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Rat connectome



Cerebral cortex left


Abbreviation
CEC
Color       
Superior regionsTelencephalon

SynonymsAbbr.Language
 Cx 
Cerebral cortexCECEng
Entire cortical mantle Eng

SubregionsSide
Allocortexleft
Cytoarchitectonic layersleft
Mesocortexleft
Neocortexleft
Area between retrosplenial cortex and secondary visual cortex medial arealeft
Border region between precentral cortex and agranular retrosplenial cortex left
Caudomedial cortical region located between the posterior boundary of somatosensory cortex and visual cortexleft
Persisting white matter subplate neuronsleft

Output to

NameSideAbbr.WeightDetails
Interstitial nucleus of medial longitudinal fasciculusipsiIMLF3
Periaqueductal grayipsiPAG0
Red nucleusipsiR1
Superior colliculusipsiSC0
Subdural space around the superior colliculusipsiSCsdc0
Substantia nigra A9ipsiSN2
Substantia nigra compact partipsiSNC2.5
Substantia nigra lateral partipsiSNL1
Substantia nigra reticular partipsiSNR2.5
Cerebellar hemisphereipsiCEREBH-0.5
Reticulotegmental nucleus of the ponsipsiRtTg-0.5
Pontine nucleiipsiPn-0.5
Prepositus nucleusipsiPr1
Pontine reticular nucleus oral partipsiPnO-0.5
Ventrolateral pontine reticular formationipsivlPRF1
Pontine reticular nucleus caudal partipsiPNC-0.5
Gigantocellular reticular nucleusipsiGi0
Lateral reticular nucleusipsiLRt-0.5
Parvicellular reticular nucleusipsiPCRt1
Facial nucleusipsi7-0.5
Spinal vestibular nucleusipsiSpVe2
Superior vestibular nucleusipsiSuVe0
Medial vestibular nucleus caudal partipsiMVeP2
Medial vestibular nucleus rostral partipsiMVeR0
Lateral vestibular nucleusipsiLVe0
Nucleus of the solitary tractipsiSol-0.5
Dorsal motor nucleus of vagusipsi10-0.5
Raphe magnus nucleusipsiRMg1
Raphe obscurus nucleusipsiROb1
Raphe pallidus nucleusipsiRPa1
Nucleus XipsiX2
Inferior oliveipsiIO2
Inferior olive dorsal nucleus lateral partipsiIODL3
Inferior olive medial nucleus lateral partipsiIOML3
Basal forebrainipsiBAF-0.5
Endopiriform systemipsiEnN-0.5
Paraventricular hypothalamic nucleusipsiPa0
Ventrolateral thalamic nucleusipsiVL-0.5
Ventromedial thalamic nucleusipsiVM-0.5
Ventromedial thalamic nucleus caudal partipsiVMc2
Ventromedial thalamic nucleus caudal two thirdsipsiVMctt2
Reticular thalamic nucleus visual sectoripsiRtvi-1
Zona incertaipsiZI1
Cerebral peduncle basal partipsicp-0.5
Dorsal columnipsidoco-0.5
Bed nucleus of the stria terminalis lateral division ventral partipsiBSTLV-0.5
Central amygdaloid nucleusipsiCe-0.5
Globus pallidusipsiGP0.5
Lateral globus pallidusipsiLGP0
Medial globus pallidusipsiMGP-0.5
Globus pallidus rostrocaudal middleipsiGPrcm0.5
Caudate putamenipsiCPu3
Medial striatumipsiCPum0.5
Dorsal striatumipsiCPud-0.5
Dorsolateral striatumipsiCPudl-0.5
Ventral striatumipsiCPuv-0.5
Lateral striatumipsiCPul-0.5
Subthalamic nucleusipsiSTh3
