University of Rostock

Department of Anatomy

Neuroscience Group

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Rat connectome



Habenula left


Abbreviation
HAB
Color       
Superior regionsEpithalamus

SynonymsAbbr.Language
Zügel Ger
Zügelchen Ger
Zügelkerne Ger
Habenular complex  
Habenula region Eng
Habenular nucleus of the thalamus Eng
Habenular Eng
HabenulaHABEng
Habenular nuclei  

SubregionsSide
Habenular commissureleft
Lateral habenular nucleusleft
Medial habenular nucleusleft
Posterior habenulaleft
Anteroposterior habenulaleft
Junction medial and lateral habenulaleft

Output to

NameSideAbbr.WeightDetails
Central gray lateral partipsiCGL2
Central grey rostral areaipsirCG0
Oculomotor systemipsiOCS0
Periaqueductal grayipsiPAG-0.5
Dorsolateral periaqueductal grayipsiDLPAG2
Periaqueductal gray lateroventral partipsiPAGLV1
Ventral periaqueductal grayipsiVPAG0
Periventricular gray matteripsiPVG2
Red nucleusipsiR0.5
Tegmental areaipsiTGA0
Nucleus intercruralisipsiNICr2
Peduncularpontine nucleusipsiPPN-0.5
Ventral tegmental area A10ipsiVTA2
Interfascicular nucleusipsiIF-0.5
Paranigral nucleusipsiPN-0.5
Ventral tegmental nucleusipsiVTg3
Dorsal tegmental nucleusipsiDTg2
Cerebellar cortexipsiCERC0
Cerebellar lobule 9ipsiCERL9-0.5
Cerebellar lobule 10ipsiCERL10-0.5
Pons oral partipsiPor3
Nucleus pontis oralis medial partipsiPorM3
Nucleus pontis oralis dorsomedial partipsiPorDM-0.5
Pontine reticular nucleusipsiPRN3
Pontine reticular nucleus oral part dorsal partipsiPnOd2
Pontine reticular nucleus oral part dorsomedial partipsiPnOdm2
Pontine reticular nucleus oral part medial partipsiPnOm2
Dorsalmost part of the pontine reticular nucleus oral partipsiPnOdom-0.5
Parabrachial nucleus medialipsiPBnMe2
Raphe nucleiipsiRAN3
Dorsal raphe nucleusipsiDR2
Dorsal raphe nucleus median partipsiDRM-0.5
Median raphe nucleusipsiMnR2
Superior central raphe nucleusipsiCS-0.5
Superior central raphe nucleus lateral partipsiCSl3
Paramedian raphe nucleusipsiPMnR3
Pontine raphe nucleusipsiPnR0
Raphe magnus nucleusipsiRMg0
Endopiriform systemipsiEnN-0.5
Basal nucleus Meynert medial partipsiBmp2
Lateral preoptic areaipsiLPO-0.5
Lateral hypothalamic areaipsiLH-0.5
Lateral hypothalamic area posterior partipsiLHAp2
Paraventricular hypothalamic nucleusipsiPa-0.5
Supramammillar nucleus anterior partipsiSuMa2
Supramammillar nucleus posterior partipsiSuMp2
Central medial thalamic nucleusipsiCM0
Midline in the central medial thalamic nucleusipsiCMmi0
Parafascicular thalamic nucleusipsiPF-2
Mediodorsal thalamic nucleusipsiMD0
Intermediodorsal thalamic nucleusipsiIMD0
Zona incertaipsiZI-0.5
Pineal glandipsiPi-0.5
Stria medullaris of the thalamusipsism3
Basal nucleus anterior subdivisionipsiBncA2
Basolateral amygdaloid nucleusipsiBL-0.5
Bed nucleus of the stria terminalisipsiBST-0.5
Bed nucleus of the stria terminalis intraamygdaloid divisionipsiBSTIA2
Central amygdaloid nucleusipsiCe2
Capsule like area surrounding central amygdaloid nucleusipsiCec2
Anterior cortical amygdaloid nucleusipsiACo0.5
Medial amygdaloid nucleus anterior partipsiMeAn0.5
Amygdalohippocampal areaipsiAHi2
Rostral part of claustrumipsiRCl0
Globus pallidusipsiGP0
Retrosplenial regionsipsiRS0
Agranular insular cortex layer 1ipsiAIL11
Agranular insular cortex layer 3ipsiAIL32
Agranular insular cortex layer 4ipsiAIL42
Medial prefrontal cortex layer 3ipsimPFCL32
Medial prefrontal cortex layer 4ipsimPFCL42
Medial prefrontal cortex layer 1ipsimPFCL12
Interpeduncular nucleusipsiIP3
Interpeduncular nucleus apical subnucleusipsiIPA0.5
Interpeduncular nucleus central subnucleusipsiIPRc2
Interpeduncular nucleus intermediate subnucleusipsiIPI2
Periaqueductal gray lateroventral partcontraPAGLV1
Ventral tegmental nucleuscontraVTg2
Paraflocculus ventral partcontraPFlv1
FlocculuscontraFl1
Pontine reticular nucleus oral part medial partcontraPnOm2
Dorsal raphe nucleuscontraDR2
Superior central raphe nucleus lateral partcontraCSl2
Supramammillar nucleus anterior partcontraSuMa2
HabenulacontraHAB0
RetinacontraRET-0.5
Interpeduncular nucleuscontraIP3
Vitreous humor of eyeipsiOrgVHEye2
Femoral bone marrowipsiOrgSkFemM1

