Version 7.7 - Released: 04/08/2019 - Content: 107395 neurons
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What's new in version 7.7 ?
  • Sixty-eight data sets (5894 reconstructions) have been added:
  • The following new Species have been added :
    • Grasshopper
    • Apis mellifera (Western Honey bee)
    • Silkmoth
  • The following new Strains of species have been added:
    • drosophila melanogaster: dar1-3010 mutant, dar1-3232 mutant, dar1 mutant, KhcKOattP, w1118
    • grasshopper: American bird
    • monkey: Squirrel
    • mouse: ApoE-Knockout, B6;129S-Pdyntm1.1(cre)Mjkr/LowlJ, BTBR, C57B6, C57Bl/6J + SVCJ129, C57BL/J, CGG, Chrna2-Tom, DAT-Cre, B6.SJL-Slc6a3tm1.1(cre)Bkmn/J ,Df(h15q13)/+, Esr2-IRES2-Cre, Gpr158tm1(KOMP)Vlcg, Hmx3cre::R26-tdTOMflox;Htr3a-GFP, Humanized ApoE3, Humanized ApoE4, Lhx6-iCre+/-; RCE-EGFP+/-, Ndnf-IRES2-dgCre, Neto2 -/-, Nkx2-1-CreERT2, Ntsr1-Cre, Penk-IRES2-Cre-neo, Sema6-/-, Sema6+/-, Sim1-Cre_KJ18, T4826I-RYR1, T4826I-RYR1 + FMR1 premutation, Tlx3-Cre_PL56 VGAT-Cre, Slc32a1tm2(cre)Lowl/J, VIP-IRES-cre
    • Silkmoth: Kinshu-Showa
    • Zebra finch: Wildtype
    • zebrafish: Et(E1b:Gal4-VP16)s1101t, Tg(UAS:loxP-tdTomato_CAAX-loxP-EGFP_CAAX)mpn128, otx1b:Cre, Gal4s1013t, UAS:Optobow, mnx1:Gal4; UAS:H2B-Cerulean-p2a-mKO2-CAAX, mnx1:eGFP-hTDP43wt, mnx1-GFP, mnx1:mVenus-zTDP43, Tg(pet1:gal4-p2A-EGFP)gy1 & Tg(UAS:Kaede)s1999t
  • The following new Primary Brain Regions have been added:
    • accessory lobe
    • Central complex
    • Central nervous system
    • forebrain
    • subesophageal zone-(SEZ)
  • The following new Secondary Brain Regions have been added:
    • accessory lobe: lateral, Mori cluster
    • antennal lobe: dorsolateral, glomerulus DA4, glomerulus DC4, glomerulus DL2, glomerulus DM4, glomerulus DP1 , glomerulus V, glomerulus VA1, glomerulus VA4, glomerulus VA5, glomerulus VA7, glomerulus VC1, glomerulus VC3 , glomerulus VC4 , glomerulus VL1, glomerulus VL2, glomerulus VM4, glomerulus VM5, glomerulus VM6, glomerulus VP1, glomerulus VP2, glomerulus VP3, glomerulus VP4, lateral cell cluster, Medial cell cluster
    • basal forebrain: medial septum
    • Central complex: posterior
    • Central nervous system: ventral
    • main olfactory bulb: dorsal
    • optic Lobe: lobula
    • peripheral nervous system: anterior, inter-parapodial, left, pygidial cirrus, Pygidial cirrus, right, segment 0, segment 1, segment 2, segment 3, ventral nerve cord
    • subesophageal ganglion: posterior protocerebral lobe
    • subiculum: Polymorphic layer
  • The following new Tertiary Brain Regions have been added:
    • (accessory lobe → lateral) posterior surface, (accessory lobe → Mori cluster) lateral, (antennal lobe → glomerulus DA4) lateral, (antennal lobe → glomerulus DA4) medial, (antennal lobe → glomerulus DL2) dorsal, (antennal lobe → glomerulus DL2) ventral, (antennal lobe → glomerulus DP1) lateral, (antennal lobe → glomerulus DP1) medial,(antennal lobe → glomerulus VA1) dorsal,(antennal lobe → glomerulus VA1) ventral, (antennal lobe → glomerulus VA7) medial, (antennal lobe → glomerulus VA7) lateral, (antennal lobe → glomerulus VC3) lateral, (antennal lobe → glomerulus VC3) medial, (antennal lobe → glomerulus VL2) posterior, (antennal lobe → glomerulus VM5) dorsal, (antennal lobe → glomerulus VM5) ventral, (antennal lobe → glomerulus VM7) dorsal, (antennal lobe → glomerulus VM7) ventral, (basal ganglia → substantia nigra) Dorsal, (basal ganglia → substantia nigra) Lateral, (brainstem → reticular formation) Intermediate zone, (Central nervous system → ventral) anterior, (Central nervous system → ventral) medial, (main olfactory bulb → dorsal) right, (mesencephalon → tectum) Dorsal cortex, (mesencephalon → tectum) External cortex, (neocortex → medial prefrontal) layer 2, (neocortex → medial prefrontal) layer 3, (neocortex → occipital) visual cortex (V1 and V2 / Brodmann areas 17 and18), (neocortex → somatosensory) Brodmann area 1 and 3b,(neocortex → somatosensory) hand representation, (optic Lobe → lobula) posterior, (peripheral nervous system → abdominal) segment 2-4, (peripheral nervous system → anterior) left, (peripheral nervous system → enteric) distal colon, (peripheral nervous system → inter-parapodial) left, (peripheral nervous system → inter-parapodial) right, (peripheral nervous system → inter-parapodial) segment 1, (peripheral nervous system → left) anterior, (peripheral nervous system → Pygidial cirrus) left, (peripheral nervous system → Pygidial cirrus) not reported, (peripheral nervous system → pygidial cirrus) right, (peripheral nervous system → Pygidial cirrus) right, (peripheral nervous system → Pygidial cirrus) ventral, (peripheral nervous system → pygidial cirrus) ventral, (peripheral nervous system → right) anterior, (peripheral nervous system → segment 0) right, (peripheral nervous system → segment 1) left, (peripheral nervous system → segment 1) not reported, (peripheral nervous system → segment 1) right, (peripheral nervous system → segment 2) left, (peripheral nervous system → segment 2) right, (peripheral nervous system → segment 3) left, (peripheral nervous system → segment 3) right, (peripheral nervous system → ventral nerve cord) decussating trunk, (peripheral nervous system → ventral nerve cord) ipsilateral, (peripheral nervous system → ventral nerve cord) segment 2, (peripheral nervous system → ventral nerve cord) segment 3, (protocerebrum → mushroom body) Calyx Pedunculus, (protocerebrum → mushroom body) contralateral, (protocerebrum → mushroom body) gamma, (spinal cord → lumbar) L5-L6, (spinal cord → lumbar) mid-lumbar, (subesophageal ganglion → posterior protocerebral lobe) dorsal central body, (subiculum → Polymorphic layer) dorsal
  • The following new Secondary Cell Types have been added:
    • Glia: Radial
    • interneuron: arc, ciliomotor, Commissural, Commissural-T, periventricular, rope, Vibration sensitive
    • principal cell: Antennal lobe projection neuron-(adPN), Columnar, kenyon cell, motoneuron , Multiglomerular projection, superficial tufted
    • sensory receptor: biciliated, collar receptor neuron, not reported
  • The following new Tertiary Cell Types have been added
    • (Glia → astrocyte) Protoplasmic, (interneuron → amacrine) Orientation selective, (interneuron → cholinergic) GABAergic, (interneuron → collar receptor neuron) split, (interneuron → Commissural) cross, (interneuron → Commissural) Up, (interneuron → dopaminergic) GABAergic, (interneuron → oriens-lacunosum moleculare) acetylcholine receptor alpha-2 (Chrna2)-positive, (interneuron → periglomerular) oligoglomerular, (interneuron → periventricular) bistratified, (interneuron → periventricular) tristratified, (interneuron → Somatostatin (SOM)-positive) nicotinic acetylcholine receptor alpha2 subunit (Chrna2)-positive, (None → medium spiny) projection, D1-type dopamine receptor-expressing, (principal cell → GABAergic) hyperpolarization-activated cyclic nucleotide gated channel 4 (HCN4)-positive, (principal cell → GABAergic) Orchid, (principal cell → GABAergic) SATB1-positive, (principal cell → GABAergic) Sharp Wave Ripple (SWR)-active, (principal cell → GABAergic) Sharp Wave Ripple (SWR)-unchanged, (principal cell → glutamatergic) Area X-projecting, (principal cell → glutamatergic) robust nucleus of the arcopallium- and area X-projecting, (principal cell → Induced Neurons) H9-derived, (principal cell → kenyon cell) a'B'c, (principal cell → kenyon cell) a'B's, (principal cell → motoneuron) arm, (principal