Primary somatosensory cortexipsiS13
Primary somatosensory cortex layer 6aipsiS1L6a2
Dorsal geniculate nucleus lateral partipsiDLGl-1
Lateral septal nucleus rostral partipsiLSr-0.5
Lateral ventricleipsiLV-0.5
Spinal cordipsiMES3
Pyramidal tractipsipy-0.5
Cervical segmentsipsiCSeg-0.5
Spinal cord layer 3 C1ipsiSCL3C13
Spinal cord layers C5ipsiSCLC51
Spinal cord layers C6ipsiSCLC61
Spinal cord layers C7ipsiSCLC71
Spinal cord layers C8ipsiSCLC81
Thoracal segmentsipsiTSeg-0.5
Spinal cord layers T1ipsiSCLT11
Lumbar segmentsipsiLSeg-0.5
Superior colliculuscontraSC0
Cerebellar hemispherecontraCEREBH-0.5
Reticulotegmental nucleus of the ponscontraRtTg-0.5
Pontine nucleicontraPn0.5
Prepositus nucleuscontraPr1
Pontine reticular nucleus oral partcontraPnO-0.5
Ventrolateral pontine reticular formationcontravlPRF0
Pontine reticular nucleus caudal partcontraPNC-0.5
Lateral reticular nucleuscontraLRt-0.5
Facial nucleuscontra7-0.5
Spinal vestibular nucleuscontraSpVe3
Superior vestibular nucleuscontraSuVe0
Medial vestibular nucleus caudal partcontraMVeP3
Medial vestibular nucleus rostral partcontraMVeR0
Lateral vestibular nucleuscontraLVe0
Nucleus of the solitary tractcontraSol-0.5
Dorsal motor nucleus of vaguscontra10-0.5
Raphe magnus nucleuscontraRMg-0.5
Nucleus XcontraX3
Inferior olivecontraIO-0.5
Inferior olive dorsal nucleus lateral partcontraIODL1
Inferior olive medial nucleus lateral partcontraIOML1
Inferior olive principal nucleus rostral partcontraIOPrR1
Ventromedial thalamic nucleus caudal partcontraVMc0.5
Ventromedial thalamic nucleus caudal two thirdscontraVMctt0.5
Caudate putamencontraCPu0.5
Temporal association area 2 dorsal partcontraTe2D-0.5
Auditory regions layer 1contraAUL10
Spinal cord layer 1 C1contraSCL1C11
Spinal cord layer 2 C1contraSCL2C11
Ventral horn C1contraVHC11
Spinal cord layer 7 C1contraSCL7C13
Spinal cord layer 3 C2contraSCL3C23
Spinal cord layer 1 C2contraSCL1C21
Spinal cord layer 2 C2contraSCL2C21
Ventral horn C2contraVHC21
Spinal cord layer 7 C2contraSCL7C23
Spinal cord layer 3 C3contraSCL3C33
Spinal cord layer 1 C3contraSCL1C31
Spinal cord layer 2 C3contraSCL2C31
Ventral horn C3contraVHC31
Spinal cord layer 7 C3contraSCL7C33
Spinal cord layers C4contraSCLC42
Spinal cord layer 3 C4contraSCL3C43
Spinal cord layer 1 C4contraSCL1C41
Spinal cord layer 2 C4contraSCL2C41
Ventral horn C4contraVHC41
Spinal cord layer 7 C4contraSCL7C43
Spinal cord layers C5contraSCLC52
Spinal cord layer 3 C5contraSCL3C53
Spinal cord layer 1 C5contraSCL1C51
Spinal cord layer 2 C5contraSCL2C51
Ventral horn C5contraVHC51
Spinal cord layer 7 C5contraSCL7C53
Spinal cord layers C6contraSCLC62
Spinal cord layer 3 C6contraSCL3C63
Spinal cord layer 1 C6contraSCL1C61
Spinal cord layer 2 C6contraSCL2C61
Ventral horn C6contraVHC61
Spinal cord layer 7 C6contraSCL7C63
Spinal cord layers C7contraSCLC72