Input from

NameSideAbbr.WeightDetails
Central grayipsiCG2
Fasciculus retroflexusipsifr-2
Superior colliculusipsiSC0.5
Superior colliculus superficial layersipsiSCs-0.5
Central tegmental fieldipsiTGAC1
Mesopontine tegmental areaipsiTGAm2
Ventral tegmental area A10ipsiVTA3
Interfascicular nucleusipsiIF-0.5
Ventral tegmental area A10 paranigral divisionipsiVTApn-0.5
Caudal linear nucleus of the rapheipsiCLi-0.5
Ventral tegmental nucleusipsiVTg-0.5
Dorsal tegmental nucleus lateral partipsiDLTN2
Pedunculopontine tegmental nucleusipsiPPTg2
A4 noradrenaline cellsipsiA40.5
Locus coeruleusipsiLC2
Locus coeruleus dorsal partipsiLCD3
Intermediate reticular nucleusipsiIRt-0.5
Gigantocellular reticular nucleusipsiGi0
Subcoeruleus nucleusipsiSubC0.5
MyelencephalonipsiMYC2
Nucleus of the solitary tractipsiSol-0.5
Nucleus of the solitary tract caudal partipsiSolca-0.5
Raphe nucleiipsiRAN3
Dorsal raphe nucleusipsiDR2
Median raphe nucleusipsiMnR2
Median raphe nucleus midrostrocaudal partipsiMnRmrc3
Paramedian raphe nucleusipsiPMnR-0.5
Ventral lateral medulla oblongataipsiMVL-0.5
Nucleus interfascicularis hypoglossiipsiNIFH-0.5
Diagonal band of BrocaipsiDBB2
Nucleus of the horizontal limb of the diagonal bandipsiHDB2
Nucleus of the vertical limb of the diagonal bandipsiVDB2.5
Medial septal nucleusipsiMS2.5
Substantia innominataipsiSI2
Lateral preoptic areaipsiLPO2
Medial preoptic areaipsiMPA-0.5
Magnocellular preoptic nucleusipsiMCPO2
Dorsomedial hypothalamic nucleusipsiDMHy1
Lateral hypothalamic areaipsiLH2.5
Subparaventricular zone ventral partipsiSuPZv2
Lateral part of ventral subparaventricular zoneipsiSuPZvL1.5
Subparaventricular zone ventromedial partipsiSuPZvm0.5
Subparaventricular zone dorsomedial partipsiSuPZdm0
Subparaventricular zone dorsolateral partipsiSuPZdL1.5
Ventromedial hypothalamic nucleusipsiVMH-0.5
Dorsal caudal extent of the subfornical organipsiSFOdc-0.5
Reticular thalamic nucleusipsiRt2.5
Pretectal regionipsiPRT1
Bed nucleus of the stria terminalisipsiBST1
Central amygdaloid nucleusipsiCe2
Anterior cortical amygdaloid nucleusipsiACo2
Medial amygdaloid nucleusipsiMe2
Globus pallidusipsiGP1
Medial globus pallidusipsiMGP2.5
Medial globus pallidus rostral partipsiMGPr2
Caudal subpallidal regionipsiCaSuPa-0.5
Ventral pallidumipsiVP-0.5
Accumbens nucleusipsiAc1
Medial accumbensipsiAcbM3
Caudate putamenipsiCPu-0.5
Ventral psalteriumipsivps3
Cingulate cortexipsiCg3
Frontal polar cortexipsiFP-0.5
Agranular insular cortexipsiAI1
Perirhinal cortexipsiA351
Anterior medial frontal cortexipsiAMFC1
Orbital cortexipsiOrC1
Interpeduncular nucleusipsiIP3
Olfactory tubercleipsiTuO1
Olfactory tubercle polymorph layer rostral partipsiTuOpoR-0.5
