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Rat connectome



Superior central raphe nucleus right


Abbreviation
CS
Color       
Superior regionsMedial raphe nucleus

SynonymsAbbr.Language
Raphe centralis superior  
Nucleus centralis raphe superior Eng
Superior central raphe nucleusCSEng
Superior central nucleus raphe Eng
Nucleus centralis superiorRCSEng
Central superior raphe nucleus Eng
Superior central nucleus  

SubregionsSide
Superior central raphe nucleus compact subnucleusright
Superior central raphe nucleus dorsal regionright
Superior central raphe nucleus lateral partright
Superior central raphe nucleus medial partright
Superior central raphe nucleus rostrodorsal portionright
Caudal nucleus raphe centralis superiorright
Cranial nucleus raphe centralis superiorright

Output to

NameSideAbbr.WeightDetails
Periaqueductal gray lateroventral partcontraPAGLV1
Midbrain extrapyramidal areacontraMEA1.5
Pedunculopontine tegmental nucleuscontraPPTg1
Lateral cerebellar nucleuscontraCERL1
Nucleus incertus pars dissipatacontraNId2
Pontine tegmental fieldcontraPTF0
Parabrachial nucleuscontraPB1
Superior central raphe nucleuscontraCS-0.5
Basal forebraincontraBAF0.5
Nucleus of the horizontal limb of the diagonal bandcontraHDB0
Nucleus of the vertical limb of the diagonal bandcontraVDB0
Medial septal nucleuscontraMS0
Substantia innominatacontraSI0
Magnocellular preoptic nucleuscontraMCPO0
Posterior mammillay nucleuscontraPMAM2
Supramammillar nucleuscontraSuM-0.5
A8 dopamine cells retrorubral groupcontraRRF2
Lateral habenular nucleuscontraLHb0.5
Lateral habenular nucleus lateral partcontraLHbL0.5
Lateral habenular nucleus caudal subfieldcontraLHbcs0.5
Medial forebrain bundlecontramfb-2
Medial globus palliduscontraMGP0
Ventral pallidumcontraVP0
Anterodorsal hippocampal formationcontraHIPPad1
Intermediomedial cell column L1contraIMML11
Intermediomedial cell column L2contraIMML21
Intermediomedial cell column L3contraIMML31
Intermediomedial cell column L4contraIMML41
Intermediomedial cell column L5contraIMML51
Intermediomedial cell column L6contraIMML61
Central grayipsiCG3
Central gray dorsal partipsiCGD1
Central gray lateral partipsiCGL1
Central gray ventral areaipsiCGva2
Periaqueductal grayipsiPAG2
Periaqueductal gray lateroventral partipsiPAGLV1
Prerubral fieldipsiPR2
Inferior colliculusipsiICOL3
Superior colliculusipsiSC1
Midbrain extrapyramidal areaipsiMEA1.5
Substantia nigra compact partipsiSNC2
Substantia nigra compact part dorsal tieripsiSNCD2
Substantia nigra reticular partipsiSNR1.5
Substantia nigra reticular part dorsolateral tieripsiSNRDL1.5
Ventral tegmental area A10ipsiVTA2
Ventral tegmental area A10 ventrolateral partipsiVTAvl2
Ventral tegmental area anterior partipsiVTAA3
Caudal linear nucleus of the rapheipsiCLi-0.5
Dorsal portion of the caudal linear nucleus of the rapheipsiCLiD-0.5