Spinal cord layer 3 C7contraSCL3C73
Spinal cord layer 1 C7contraSCL1C71
Spinal cord layer 2 C7contraSCL2C71
Ventral horn C7contraVHC71
Spinal cord layer 7 C7contraSCL7C73
Spinal cord layers C8contraSCLC82
Spinal cord layer 3 C8contraSCL3C83
Spinal cord layer 1 C8contraSCL1C81
Spinal cord layer 2 C8contraSCL2C81
Ventral horn C8contraVHC81
Spinal cord layer 7 C8contraSCL7C83
Spinal cord layers T1contraSCLT12
Spinal cord layer 3 T1contraSCL3T13
Spinal cord layer 1 T1contraSCL1T11
Spinal cord layer 2 T1contraSCL2T11
Ventral horn T1contraVHT11
Spinal cord layer 7 T1contraSCL7T13
Spinal cord layer 3 T2contraSCL3T23
Spinal cord layer 1 T2contraSCL1T21
Spinal cord layer 2 T2contraSCL2T21
Ventral horn T2contraVHT21
Spinal cord layer 7 T2contraSCL7T23
Spinal cord layer 3 T3contraSCL3T33
Spinal cord layer 1 T3contraSCL1T31
Spinal cord layer 2 T3contraSCL2T31
Ventral horn T3contraVHT31
Spinal cord layer 7 T3contraSCL7T33
Spinal cord layer 3 T4contraSCL3T43
Spinal cord layer 1 T4contraSCL1T41
Spinal cord layer 2 T4contraSCL2T41
Ventral horn T4contraVHT41
Spinal cord layer 7 T4contraSCL7T43
Spinal cord layer 3 T5contraSCL3T53
Spinal cord layer 1 T5contraSCL1T51
Spinal cord layer 2 T5contraSCL2T51
Ventral horn T5contraVHT51
Spinal cord layer 7 T5contraSCL7T53
Spinal cord layer 3 T6contraSCL3T63
Spinal cord layer 1 T6contraSCL1T61
Spinal cord layer 2 T6contraSCL2T61
Ventral horn T6contraVHT61
Spinal cord layer 7 T6contraSCL7T63
Spinal cord layer 3 T7contraSCL3T73
Spinal cord layer 1 T7contraSCL1T71
Spinal cord layer 2 T7contraSCL2T71
Ventral horn T7contraVHT71
Spinal cord layer 7 T7contraSCL7T73
Spinal cord layer 3 T8contraSCL3T83
Spinal cord layer 1 T8contraSCL1T81
Spinal cord layer 2 T8contraSCL2T81
Ventral horn T8contraVHT81
Spinal cord layer 7 T8contraSCL7T83
Spinal cord layer 3 T9contraSCL3T93
Spinal cord layer 1 T9contraSCL1T91
Spinal cord layer 2 T9contraSCL2T91
Ventral horn T9contraVHT91
Spinal cord layer 7 T9contraSCL7T93
Spinal cord layer 3 T10contraSCL3T103
Spinal cord layer 1 T10contraSCL1T101
Spinal cord layer 2 T10contraSCL2T101
Ventral horn T10contraVHT101
Spinal cord layer 7 T10contraSCL7T103
Spinal cord layer 3 T11contraSCL3T113
Spinal cord layer 1 T11contraSCL1T111
Spinal cord layer 2 T11contraSCL2T111
Ventral horn T11contraVHT111
Spinal cord layer 7 T11contraSCL7T113
Spinal cord layer 3 T12contraSCL3T123
Spinal cord layer 1 T12contraSCL1T121
Spinal cord layer 2 T12contraSCL2T121
Ventral horn T12contraVHT121
Spinal cord layer 7 T12contraSCL7T123
Spinal cord layer 3 T13contraSCL3T133
Spinal cord layer 1 T13contraSCL1T131
Spinal cord layer 2 T13contraSCL2T131
Ventral horn T13contraVHT131
Spinal cord layer 7 T13contraSCL7T133
Spinal cord layer 3 L1contraSCL3L13
Spinal cord layer 1 L1contraSCL1L11
Spinal cord layer 2 L1contraSCL2L11
Ventral horn L1contraVHL11
Spinal cord layer 7 L1contraSCL7L13
