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Rat connectome



Pontine raphe nucleus left


Abbreviation
PnR
Color       
Superior regionsRaphe nuclei

SynonymsAbbr.Language
Nucleus raphe pontisRPOLat
Raphe pontisRP 
N. raphe pontis  
Raphe pontis nucleusRpNEng
B5 cell groupB5CG 
Raphe pontis nucleiRPn 
Raphe pontis nucleus Eng
Nucleus raphe pontisRaPnEng
Nucleus of the raphe pontis  
Pontine raphe nucleusPnREng
Pontine raphe area Eng

SubregionsSide
Caudal pontine raphe nucleusleft
Lateral margin of the nucleus raphe pontisleft
Pontine raphe nucleus ventral partleft
Pontine raphe nucleus oral partleft

Output to

NameSideAbbr.WeightDetails
Nuclei of the lateral lemniscusipsiNLL1
Nucleus of DarkschewitschipsiDk0
Oculomotor nucleusipsi30
Rostral interstitial nucleus of medial longitudinal fasciculusipsiRI0
Periaqueductal grayipsiPAG-0.5
Dorsal periaqueductal grayipsiDPAG-0.5
Periaqueductal gray lateroventral partipsiPAGLV1
Ventral periaqueductal grayipsiVPAG-0.5
Periventricular gray matteripsiPVG0
Red nucleusipsiR1
Inferior colliculusipsiICOL-0.5
Superior colliculusipsiSC-0.5
Superior colliculus superficial layersipsiSCs0
Superior colliculus intermediate layersipsiSCi0
Central tegmental field dorsal partipsiTGACd1
Substantia nigra A9ipsiSN1
Ventral tegmental area A10ipsiVTA1
Interfascicular nucleusipsiIF0
Caudal linear nucleus of the rapheipsiCLi0
Laterodorsal tegmental nucleusipsiLDTg1.5
Ventral tegmental nucleusipsiVTg2
Dorsal tegmental nucleusipsiDTg1.5
Pedunculopontine tegmental nucleusipsiPPTg1
Edinger Westphal nucleusipsiEW1
Cerebellar lobule 7ipsiCERL71
Cerebellar lobule 8ipsiCERL80
Cerebellar lobule 9ipsiCERL91
Cerebellar lobule 6aipsiCERL6a2
Cerebellar lobule 6bipsiCERL6b2
Cerebellar lobule 6cipsiCERL6c2
Lateral cerebellar nucleusipsiCERL1
FlocculusipsiFl3
Barringtons nucleusipsiBar0.5
Locus coeruleusipsiLC2
Locus coeruleus dorsomedial partipsiLCdm2
Locus coeruleus ventrolateral partipsiLCvL2.5
Pericoerulear regionipsiPCR2
Mesencephalic reticular formationipsiMRF0
Parabrachial nucleusipsiPB0.5
Lateral parabrachial nucleusipsiLPB0.5
Parvicellular reticular nucleusipsiPCRt1.5
Hypoglossal nucleus ventral partipsi12SV-0.5
Mesencephalic trigeminal nucleusipsiMe51
Mesencephalic trigeminal nucleus rostral ponsipsiMe5rp2
Pontine part of the mesencephalic trigeminal nucleusipsiMe5P-0.5
Motor trigeminal nucleusipsiMo51
Spinal trigeminal nucleusipsiSp5nc1
Trigeminal subnucleus caudalisipsi5SSC0
Cochlear nucleusipsiCON3
Dorsal cochlear nucleusipsiDC-0.5
Medial vestibular nucleusipsiMVe0.5
Nucleus of the solitary tract lateral partipsiSolL1
Dorsal raphe nucleusipsiDR3
Median raphe nucleusipsiMnR2
Raphe magnus nucleusipsiRMg2
Raphe pallidus nucleusipsiRPa2
Rostral ventral respiratory groupipsiRVRG0
Nucleus of the horizontal limb of the diagonal bandipsiHDB3
Medial septal nucleusipsiMS3
Substantia innominataipsiSI0.5