Lateral tegmental field retroambigual areaipsiLTfr1
Laterodorsal tegmental nucleusipsiLDTg1
Ventral tegmental nucleusipsiVTg3
Dorsal tegmental nucleusipsiDTg3
Dorsal tegmental nucleus central partipsiDTgC1
Dorsal tegmental nucleus ventromedial partipsiDTgVM-0.5
Pedunculopontine tegmental nucleusipsiPPTg1
Edinger Westphal nucleusipsiEW1
CerebellumipsiCERE1
Cerebellar lobule 4ipsiCERL42
Cerebellar lobule 5ipsiCERL52
Cerebellar lobule 7ipsiCERL72
Cerebellar lobule 8ipsiCERL82
Cerebellar lobule 9ipsiCERL92
Cerebellar lobule 10ipsiCERL102
Cerebellar lobule 6ipsiCERL62
Lateral cerebellar nucleusipsiCERL1
Locus coeruleusipsiLC1
Nucleus incertus pars dissipataipsiNId2
Pontine tegmental fieldipsiPTF0
Reticulotegmental nucleus of the ponsipsiRtTg2
Prepositus nucleusipsiPr2
Medial reticular formationipsiRFm-0.5
Ventral reticular formationipsiVRF2
Pontine reticular nucleusipsiPRN1
Pontine reticular nucleus central partipsiNRTPc-0.5
Pontine reticular nucleus oral partipsiPnO2
Pontine reticular nucleus caudal partipsiPNC1
Cuneiforme nucleusipsiCnF1
Parabrachial nucleusipsiPB1
Gigantocellular reticular nucleusipsiGi1
Lateral reticular nucleusipsiLRt2
Supratrigeminal nucleusipsiSu51
Mesencephalic trigeminal nucleusipsiMe51
Spinal trigeminal nucleusipsiSp5nc-0.5
Cochlear nucleusipsiCON3
Dorsal raphe nucleusipsiDR2
Superior central raphe nucleusipsiCS-0.5
Pontine raphe nucleusipsiPnR3
Raphe magnus nucleusipsiRMg2
Raphe obscurus nucleusipsiROb-0.5
Rostral ventrolateral medullaipsiRVLM3
Linear nucleus of the medullaipsiLi2
Inferior oliveipsiIO1
Superior oliveipsiSuOLi2
Basal forebrainipsiBAF1
Median eminenceipsiME1.5
Diagonal band of BrocaipsiDBB2
Nucleus of the horizontal limb of the diagonal bandipsiHDB3
Nucleus of the vertical limb of the diagonal bandipsiVDB3
Medial septal nucleusipsiMS1.5
Substantia innominataipsiSI1
Medial preoptic areaipsiMPA1.5
Lateral preoptic nucleusipsiLPN2
Magnocellular preoptic nucleusipsiMCPO1
Tuberomammillary nucleusipsiTuM2
Subcommissural organipsiSCO2
Lateral hypothalamic areaipsiLH2
Anterior hypothalamic areaipsiAHA1.5
Anterior hypothalamic area posterior partipsiAHAP2
Anterior hypothalamic nucleusipsiAHn1.5
Dorsal hypothalamic areaipsiDA2
Dorsomedial hypothalamic nucleus [Medial zone]ipsiDM2
Posterior hypothalamic nucleusipsiPH2
Tuberal areaipsiTA2
Ventromedial hypothalamic nucleusipsiVMH1
Arcuate nucleusipsiArc2
Paraventricular hypothalamic nucleusipsiPa1
Periventricular hypothalamic nucleusipsiPe2
Suprachiasmatic nucleusipsiSCh2
Suprachiasmatic nucleus ventral divisionipsiSChv2
Supraoptic nucleus [Supraoptic region]ipsiSO2
Mammillary bodyipsiCMAM3
Lateral mammillary nucleusipsiLM2
Medial mammillary nucleusipsiMMn1
Medial mammillary nucleus lateral partipsiML2
Medial mammillary nucleus medial partipsiMM2
Lateral part of pars medialis of the medial mammillary nucleusipsiMLM-0.5
Medial mammillary nucleus posterior partipsiMMNp1