cell → motoneuron) bow, (principal cell → motoneuron) crab, (principal cell → motoneuron) hose, (principal cell → Motoneuron) mnx1 expressing, (principal cell → motoneuron) ring, (principal cell → motoneuron) spider, (principal cell → projection) bilateral, (principal cell → projection) macroglomerular complex-targeting, (principal cell → projection) bistratified, (principal cell → projection) monostratifed, (principal cell → projection) multiglomerular, (principal cell → projection) non-stratified, (principal cell → projection) periventricular, (principal cell → projection) Pre-hypoglossal, (principal cell → projection) tristratified, (principal cell → pyramidal) Ctip2-negative, (principal cell → pyramidal) peritumoral, (principal cell → robust nucleus of the arcopallium projecting) glutamatergic (principal cell → superficial tufted) horizontal, (principal cell → superficial tufted) vertical, (principal cell → uniglomerular projection) t5, (sensory receptor → biciliated) unpaired, (sensory receptor → collar receptor neuron) biciliated, (sensory receptor → collar receptor neuron) unpaired, (sensory receptor → Multidendritic-dendritic arborization (DA)) ddaB
  • The following new stains have been added:
    • AAV2-EF1a-DIO-mCherry, Adeno-associated virus (AAV), Alexa Fluor 647 hydrazide, Kaede fluorescent protein, mTurquoise2 + enhanced yellow fluorescent protein + tdTomato, Phase contrast, Steptavidin-Alexa Fluor 555, td tomato + photoactivatable green fluorescent protein (paGFP)
  • The following reconstruction softwares have been added:
    • GTree
  • The following original formats have been added
    • GTree.swc, Neuronstudio.nst
  • The following new experimental conditions have been added
    • 2,4-di-nitrobenzene sulfonic acid-(DNBS) colitis model, 2,4-di-nitrobenzene sulfonic acid-(DNBS) colitis model + GR159897 once daily, IP, 78Q + CrebA Overexpression, 78Q Overexpression, 78Q + Rac1 + CrebA Overexpression, 78Q + Rac1 Overexpression, Bisphenol A-(BPA), CrebA + Rac1 Overexpression, CREB Overexpression + Mecp2 KO, CREB Overexpression + Mecp2 V247fs mutation, CRISPR/Cas9-corrected Mecp2 V247fs mutation, DNMT3A-KO, Electrical field stimulation at 2000Hz, Electrical field stimulation at 20Hz, Electrical field stimulation at 5Hz, Floxed-stop Dcx-shRNA electroporation + Tamoxifen-inducible Cre recombinase + mCherry + Tamoxifen, GluA2CTP, GR159897 once daily IP, Mecp2 KO + Rolipram, Mecp2 T158M mutation, Mecp2 T158M mutation + Rolipram, Mecp2 T158M mutation + WNT2 Overexpression, Mecp2 V247fs mutation, Mecp2 V247fs mutation + Rolipram, Mecp2 V247fs mutation + WNT2 Overexpression, Mettl14 f/f, Negr1 shRNA, Pah^enu2 KO, Pah^enu2 KO rAvPAL-RBC treated, Rac1 Overexpression, Repeated Cross Fostering-(RCF) + Cocaine, Retinoic acid, shNova2, shNova2 + X1, shNova2 + X1 mutant, shNova2 + X5, shRNA electroporation targeting Dcx + mCherry, shRNA in utero electroporation targeting Dcx + GFP, shX1 + X1, shX1 + X1 mutant, shX1 + X5, trkB IgG, zTDP-43 (wt) expression
  • Secondary brain region for Kole cells (38 neurons related to PMID=15062977) corrected from CA1 to CA3.
  • Literature Coverage has been updated to include publications through April 2019.
  • Added FAQ: How do you compute the ticker tape statistics?
  • The following major errors were corrected:
    • 78 cells with Class3: "NG2-expressing" was changed to the existing entry "Nerve/Glial proteoglycan 2 (NG2)-positive"
    • In existing Tenner archive, Objective changed from dry to oil and 2 duplicate neurons removed
    • "Whole mount" removed from Slicing Thickness menu/table. All 373 cases which had that value had Slicing direction set to "Whole Mount" and Slicing Thickness set to "Not applicable"

What's new in version 7.6 ?