Spinal cord layer 3 L2contraSCL3L23
Spinal cord layer 1 L2contraSCL1L21
Spinal cord layer 2 L2contraSCL2L21
Ventral horn L2contraVHL21
Spinal cord layer 7 L2contraSCL7L23
Spinal cord layer 3 L3contraSCL3L33
Spinal cord layer 1 L3contraSCL1L31
Spinal cord layer 2 L3contraSCL2L31
Ventral horn L3contraVHL31
Spinal cord layer 7 L3contraSCL7L33
Spinal cord layer 3 L4contraSCL3L43
Spinal cord layer 1 L4contraSCL1L41
Spinal cord layer 2 L4contraSCL2L41
Ventral horn L4contraVHL41
Spinal cord layer 7 L4contraSCL7L43
Spinal cord layer 3 L5contraSCL3L53
Spinal cord layer 1 L5contraSCL1L51
Spinal cord layer 2 L5contraSCL2L51
Ventral horn L5contraVHL51
Spinal cord layer 7 L5contraSCL7L53
Spinal cord layer 3 L6contraSCL3L63
Spinal cord layer 1 L6contraSCL1L61
Spinal cord layer 2 L6contraSCL2L61
Ventral horn L6contraVHL61
Spinal cord layer 7 L6contraSCL7L63
Spinal cord layer 3 S1contraSCL3S13
Spinal cord layer 1 S1contraSCL1S11
Spinal cord layer 2 S1contraSCL2S11
Ventral horn S1contraVHSa11
Spinal cord layer 7 S1contraSCL7S13
Spinal cord layer 3 S2contraSCL3S23
Spinal cord layer 1 S2contraSCL1S21
Spinal cord layer 2 S2contraSCL2S21
Ventral horn S2contraVHSa21
Spinal cord layer 7 S2contraSCL7S23
Spinal cord layer 3 S3contraSCL3S33
Spinal cord layer 1 S3contraSCL1S31
Spinal cord layer 2 S3contraSCL2S31
Ventral horn S3contraVHSa31
Spinal cord layer 7 S3contraSCL7S33
Spinal cord layer 3 S4contraSCL3S43
Spinal cord layer 1 S4contraSCL1S41
Spinal cord layer 2 S4contraSCL2S41
Ventral horn S4contraVHSa41
Spinal cord layer 7 S4contraSCL7S43
Spinal cord layer 3 Co1contraSCL3Co13
Spinal cord layer 1 Co1contraSCL1Co11
Spinal cord layer 2 Co1contraSCL2Co11
Ventral horn Co1contraVHCo11
Spinal cord layer 7 Co1contraSCL7Co13
Spinal cord layer 3 Co2contraSCL3Co23
Spinal cord layer 1 Co2contraSCL1Co21
Spinal cord layer 2 Co2contraSCL2Co21
Ventral horn Co2contraVHCo21
Spinal cord layer 7 Co2contraSCL7Co23
Spinal cord layer 3 Co3contraSCL3Co33
Spinal cord layer 1 Co3contraSCL1Co31
Spinal cord layer 2 Co3contraSCL2Co31
Ventral horn Co3contraVHCo31
Spinal cord layer 7 Co3contraSCL7Co33
Bulbospongiosus muscleipsiMuscbsp1
CervixipsiOrgUTC-10
Uterine hornipsiOrgUTh-10
Uterus bodyipsiOrgUTB-10
Urinary bladderipsiOrgUrBLa-0.5
Trigone of the urinary bladderipsiOrgUrBLaT-10
Pancreas sideipsiOrgsPancs-10

Input from

NameSideAbbr.WeightDetails
MesencephalonipsiMEC0
Central grayipsiCG-0.5
Central gray lateral ventral partipsiCGVD1
Central grey caudal area ventral partipsicCGv-0.5
Ventral periaqueductal grayipsiVPAG1
Red nucleusipsiR-10
Central nucleus of the inferior colliculusipsiCIC-0.5
Dorsal peduncular pontine nucleusipsiDPPn3
Ventral peduncular pontine nucleusipsiVPPn3
Substantia nigra A9ipsiSN3
Substantia nigra compact partipsiSNC-0.5
Substantia nigra compact part medial tieripsiSNCM0
Substantia nigra lateral partipsiSNL-0.5