Posterior mammillay nucleusipsiPMAM1.5
Premammillary nucleusipsiPMAN1.5
Supramammillar nucleusipsiSuM3
A8 dopamine cells retrorubral groupipsiRRF2
Retrochiasmatic areaipsiRCh2
Parafascicular thalamic nucleusipsiPF2
Rhomboid thalamic nucleusipsiRh1
Mediodorsal thalamic nucleus medial partipsiMDM3
Midline group of the dorsal thalamusipsiMTN2
Paratenial thalamic nucleusipsiPT1
Reuniens thalamic nucleusipsiRe1
Ventromedial thalamic nucleusipsiVM2
Intralaminar nucleiipsiILN2
Lateral thalamic nuclear groupipsiLTNG1
Mediolateral thalamic nucleusipsiMeLT2
Posteromedian thalamic nucleusipsiPoMn1
Ventral thalamusipsiVNT1
Reticular thalamic nucleusipsiRt1.5
Subparafascicular thalamic nucleus parvicellular partipsiSPFp2
Zona incertaipsiZI2
Lateral habenular nucleusipsiLHb3
Lateral habenular nucleus lateral partipsiLHbL1
Lateral habenular nucleus caudal subfieldipsiLHbcs1
Medial habenular nucleusipsiMHb2
Medial forebrain bundleipsimfb-2
Amygdaloid complexipsiAC2
Basal nucleusipsiBnc2
Basolateral amygdaloid nucleusipsiBL2
Anterior basolateral nucleusipsiBLA0.5
Basomedial amygdaloid nucleusipsiBM2
Amygdalopiriform transition areaipsiAPir1
Medial amygdaloid nucleusipsiMe2
Medial amygdaloid nucleus dorsal tipipsiMeDT-0.5
ClaustrumipsiCl1
Globus pallidusipsiGP2
Medial globus pallidusipsiMGP2
Ventral pallidumipsiVP1
Caudate putamenipsiCPu1.5
Subthalamic nucleusipsiSTh1.5
Cerebral cortexipsiCEC3
HippocampusipsiHIPP3
Anterodorsal hippocampal formationipsiHIPPad-0.5
Dentate gyrusipsiDG3
Ventral hippocampusipsiHIPPv-0.5
Piriform cortexipsiPir1.5
Retrosplenial regionsipsiRS1
Cingulate cortexipsiCg3
Dorsal anterior cingulate cortexipsiDACC-0.5
Prelimbic cortexipsiPrL-0.5
Infralimbic cortexipsiIL-0.5
NeocortexipsiNEOCX1
Frontal association cortexipsiFrA2
Frontal cortex area 2ipsiFr23
Prefrontal cortexipsiPFC3
Motoric regionsipsiM2
Medial agranular prefrontal cortexipsiAGm-0.5
Sensory regionsipsiSR1
Visual regionsipsiVR3
Ventral lateral geniculate nucleusipsiVLG1
Ventral lateral geniculate nucleus lateral partipsiVLGl-0.5
Medial geniculate nucleusipsiMG1
Interpeduncular nucleusipsiIP3
Interpeduncular nucleus dorsal subnucleusipsiIPRd3
Interpeduncular nucleus lateral subnucleusipsiIPL0
Interpeduncular nucleus ventral partipsiIPv0
Glomerular layer of the olfactory bulbipsiOBglo2
Anterior olfactory nucleusipsiAON1.5
Olfactory tubercleipsiTuO1.5
Septal regionipsiSER2
Lateral septal nucleusipsiLS3
Lateral septal nucleus caudal partipsiLSc3
Lateral septal nucleus ventral partipsiLSV1
Ependyma and subependymal layeripsiE1
Intermediomedial cell column C4ipsiIMMC43
Intermediomedial cell column C5ipsiIMMC53
Intermediomedial cell column L1ipsiIMML12
Intermediomedial cell column L2ipsiIMML22
Intermediomedial cell column L3ipsiIMML32
Intermediomedial cell column L4ipsiIMML42
Intermediomedial cell column L5ipsiIMML52
Intermediomedial cell column L6ipsiIMML62