  • The following new Species have been added: capuchin monkey
  • The following new Strains of species have been added:
    • C. elegans: sax-7(dz156), dma-1(tm5159):mnr-1(dz175), dma-1(tm5159):sax-7(dz156), mnr-1(dz175):sax-7(dz156)
    • mouse: PDE1c-tdTomato, Wnt3a-tdTomato, Arctic48, Arctic48/C5aR1KO, B6.Cg-Tg(Scnn1a-Cre)3Aibs/J, C5aR1KO, Chat-IRES-Cre-neo, h-GFAP-Cre;Frs2(fl/fl);Frs3-/-
  • The following new Brain Regions have been added:
    • Secondary brain region: Area X, subthalamic nucleus
    • Tertiary brain region: Reeler barrel equivalent
  • The following new Cell Types have been added:
    • Tertiary cell type: 6 month old, CamKIIalpha-negative, CamKIIalpha-positive, D2-type dopamine receptor-expressing, Microtubule-associated protein 2 (MAP2)-positive, Spontaneously firing
  • The following new Experimental Conditions have been added: Arctic(E22G) mutations, Arctic(E22G) mutations + C5a receptor 1 knockout, cocaine, Swedish(K670N+M671L), 1 dendrite branch severed + dendrites regenerated, 13 weeks post-lesion, 16 weeks post-lesion, 3-double mutant, 45 minute left (controlateral) middle cerebral artery occlusion 60 days prior, 45 minute left (ipsilateral) middle cerebral artery occlusion 60 days prior, 6-hydroxydopamine (6-OHDA)-lesion, ACEA+GP1a-Treated, ACEA-Treated, Acetylcholine, Kynurenic acid, Acetylcholinesterase, alpha-bungarotoxin 50nM, angled/circular micro-pattern plating, Ank2-IR, Antalarmin hydrochloride, Anterior thalamic nuclei lesion, anti-DENV2 hyperimmune serum, antibody-enhanced dengue disease, APP Knockout, APP Swedish mutation, APP Swedish mutation + seleginine, APP Swedish/Indiana double mutation (TgTRND8), ATXN1-knockout, axotomy of olfactory sensory neurons, bead injection, beta-actin morpholino, beta-actin morpholino + beta-actin rescue, Both ear clip, Brn3b+/-; Brn3a CKOAP/+, Brn3b+/-; Brn3a CKOAP/-, Brn3b+/
  • The following new Slicing thickness values have been added: 0.029
  • The following new Stain values have been added: mRuby2, Streptavidin Alexa 633
  • One cell from Keyvani archive (34-8-2-KD) and three from Markram archive (SM100428A1-3-RPINT-IDF, SM081009A1-7-IDC, SM081009A1-7-IDB) were removed from the repository due to duplicity with other cells in the same archives (Keyvani, 34-8-1-KD; Markram, SM100428A1-3-IDF, SM081009A2, SM081009A4).



Version 7.5 released on 08/02/2018 contained 96831 neurons

What's new in version 7.5 ?
