmLambda -1.60 mm
Rat P1
mpc
py
4V
IC
Page 49
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 51
Bregma -5.60 mmLambda -1.80 mm
Rat P1
mpc
py
4V
IC
Page 50
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 52
Bregma -5.80 mmLambda -2.00 mm
Rat P1
py
4V
IC
icp
Page 51
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 53
Bregma -6.00 mmLambda -2.20 mm
Rat P1
4V
py
IC
icp
Page 52
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 54
Bregma -6.20 mmLambda -2.40 mm
Rat P1
4V
py
icp
Page 53
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 55
Bregma -6.40 mmLambda -2.60 mm
Rat P1
4V
py
Page 54
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 56
Bregma -6.60 mmLambda -2.80 mm
Rat P1
4V
pyIO
Page 55
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 57
Bregma -6.80 mmLambda -3.00 mm
Rat P1
4V
pyIO
Page 56
0 1 2 3 4 5 6123456
0 1 2 3 4 5 6123456
0+5 -5 -10Bregma
0 -5Lambda 5
mm
mm
mm mm
mmmm
Figure 58
Bregma -7.00 mmLambda -3.20 mm
Rat P1
py
CC
IO