Input from

NameSideAbbr.WeightDetails
Periaqueductal graycontraPAG0
Dorsal periaqueductal gray caudal partcontraDPAGC0
Dorsolateral periaqueductal gray caudal partcontraPAGdlc0
Dorsolateral periaqueductal gray rostral partcontraPAGdlr0
Ventrolateral periaqueductal gray caudal partcontraPAGvlc3
Ventrolateral periaqueductal gray rostral partcontraPAGvlr0
Lateral cerebellar nucleuscontraCERL-0.5
Pons oral partcontraPor1
Lateral parabrachial nucleuscontraLPB2
Supragenual nucleuscontraSGe0.5
Superior central raphe nucleuscontraCS-0.5
Lateral hypothalamic area [Lateral zone mammillary level]contraLHLZM1
Premammillary nucleus dorsal partcontraPMD0.5
Infralimbic cortexcontraIL-0.5
Central grayipsiCG-0.5
Periaqueductal grayipsiPAG0.5
Dorsal periaqueductal gray caudal partipsiDPAGC0
Dorsolateral periaqueductal gray caudal partipsiPAGdlc0
Dorsolateral periaqueductal gray rostral partipsiPAGdlr0.5
Ventrolateral periaqueductal gray caudal partipsiPAGvlc1
Ventrolateral periaqueductal gray rostral partipsiPAGvlr0.5
Red nucleusipsiR-0.5
Peduncularpontine nucleusipsiPPN-0.5
Substantia nigra A9ipsiSN2
Substantia nigra compact partipsiSNC-0.5
Substantia nigra reticular partipsiSNR-0.5
Caudal linear nucleus of the rapheipsiCLi-0.5
Ventral tegmental nucleusipsiVTg-0.5
Dorsal tegmental nucleusipsiDTg-0.5
Lateral cerebellar nucleusipsiCERL-0.5
Locus coeruleusipsiLC-0.5
Pons caudal partipsiPca-0.5
Pons oral partipsiPor3
Medial reticular formationipsiRFm-0.5
Nucleus reticularis subcuneiformisipsiRScf-0.5
Lateral parabrachial nucleusipsiLPB2
Gigantocellular reticular nucleusipsiGi-0.5
Medullary reticular nucleus dorsal partipsiMdDd4
Subcoeruleus nucleusipsiSubC-0.5
Dorsal raphe nucleusipsiDR3
Dorsal raphe nucleus intermediate partipsiDRim-0.5
Dorsal raphe nucleus lateral wingipsiDRlw3
Linear nucleus of the rapheipsiLIR3
Rostral linear nucleus of the rapheipsiRLi-0.5
Superior central raphe nucleusipsiCS-0.5
Raphe magnus nucleusipsiRMg3
Raphe magnus nucleus rostral partipsiRMgR-0.5
Raphe nuclei rostral partipsiRANR-0.5
Raphe obscurus nucleusipsiROb1
Rostral part of the ventromedial medulla oblongataipsiRMeObvm3
Medial septal nucleusipsiMS-0.5
Substantia innominataipsiSI3
Lateral preoptic areaipsiLPO3
Medial preoptic areaipsiMPA1
Medial preoptic area dorsolateral partipsiMPADL1
Rostral part of the ventrolateral preoptic nucleusipsiVLPOr1
Midcaudal part of the ventrolateral preoptic nucleusipsiVLPOmc1
Lateral hypothalamic area anterior part [Preoptic anterior region]ipsiLHAapar2
Lateral hypothalamic area posterior part [Preoptic anterior region]ipsiLHApPAR2
Lateral hypothalamic area premammillary subfornical region [Preoptic anterior region]ipsiLHAsfp1
Lateral zoneipsiLHA1
Lateral hypothalamic area motor related juxtaventromedial regionipsiLHAjvm2
Lateral hypothalamic area subfornical region anterior zoneipsiLHAsfa2
Lateral hypothalamic area posterior partipsiLHAp2
Lateral hypothalamic area [Lateral zone mammillary level]ipsiLHLZM1
Medial division of the hypothalamusipsiMdH-0.5
Dorsomedial hypothalamic nucleus [Medial zone]ipsiDM-0.5
Ventromedial hypothalamic nucleusipsiVMH-0.5
Mammillary bodyipsiCMAM-0.5
Premammillary nucleus dorsal partipsiPMD1
Anteroventral thalamic nucleusipsiAV-0.5
Parafascicular thalamic nucleusipsiPF-0.5
Zona incertaipsiZI2
HabenulaipsiHAB-0.5
Bed nucleus of the stria terminalis ventral tipipsiBNSTvt1
Subthalamic nucleus medial partipsiSThM2
Anterior cingulate cortexipsiACC3
Infralimbic cortexipsiIL-0.5
Frontal cortex area 2ipsiFr22
Primary auditory cortexipsiAu11
Somatomotoric regionsipsiSMR-0.5
Hindlimb motor cortexipsiHMCx-0.5
Medial prefrontal cortexipsimPFC2
Medial agranular prefrontal cortexipsiAGm2
Medial agranular prefrontal cortex caudal partipsicAGm3
Ventral lateral geniculate nucleus ventrolateral partipsiVLGvL2
Interpeduncular nucleus caudal subnucleusipsiIPC2
Interpeduncular nucleus dorsal subnucleus magnocellular partipsiIPRm2
Interpeduncular nucleus dorsal subnucleus parvocellular partipsiIPRdp2
Interpeduncular nucleus lateral subnucleusipsiIPL2
Interpeduncular nucleus medial partipsiIPM2
Interpeduncular nucleus paramedian partipsiIPPM2

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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