Olfactory tubercle rostral partipsiTuOr-0.5
Septal regionipsiSER3
Dorsal medial septumipsiDMS-0.5
Lateral septal nucleus caudal partipsiLSc-0.5
Lateral septal nucleus caudal part dorsal zoneipsiLScd-0.5
Lateral septal nucleus dorsal partipsiLSD0
Lateral septal nucleus intermediate partipsiLSI0
Lateral septal nucleus ventral partipsiLSV0
Anteroposterior extension of the lateral septal nucleusipsiLSap0
Ventroposterior extension of the lateral septal nucleusipsiLSvp0
Posterior septal complexipsiPSC-0.5
Septofimbrial nucleusipsiSFi2
Triangular septal nucleusipsiTS3
Dorsal triangular septal nucleusipsiDTS-0.5
Triangular septal nucleus dorsal halfipsiTSdh-0.5
Caudal septumipsiCSER0.5
Cervical segment 6ipsiCS6-0.5
Cervical segment 7ipsiCS7-0.5
Cervical segment 8ipsiCS8-0.5
Thoracal segment 1ipsiT1-0.5
Thoracal segment 10ipsiT10-0.5
Lumbar segment 3ipsiL3-0.5
Lumbar segment 4ipsiL4-0.5
Fasciculus retroflexuscontrafr0
Mesopontine tegmental areacontraTGAm1
Dorsal tegmental nucleus lateral partcontraDLTN1
Pedunculopontine tegmental nucleuscontraPPTg1
Locus coeruleuscontraLC0.5
Dorsal raphe nucleuscontraDR1
Median raphe nucleuscontraMnR1
Diagonal band of BrocacontraDBB1
Preoptic regioncontraPREO1
Reticular thalamic nucleuscontraRt2
HabenulacontraHAB0
Medial accumbenscontraAcbM1
Agranular insular cortexcontraAI0
Anterior medial frontal cortexcontraAMFC0
Orbital cortexcontraOrC0
Triangular septal nucleuscontraTS-0.5
Cervical segment 1contraCS14
Cervical segment 2contraCS24
Cervical segment 3contraCS33
Cervical segment 4contraCS42
Cervical segment 5contraCS52
Cervical segment 6contraCS61
Cervical segment 7contraCS72
Cervical segment 8contraCS82
Thoracal segment 1contraT11
Thoracal segment 2contraT21
Thoracal segment 3contraT31
Thoracal segment 4contraT40.5
Thoracal segment 5contraT50.5
Thoracal segment 6contraT60.5
Thoracal segment 7contraT71
Thoracal segment 8contraT80.5
Thoracal segment 9contraT92
Thoracal segment 10contraT102
Thoracal segment 11contraT112
Thoracal segment 12contraT121
Thoracal segment 13contraT131
Lumbar segment 1contraL13
Lumbar segment 2contraL23
Lumbar segment 3contraL33
Lumbar segment 4contraL42
Lumbar segment 5contraL52
Lumbar segment 6contraL63
Sacral segment 1contraSa13
Sacral segment 2contraSa23
Sacral segment 3contraSa31
Sacral segment 4contraSa41
Coccygeal segment 1contraCo11
Coccygeal segment 2contraCo21
Coccygeal segment 3contraCo31

Key for weights

ValueWeight
-3 unknown
-2 fibers of passage
-1 not clear
-0.5 exists
0 not present
0.5 very light
1 light / sparse
1.5 light / moderate
2 moderate / dense
2.5 moderate / strong
3 strong
4 very strong





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