Medial preoptic areaipsiMPA3
Medial preoptic nucleusipsiMPO-0.5
Median preoptic nucleusipsiMnPO-0.5
Periventricular area of the preoptic regionipsiPVPREO-0.5
Tuberomammillary nucleus dorsomedial partipsiTBMdm1
Ventral tuberomammillary nucleusipsiVTM1
Glia limitans ventral to the ventral tuberomammillary nucleusipsiTuMgL1
HypothalamusipsiHYPO0.5
Dorsomedial hypothalamic nucleusipsiDMHy1
Lateral zoneipsiLHA2
Lateral hypothalamic areaipsiLH-0.5
Lateral hypothalamus adjacent to the ventral tuberomammillary nucleusipsiLHVTM1
Mediobasal hypothalamusipsiMeHypo-0.5
Medial preoptic anterior regionipsiMPAr2
Anteroventral periventricular nucleus [Anterior hypothalamic area]ipsiAVPe0
Anterior hypothalamic nucleusipsiAHn0
Anterior hypothalamic nucleus rostral zoneipsiAHnR1
Dorsomedial hypothalamic nucleus [Medial zone]ipsiDM1.5
Posterior hypothalamic nucleusipsiPH1.5
Medial basal hypothalamusipsiMBH-0.5
Ventromedial hypothalamic nucleusipsiVMH0
Ventromedial hypothalamic nucleus central partipsiVMHC0
Ventromedial hypothalamic nucleus shellipsiVMS1
Arcuate nucleusipsiArc3
Arcuate nucleus caudal halfipsiArcch1
Paraventricular hypothalamic nucleusipsiPa0
Periventricular hypothalamic nucleusipsiPe1
Suprachiasmatic nucleusipsiSCh2
Lateral mammillary nucleusipsiLM1
Medial mammillary nucleusipsiMMn0
Premammillary nucleus dorsal partipsiPMD1
Premammillary nucleus ventromedial partipsiPMvm1
Supramammillar nucleus lateral partipsiSuML1
Supramammillar nucleus medial partipsiSuMM0
Retrochiasmatic areaipsiRCh1
Anterodorsal thalamic nucleusipsiAD0
Anteromedial thalamic nucleusipsiAM0
Anteroventral thalamic nucleusipsiAV0
Central medial thalamic nucleusipsiCM1.5
Centre median nucleusipsiCeMe0
Centrolateral thalamic nucleusipsiCL1.5
Paracentral thalamic nucleusipsiPC1.5
Parafascicular thalamic nucleusipsiPF1
Rhomboid thalamic nucleusipsiRh1
Mediodorsal thalamic nucleusipsiMD1
Mediodorsal thalamic nucleus lateral partipsiMDL0
Mediodorsal thalamic nucleus medial partipsiMDM0
Submedius thalamic nucleusipsiSub1
Paratenial thalamic nucleusipsiPT1
Paraventricular thalamic nucleusipsiPV2
Reuniens thalamic nucleusipsiRe1
Subfascicular nucleusipsiSFN-0.5
Ventrolateral thalamic nucleusipsiVL0
Ventral posterior thalamic complexipsiVPT0
Ventrobasal complexipsiVB0
Ventromedial thalamic nucleusipsiVM0
Intralaminar nucleiipsiILN1
Lateral posterior thalamic nucleusipsiLP0
Laterodorsal thalamic nucleusipsiLD0
Posteromedial thalamic nucleusipsiPMTN0
Reticular thalamic nucleusipsiRt1.5
Subparafascicular thalamic nucleusipsiSPF0
Zona incertaipsiZI0
Forel field H1ipsiFFH10
Forel field H2ipsiFFH20
Lateral habenular nucleusipsiLHb1.5
Medial habenular nucleusipsiMHb0
Pretectal regionipsiPRT1.5
Medial forebrain bundleipsimfb-2
Stria medullaris of the thalamusipsism-2
Cisterna cerebellomedullarisipsiCistcm-3
Medial terminal nucleus of the accessory optic tractipsiMT1