  • The following new Species have been added: Calango lizard, Steller's Sculpin, zebra finch
  • The following new Strains of species have been added:
    • Calango lizard: Wild-caught
    • drosophila melanogaster: GAL4[221],UAS-mCD8::GFP (x) UAS-Trio GEF2, GAL4[221],UAS-mCD8::GFP (x) UAS-Trio-IR, GAL4[477],UAS-mCD8::GFP (x) UAS-Trio, GAL4[477],UAS-mCD8::GFP (x) UAS-Trio GEF2, GAL4[477],UAS-mCD8::GFP (x) UAS-Trio-IR, GAL4[221],UAS-mCD8::GFP (x) UAS-Trio, GAL4[221],UAS-mCD8::GFP (x) UAS-Trio GEF1, GAL4[477],UAS-mCD8::GFP (x) UAS-Trio GEF1
    • mouse: C57BL/6JRj, B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J (JAX# 007914), Nkx2.1-cre:RCE, C57BL6 x B6.129P2(C)-Mecp2+/y, L7-tau-GFP, C57BL6 x B6.129P2(C)-Mecp2-/y, VGAT-Cre, B6.129S4-Grin1tm2Stl/J, hGFAP::CreERT2; Rosa26R-YFP
    • zebrafish: Tg(6.7FRhcrtR:gal4VP16), Tg(pkd2l1:Gal4)icm10
  • The following new Brain Regions have been added:
    • Secondary brain region: Apical nervous system, enteric
    • Tertiary brain region: dorsolateral sensory cluster, high vocal center, inferior, lobule IX, lobule V, medial frontal gyrus, myenteric plexus, nasal, oculomotor, peptidergic circuit, proximal, segment 8, smooth muscle layers
  • The following new Cell Types have been added:
    • Secondary cell type: asymmetric, biciliary, ciliary photoreceptor, glial fibrillary acidic protein (GFAP)-expressing, IRP2-positive, long-branched ciliary, myoinhibitory peptide (MIP)-positive, persistent activity neuron (PAN), robust nucleus of the arcopallium projecting, Type IV (bipolar), unciliated, uniciliary
    • Tertiary cell type: 14 days old, allatostatin-C (ASTC)-positive, Bursicon-positive, bushy, cerebrospinal fluid-contacting neurons (CSF-cNs), corticopontine, F-mini-Off, F-mini-On, FMRFamide-positive, hypertrophic, J type, M2 type, Medial Ganglionic Eminence (CGE)-derived, myoinhibitory peptide (MIP)-positive, NADPH diaphorase-expressing, Nerve/Glial proteoglycan 2 (NG2)-positive, Nitrergic, Nonclassical transient On, pentaciliary, persistent activity neuron (PAN), putative, RGWamide-positive, S100beta-expressing, Sox10-expressing, tOn-alpha, Type 3, Type 4, Type 5, Type 6, Type I (protoplasmic), Type II (fibrous), Type III (extraganglionic)
  • The following new Experimental Conditions have been added: Brn3b+/-; Brn3a CKOAP/+, Brn3b+/-; Brn3a CKOAP/-, Brn3b+/-; Brn3c CKOAP/+, Brn3b+/-; Brn3c CKOAP/-, Brn3b-/-; Brn3a CKOAP/+, Brn3b-/-; Brn3a CKOAP/-, Brn3b-/-; Brn3c CKOAP/+, Brn3b-/-; Brn3c CKOAP/-, caspase3, cavernous hemangioma, Cdkl5 knockout, chronic restraint stress, crmp+/-, crmp+/-;crmp2+/-, crmp-/-, crmp1+/-;sema3a+/-, crmp2+/-, crmp2-/-, Cyst, Dichlobenil + Minocycline, environmental enrichment + Piry virus-infected, Erythropoietin, Erythropoietin + chronic restraint stress, glioma, high fever, HUCPVC Conditioned Media, intractable seizures, in utero exogenous cannabinoid exposure, Lennox-Gastaut syndrome, Mecp2 KO, miR-196a transgene, Naris Occlusion, Neurilemmona in the middle cranial fossa, NR1 knockout, oligodendroglioma, Pilocytic astrocytoma, Piry virus-infected, sema3a+/-, sema3a+/-;crmp2+/-, sema3a-/-, siRNA NaV1.1-1.3 knock-down
  • The following new Original Format of reconstruction files have been added: EyeWire.mat, Farsight.swc
  • The following new Slicing thickness values have been added: 0.03
  • The following new Stain values have been added: horseradish peroxidase + diaminobenzidine, mcherry
  • The following new Reconstruction Software have been added: EyeWire, Farsight



Version 7.4 released on 04/16/2018 contained 86893 neurons

What's new in version 7.4 ?