Substantia nigra reticular partipsiSNR-0.5
Ventral tegmental area A10ipsiVTA3
Ventrolateral tegmental areaipsiVLTg3
Laterodorsal tegmental nucleusipsiLDTg0.5
Ventral tegmental nucleusipsiVTg-0.5
Dorsal tegmental nucleusipsiDTg0
Pedunculopontine tegmental nucleusipsiPPTg1
Pedunculopontine tegmental nucleus rostral partipsiPPTgR-0.5
A4 noradrenaline cellsipsiA4-0.5
A5 noradrenaline cellsipsiA51
Barringtons nucleusipsiBar0
Locus coeruleusipsiLC3
Locus coeruleus dorsal partipsiLCD3
Locus coeruleus ventral partipsiLCv3
Pontine grayipsiPG-0.5
Medial portion of the reticulotegmental nucleusipsiMRETn-0.5
Prepositus nucleusipsiPr1
Reticular systemipsiRF0
Nucleus reticularis subcuneiformisipsiRScf-0.5
Pontine reticular nucleusipsiPRN0
Pontine reticular nucleus oral part lateral partipsiPnOL-0.5
Pontine reticular nucleus oral part medial partipsiPnOm1
Ventrolateral pontine reticular formationipsivlPRF0
Pontine reticular nucleus caudal part betaipsiPnOcb1
Peribrachial regionipsiPBR2
Cuneiforme nucleusipsiCnF-0.5
Cuneiforme nucleus dorsal partipsiCnFD-0.5
Parabrachial nucleusipsiPB-0.5
Koelliker Fuse nucleusipsiKF-0.5
Lateral parabrachial nucleusipsiLPB-0.5
Parabrachial nucleus medialipsiPBnMe3
Gigantocellular reticular nucleusipsiGi1
Medial subnucleus reticularis ventralisipsiMSRV-0.5
Medial subnucleus reticularis ventralis dorsal partipsiMSRVd1
Parvicellular reticular nucleusipsiPCRt-0.5
Region around lateral reticular nucleusipsiCBRFa-0.5
Subcoeruleus nucleusipsiSubC1
Principal sensory trigeminal nucleusipsiPr5-0.5
Principal sensory trigeminal nucleus dorsal partipsiPr5D0
Raphe nucleiipsiRAN-0.5
Dorsal raphe nucleusipsiDR3
Dorsal raphe nucleus ventral partipsiDRV-0.5
Linear nucleus of the rapheipsiLIR1
Superior central raphe nucleusipsiCS3
Pontine raphe nucleusipsiPnR-0.5
Raphe magnus nucleusipsiRMg-0.5
Raphe obscurus nucleusipsiROb-0.5
Raphe pallidus nucleusipsiRPa-0.5
A1 noradrenergic cellsipsiA1-0.5
A2 noradrenergic cellsipsiA2-0.5
Dorsomedial superior oliveipsiSuOLiDM1
Dorsal paragigantocellular nucleusipsiDPGi-0.5
Lateral paragigantocellular nucleusipsiLPGi-0.5
Basal forebrainipsiBAF3
Nucleus of the horizontal limb of the diagonal bandipsiHDB1
Lateral portion of the diagonal band of BrocaipsiLDBB-0.5
Medial septal nucleusipsiMS-0.5
Basal nucleus MeynertipsiB3
Basal nucleus Meynert anterior partipsiBan-0.5
Basal nucleus Meynert medial partipsiBmp-0.5
Substantia innominataipsiSI2
Lateral preoptic areaipsiLPO-0.5
Magnocellular preoptic nucleusipsiMCPO1
Tuberomammillary nucleusipsiTuM-0.5
Lateral hypothalamic areaipsiLH-0.5
Lateral hypothalamic area [Lateral zone tuberal level]ipsiLHtu1
Posterior magnocellular nucleiipsiPHApm3
Ventromedian part of the anterior magnocellular part paraventricular nucleus of the hypothalamusipsiPaAMavm-0.5
ThalamusipsiT-0.5
Dorsal thalamusipsiDOR2