Lateral amygdaloid nucleusipsiLA-1
Central amygdaloid nucleusipsiCe3
Lateral accumbens shellipsiAcbShl0.5
Medial accumbens shellipsiAcbShm2
Subthalamic nucleusipsiSTh1.5
Cerebral cortexipsiCEC-0.5
Field CA1 of hippocampusipsiCA1-0.5
Fornixipsif-2
PresubiculumipsiPrS0.5
ParasubiculumipsiPaS0.5
Entorhinal cortexipsiEnt0.5
Lateral entorhinal cortexipsiLEnt0.5
Medial entorhinal cortexipsiMEnt0.5
Cingulate cortexipsiCg3
Cingulate cortex area 1ipsiCg12
Cingulate cortex area 1 caudal partipsiCg1c1
Cingulate cortex area 2 caudal partipsiCg2c1
Prelimbic cortexipsiPrL2
Infralimbic cortexipsiIL1
Frontal cortex area 2ipsiFr23
Prefrontal cortexipsiPFC3
Motoric regionsipsiM2
Medial prefrontal cortexipsimPFC0.5
Medial agranular prefrontal cortexipsiAGm1
Sensory regionsipsiSR1
Visual regionsipsiVR3
Medial orbital cortexipsiMO2
Nucleus of the posterior commissureipsiPCom1
Dorsal geniculate nucleus lateral partipsiDLGl0
Intergeniculate leafipsiIGL-0.5
Ventral lateral geniculate nucleusipsiVLG0
Medial geniculate nucleusipsiMG0
Septal regionipsiSER1
Lateral septal nucleusipsiLS1
Lateral septal nucleus rostral partipsiLSr-0.5
Prebrachial segmentsipsiPSeg0.5
Cervical segment 1ipsiCS1-0.5
Intermediate zone C1ipsiizVHC1-0.5
Cervical segment 2ipsiCS2-0.5
Thoracal segment 6ipsiT61
Lumbosacral spinal cordipsiLSSC-0.5
Ventral horn L1ipsiVHL11
Ventral horn L2ipsiVHL21
Ventral horn L3ipsiVHL31
Lumbar segment 5ipsiL53
Lumbar segment 6ipsiL63
Sacral segment 1ipsiSa11
Sacral segment 2ipsiSa21
Sacral segment 3ipsiSa31
Sacral segment 4ipsiSa41
Coccygeal segment 1ipsiCo11
Coccygeal segment 2ipsiCo21
Central gray mesencephalic part intercollicular levelcontraCGMint-0.5
Nuclei of the lateral lemniscuscontraNLL1
Red nucleuscontraR1
Central tegmental field dorsal partcontraTGACd1
Laterodorsal tegmental nucleuscontraLDTg1
Ventral tegmental nucleuscontraVTg1
Dorsal tegmental nucleuscontraDTg1
Pedunculopontine tegmental nucleuscontraPPTg1
Cerebellar lobule 7contraCERL70.5
Cerebellar lobule 8contraCERL80
Cerebellar lobule 6acontraCERL6a2
Cerebellar lobule 6bcontraCERL6b2
Cerebellar lobule 6ccontraCERL6c2
Lateral cerebellar nucleuscontraCERL1
FlocculuscontraFl3
Locus coeruleuscontraLC1
Mesencephalic trigeminal nucleuscontraMe51
Mesencephalic trigeminal nucleus rostral ponscontraMe5rp2
Median raphe nucleuscontraMnR2
Raphe pallidus nucleuscontraRPa2
Medial preoptic areacontraMPA-0.5
Medial preoptic nucleuscontraMPO-0.5
Median preoptic nucleuscontraMnPO-0.5
HypothalamuscontraHYPO0.5
Lateral zonecontraLHA-0.5
Cisterna cerebellomedullariscontraCistcm-3
Medial terminal nucleus of the accessory optic tractcontraMT1
Subthalamic nucleuscontraSTh0.5
Cingulate cortexcontraCg1
Prelimbic cortexcontraPrL0.5
Infralimbic cortexcontraIL0.5
Medial orbital cortexcontraMO0.5
Septal regioncontraSER1
Prebrachial segmentscontraPSeg0.5
Intermediate zone C1contraizVHC1-0.5
Thoracal segment 6contraT61