  • The following new Species have been added: African wild dog, Aplysia, Blue wildebeest, Caracal, Clam worm, Domestic dog, ferret, Greater kudu, Lemur, Lion, Mongoose, Wallaby, Zebra
  • The following new Strains of species have been added:
    • Aplysia: Wild
    • Clam worm: Platynereis dumerilii
    • Crab: Jonah
    • drosophila melanogaster: pJFRC-20XUAS-IVS-RFPnls-PQR-cut, UAS-shep-RNAiVDRC, RhoGAP18b-IR melanogaster, Wdb-IR melanogaster, ppkGal4,UAS-CD4-tdGFP, RpL24-IR melanogaster, RpS13-IR melanogaster, OreR, cpa-IR melanogaster, caper-CC01391 mutant, SkpA-IR melanogaster, Ank2-IR melanogaster, RhpGAP18b-IR melanogaster, ctp_cdlc-IR melanogaster, CG7033-IR melanogaster, ppk-CD4-tdTomato reporter, RpS2-IR melanogaster, shep-BG00836 mutant, Dmn-IR melanogaster, Tcp1-IR melanogaster, RpL7-IR melanogaster, RpS17-IR melanogaster, msps-IR melanogaster, RpL36A-IR melanogaster, cpb-IR melanogaster, Ret_C168/Df(Bsc312)
    • Lemur: Ring-tailed
    • Mongoose: Banded
    • monkey: Golden lion tamarin, callithrix penicillata
    • mouse: B6.Cg-Gt(ROSA)26Sortm6(CAG-ZsGreen1)Hze/J (JAX# 007906), C57BL/6JRccHsd, Transgenic EGFP, CD1, Rosa-CreER, Nestine-rtTA/Tet-Bax, Cre+ Tor1aflx/+, CCK-CreER, DLXcre/+;mGluR5f/f, Crhr1-Cre, 129/SVE, daDREAM, Dnmt3b, Hoxd10-GFP, 15q11-13patDp/+, BL/6; 129SvJ, Opn4CreERT2/+;Z/AP, VGLUT3-Cre, HRASG12V, C57BL/6 LRRK2-/- Knock-out, Thy1-YFP-G & C57BL/6{J} & OMP-ChR2:EYFP, Rhot1, ChAT-Cre, FVB, C57BL/6 LRRK2 wild-type, Igfbp5, Tbet-Cre/C57, Chrna2-Cre{;Ai3} on mixed FVB/N & Crl:CD1[ICR] & C57BL/6 background, PV / myrGFP-LDLRct, NeuroD4, C57BL/6J x GAD67-GFP, FVB-Tg(GadGFP)45704Swn/J, NHE6, C57BL/6J x Nestin-Cre/tdTomato, Tor1aflx/+, Cln5-KO, MR-transgenic, Pvcre, 5HTr6, PVFlpO+vGATiCre, Kcnip2, SCA6-84Q/84Q, Pcdh-alpha-f/f;Slc6a4::Cre, TorsinA Conditional Knockout, CB2-GFP, DAT-GFP, C57BL/6J, d Viptm1(cre)Zjh/J (VIPCre), TorsinA Heterozygous, Rhot2, PVFlpO+vGlut2, Cbln2-GFP, dlx6a-cre 1Mekk/J, kif20b magoo, C57BL6/TH-GFP, TgH(CX3CR1-EGFP)xTgN(THY1.2-EYFP), Prmt8tm1a(EUCOMM)Wtsi, Dlx5/6-Cre, GFAP-td
    • rabbit: Flemish giant
    • rat: Green, PVG hooded, Lewis
    • Wallaby: Red-necked
    • Zebra: Plains, Mountain
    • zebrafish: Tg(elavl3:GCaMP5G)a4598 transgenic, TL
  • The following new Brain Regions have been added:
    • Primary brain region: abdominal ganglion, eye circuit, olfactory pit, pallium, peptidergic circuit
    • Secondary brain region: Anterior group of the dorsal thalamus, Anterior hypothalamic nucleus, Anterodorsal nucleus, Anteromedial nucleus, Anteroventral nucleus, Central lateral nucleus of the thalamus, Central medial nucleus of the thalamus, Dorsomedial nucleus of the hypothalamus, Interanterodorsal nucleus of the thalamus, Intralaminar nuclei of the dorsal thalamus, Lateral posterior nucleus of the thalamus, Mediodorsal nucleus of thalamus, Nucleus of reunions, Paracentral nucleus, Parafascicular nucleus, Paraventricular hypothalamic nucleus, Posterior hypothalamic nucleus, Postsubiculum, Retrosplenial area, Subparaventricular zone, Ventral anterior-lateral complex of the thalamus, Ventral medial nucleus, Ventromedial hypothalamic nucleus, ciliary band I, ciliary band II, ciliary band III, ciliary zone 1, ciliary zone 2, ciliary zone 3, ciliary zone 4, ciliary zone 5, ciliary zone 6, ciliary zone 7, ciliary zone 8, cortex, dorsal cluster, epithalamus, nuchal organs, raphe nuclei