Anterior group of the dorsal thalamusipsiATN-0.5
Anterodorsal thalamic nucleusipsiAD-0.5
Intralaminar nuclei of the dorsal thalamusipsiILM2
Central medial thalamic nucleusipsiCM-0.5
Centrolateral thalamic nucleusipsiCL0.5
Paracentral thalamic nucleusipsiPC-0.5
Parafascicular thalamic nucleusipsiPF-0.5
Lateral group of the dorsal thalamusipsiLAT-0.5
Mediodorsal thalamic nucleusipsiMD-0.5
Paratenial thalamic nucleusipsiPT-0.5
Paraventricular thalamic nucleusipsiPV-0.5
Ventral group of the dorsal thalamusipsiVENT-0.5
Ventral anterior-lateral complex of the thalamusipsiVAL0.5
Ventro anterior thalamic nucleusipsiVA-0.5
Ventrolateral thalamic nucleus medial partipsiVLme-0.5
Ventrobasal complexipsiVB-0.5
Ethmoid thalamic nucleusipsiEth-0.5
Intralaminar nucleiipsiILN-0.5
Parafascicular centre-median complexipsiPFCM-0.5
Lateral posterior thalamic nucleusipsiLP-0.5
Posterior groupipsiPTG-0.5
Posteromedian thalamic nucleusipsiPoMn-0.5
Ventral thalamusipsiVNT-0.5
Perireticular thalamic nucleusipsiPRTN3
Reticular thalamic nucleusipsiRt0
Zona incertaipsiZI0
Zona incerta ventral partipsiZIV0
Ansa lenticularisipsial0.5
Internal capsuleipsiic2
Cerebral peduncle basal partipsicp0
Corpus callosumipsicc-0.5
Amygdaloid complexipsiAC-0.5
Deep amygdaloid complexipsiDAC-0.5
Basal nucleus posterior partipsiBncP-0.5
Bed nucleus of the stria terminalisipsiBST-0.5
Globus pallidusipsiGP-0.5
Medial globus pallidusipsiMGP2
Ventral pallidumipsiVP1
Caudate putamenipsiCPu-0.5
Subthalamic nucleusipsiSTh2
Subthalamic nucleus medial partipsiSThM-0.5
Field CA1 of hippocampusipsiCA13
SubiculumipsiS3
Entorhinal cortexipsiEnt3
NeocortexipsiNEOCX-0.5
Ventral temporal association cortexipsiTev3
Auditory regionsipsiAU3
Perirhinal cortexipsiA353
Primary somatosensory cortex forelimb regionipsiS1FL3
Commissural systemsipsicos0.5
Dorsal geniculate nucleus lateral partipsiDLGl-1
Medial geniculate nucleus medial partipsiMGM-0.5
Central cervical nucleusipsiMESccn-0.5
Cervical motor nucleusipsiMEScmn-0.5
Pyramidal tractipsipy-0.5
Dorsal root ganglion C2ipsiDRGC20
Cervical segment 6ipsiCS6-0.5
Cervical segment 7ipsiCS7-0.5
Cervical segment 8ipsiCS8-0.5
Thoracal segment 1ipsiT1-0.5
Ventral tegmental nucleuscontraVTg-0.5
Pedunculopontine tegmental nucleuscontraPPTg-0.5
Prepositus nucleuscontraPr1
Ventrolateral pontine reticular formationcontravlPRF0
Peribrachial regioncontraPBR2
Posterior magnocellular nucleicontraPHApm-0.5
Centrolateral thalamic nucleuscontraCL0
Paracentral thalamic nucleuscontraPC0
Mediodorsal thalamic nucleus caudal two thirdscontraMDCtt0
Lateral habenular nucleuscontraLHb0
NeocortexcontraNEOCX-0.5
Prefrontal cortexcontraPFC-0.5
Lateral agranular prefrontal cortexcontraAGl-0.5
Hindpaw skinipsiOrgHPS3
Hindpaw skincontraOrgHPS-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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