Input from

NameSideAbbr.WeightDetails
Rostral interstitial nucleus of medial longitudinal fasciculusipsiRI2
Periventricular gray matteripsiPVG0
Superior colliculusipsiSC-0.5
Substantia nigra A9 dorsal partipsiSND-0.5
Substantia nigra lateral partipsiSNL-0.5
Ventral tegmental area A10ipsiVTA3
Nucleus incertus pars compactaipsiNIc3
Mesencephalic reticular formationipsiMRF2
Deep mesencephalic nucleus medial partipsiDpMeM3
Koelliker Fuse nucleusipsiKF0
Lateral parabrachial nucleusipsiLPB2
Parabrachial nucleus medialipsiPBnMe2
Gigantocellular reticular nucleusipsiGi-0.5
Gigantocellular reticular nucleus alpha partipsiGiA-0.5
Parvicellular reticular nucleus rostral portionipsipRNr-0.5
Subcoeruleus nucleusipsiSubC3
Between subcoeruleus nucleus pars alpha and dorsal partipsiSubCAbD-0.5
Principal sensory trigeminal nucleusipsiPr51
Spinal trigeminal nucleus oral partipsiSp5O1
Dorsal raphe nucleus caudal partipsiDRC2.5
Dorsal raphe nucleus rostral partipsiDRr2.5
Median raphe nucleusipsiMnR3
Superior central raphe nucleusipsiCS3
Raphe magnus nucleus rostral partipsiRMgR-0.5
Dorsal paragigantocellular nucleusipsiDPGi-0.5
Rostral ventral respiratory groupipsiRVRG-2
Nucleus of the horizontal limb of the diagonal bandipsiHDB-2
Nucleus of the vertical limb of the diagonal bandipsiVDB-2
Medial septal nucleusipsiMS-2
Dorsomedial hypothalamic nucleusipsiDMHy1
Perifornical hypothalamic area [Preoptic anterior region]ipsiPFxPAR0
Lateral zoneipsiLHA1
Lateral hypothalamic areaipsiLH1
Lateral hypothalamic area dorsal partipsiLHd0.5
Lateral hypothalamic area perifornical partipsiPFx2
Lateral hypothalamic area ventral partipsiLHAvp1
Lateral hypothalamic area [Lateral zone mammillary level]ipsiLHLZM1
Anterior hypothalamic nucleusipsiAHn0
Dorsomedial hypothalamic nucleus [Medial zone]ipsiDM1
Dorsomedial hypothalamic nucleus dorsomedial partipsiDMDM1
Posterior hypothalamic areaipsiPHA1
Posterior hypothalamic nucleusipsiPH0
Posterior hypothalamic nucleus caudal partipsiPHCa1.5
Posterior hypothalamic nucleus rostral partipsiPHRo1
Ventromedial hypothalamic nucleusipsiVMH0
Ventromedial hypothalamic nucleus central partipsiVMHC0
Ventromedial hypothalamic nucleus shellipsiVMS1
Periventricular zoneipsiPVZ0
Arcuate nucleusipsiArc0.5
Paraventricular hypothalamic nucleus medial parvicellular part [Periventricular zone anterior region]ipsiPaMP1
Paraventricular hypothalamic nucleusipsiPa-0.5
Periventricular hypothalamic nucleusipsiPe1
Incerto hypothalamic areaipsiicHYPO-0.5
Lateral mammillary nucleusipsiLM0
Medial mammillary nucleusipsiMMn0
Supramammillar nucleus lateral partipsiSuML0
Supramammillar nucleus medial partipsiSuMM0
Medial part of the caudal perifornical areaipsiPeFCM1
Lateral part of the caudal perifornical areaipsiPeFCL1
Retrochiasmatic areaipsiRCh1
Subfascicular nucleusipsiSFN0
Zona incertaipsiZI1
Forel field H1ipsiFFH10
Forel field H2ipsiFFH20
HabenulaipsiHAB0
Lateral habenular nucleusipsiLHb1
Lateral habenular nucleus medial part parvocellular subnucleusipsiLHbMPc2.5
Midbrain periventricular fiber systemipsilftmpe1
Medial orbital cortexipsiMO2
Ventral orbital cortexipsiVO0
Nucleus of the posterior commissureipsiPCom0
Precommissural nucleusipsiPrC1
Intergeniculate leafipsiIGL0
Lateral septal nucleusipsiLS-2
Lateral septal nucleus intermediate partipsiLSI-2
Septofimbrial nucleusipsiSFi-2
Triangular septal nucleusipsiTS3
Ventral tegmental area A10contraVTA3
Lateral cerebellar nucleuscontraCERL-0.5
Subcoeruleus nucleuscontraSubC-0.5
Between subcoeruleus nucleus pars alpha and dorsal partcontraSubCAbD-0.5
Posteroventral cochlear nucleuscontraPVCON4
Dorsal raphe nucleus caudal partcontraDRC2
Dorsal raphe nucleus rostral partcontraDRr2
Dorsomedial hypothalamic nucleuscontraDMHy0
Perifornical hypothalamic area [Preoptic anterior region]contraPFxPAR0
Lateral hypothalamic area dorsal partcontraLHd-0.5
Lateral hypothalamic area ventral partcontraLHAvp-0.5
Dorsomedial hypothalamic nucleus [Medial zone]contraDM-0.5
Posterior hypothalamic nucleus caudal partcontraPHCa0.5
Posterior hypothalamic nucleus rostral partcontraPHRo0.5
Periventricular zonecontraPVZ0
Medial part of the caudal perifornical areacontraPeFCM-0.5
Lateral part of the caudal perifornical areacontraPeFCL-0.5
Lateral habenular nucleuscontraLHb0
Triangular septal nucleuscontraTS3
Stomach wallipsiOrgsStomWS-0.5

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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