    • Tertiary brain region: , Brodmann area 12, Brodmann area 24, Brodmann area 3, Brodmann area 4, Lateral habenula, Lateral longitudinal fasciculus, Medial longitudinal fasciculus, anterior, anterior macula, association area TE, fourth visual, intrinsic to the optic neuropil, juxtaglomerular space, layer 1, layer 2, layer 2-3, layer 3, left, medial, medial crista, neuromast, nucleus of medial longitudinal fasciculus, occipital projecting, oculomotor, otic, peripheral, posterior crista, posterior macula, putative, putative trigeminal, right, septal, trans optic neuropil, vestibular nucleus, visual association (TE), visual association (TEO), visual association (TEad)
  • The following new Cell Types have been added:
    • Secondary cell type: Fvamide, Myoinhibitory peptide, Neural progenitor cell, RGWamide, Schnorkel, TmY15, acrotroch, anterior paired lateral neuron, axo-axonic cell (AAC), bag cell neuron, ciliomotor, crescent, loop, metatroch, modulatory neuron, myelinated, octapaminergic, paratroch, peptidergic, photoreceptor, pigment depressing factor (PDF)-positive, prototroch
    • Tertiary cell type: CaD, CaP, CaV, D1-type dopamine receptor-expressing, Inner ear projecting, MC, MeL, MeLM, MeLc, MeLr, MeM, MeMD, MeMv, MiD, MiD2, MiD2CL, MiD2cm, MiD2i, MiD3, MiD3CL, MiD3cm, MiD3i, MiM1, MiR, MiR1, MiR2, MiT, MiV, MiV1, MiV2, On-Off, Peripheral lateral line afferent neuron, Posterior lateral line nerve projecting, Putative spinal projecting, RoI2, RoI2C, RoI2R, RoL, RoL1, RoL2, RoL3, RoM, RoM1, RoM1C, RoM1R, RoM2, RoM2L, RoM2m, RoM3, RoM3L, RoM3M, RoV3, auditory association cortex targeting, cMNATO, cMNd, ciliomotor, clasping short axon cell, contralaterally-projecting, eyespotPRCR3, heart projecting, hippocampus-projecting, infraorbital projecting, ipsilaterally-projecting, mandibular-projecting, mauthner cell, middle, occipital projecting, oculomotor projecting, optic nerve projecting, peptidergic, preoptic nucleus projecting, sensory, ser-h1, ser-tr1, thermosensory, ventral pallidum-projecting, vestibulospinal
  • The following new Experimental Conditions have been added: Early training, odor enrichment for 7 days, Acetylcholinesterase, Ank2-IR, Anterior thalamic nuclei lesion, APP Swedish mutation, beta-actin morpholino, beta-actin morpholino + beta-actin rescue, CG7033-IR
  • The following new Original Format of reconstruction files have been added: Catmaid.csv, Catmaid.swc, Knossos.nlm, Simple Neurite Tracer.ndf
  • The following new Slicing thickness values have been added: 0.06, 1, 25, 265, 270, 277, 285, 292, 295, 310, 332, 339, 356, 360, 405, 420, 425, 429, 434, 438, 593
  • The following new Stain values have been added: Streptavidin Alexa Fluor 555, immunogold, membrane-targeted GFP, Streptavidin-Alexa Fluor 488, Tag red fluorescent protein, tetramethylrodamine-dextran
  • One neuron entry (20120828SC2) from an earlier release (v.7.0) was changed from secondary cell type "basket" to "Chandelier"



Version 7.3 released on 11/28/2017 contained 80012 neurons

What's new in version 7.3 ?
  • The following new Species have been added: Crab
  • The following new Brain Regions have been added:
    • Secondary brain region: cornea, glomerulus DA2, glomerulus DL4, hindbrain, inner nuclear layer, layer 2-4, mediodorsal thalamic nucleus, neurosecretory preoptic area (NPO), posterior tuberculum (PT), preoptic nucleus, skin, tail, thoracic, trigeminal nucleus
    • Tertiary brain region: Brodmann area 20, Lateromedial Visual, Marginal zone, T3, above plexus, alpha, alpha-1, alpha-2, alpha-3, alpha-prime, apex, column 3, dorsal agranular cingulate, down, lobule III, low-threshold mechanoreceptor-recipient zone (LTMR-RZ), maxillary subregion, medial preoptic area, principal trigeminal nucleus, segment 2, segment 3, segment 4, segment 4-6, segment 5, segment 6, segment 7, subgranular zone
  • The following new Cell Types have been added:
    • Secondary cell type: Induced Neurons, Kenyon cell, Pseudounipolar, SIFamide, dorsal paired medial-(DPM), gastric mill, induced pluripotent stem cell-(iPSC)-derived, lateral gastric, lateral pyloric, lung terminal, magnocellular, neural integrators, non-Kenyon cell, oxytocinergic neuron (OXT)
    • Tertiary cell type: 2A, A-beta afferent nerve fiber, Chrna2-positive, Glomerular layer-projecting, Local edge detector type, M1 type, Osteocrin-positive, PAM, PFC-anterior cingulate projecting, PFC-orbital projecting, PFC-projecting, PPL1, Reelin secreting, SATB2-positive, Tbr2 lineage, anterior paired lateral-(APL), complex, core-targeting, cough receptor, direction-selective, hindbrain projecting, mature, midline-crossing, mixed bipolar, non-Tbr2 lineage, pituitary projecting, posterior-targeting, right main bronchus, right middle lobe, spinal projecting, surface-targeting, tOff-alpha
  • The following new Experimental Conditions have been added: GP1a-Treated, ACEA+GP1a-Treated, ACEA-Treated, Osteocrin-overxpressing, Osteocrin siRNA, 45 minute left (controlateral) middle cerebral artery occlusion 60 days prior, 45 minute left (ipsilateral) middle cerebral artery occlusion 60 days prior, lipopolysaccharide injection + PXS-4681A, mgluR5 cKO, iron-deficient, eltrombopag-treated, Opn4 expression, dendrotomy, APP Swedish mutation + seleginine, APP Swedish mutation, Morphine Sulphate self-administered, tissue-nonspecific alkaline phosphatase (TNAP) Knockout, high anxiety-like behavior + fluoxetine, high anxiety-like behavior, anti-DENV2 hyperimmune serum, antibody-enhanced dengue disease, enriched environment, Kif20b-/- Mutant, Trim9 Knockout, Transplanted embryonic neurons, Tpx2-depleted, axotomy of olfactory sensory neurons, mineralocorticoid receptors overexpression, stress + mineralocorticoid receptors overexpression, overpressure-exposed, Post-Lasik 1 month, Post-Lasik 1 week, Post-Lasik 6 months, Rorb overexpression, simulated microgravity (SMg) for 14 days, NHE6 KO, Chronic Ethanol, siTCERG1, chronic mild restraint stress, 13 weeks post-lesion, 16 weeks post-lesion, Pilocarpine-induced epilepsy, LPS-triggered, Tor1a null, Tor1a +/-, treatment, high susceptibility to apomorphine, low susceptibility to apomorphine, High licking/grooming mother, Low licking/grooming mother, Costello Syndrome, Ras hyperactivation, Fitm RNAi-1 knockdown, Deferoxamine (DFX), VK-28, spinocerebellar ataxia type 6 model, Chronic cough, normal raising for 7 days + odor enrichment for 7 days + and odor removal for 5 days, ATXN1-knockout, right ear clip + bead injection, bead injection, ear clipping, Left ear clip, Right ear clip, Both ear clip, alpha-bungarotoxin 50nM, Choline 0.1mM, Choline 1mM, Nicotine 50nM, Nicotine 50nM + alpha-bungarotoxin 50nM, PNU-282987 1uM, PNU-282987 10uM, Choline 0.1nM, capre -/-, shep-/-, shep-RNAi, saporin treated, saporin + dihydrotestosterone treated, saporin + estradiol treated, saporin + testosterone treated, early-life stressed (ES), Antalarmin hydrochloride, Polyethylene glycol, early-life stressed (ES) + Antalarmin hydrochloride, early-life stressed (ES) + Polyethylene glycol, SCH23390 + Nicotine, SCH23390, Infraorbital nerve cut, dendrites severed by 2-photon laser (balding) + dendrites regenerated, 1 dendrite branch severed + dendrites regenerated
  • The following new Original Format of reconstruction files have been added: Knossos.nml, Neurolucida.hoc, Neurolucida.xml, Raveler.swc, neuTu.swc, TrakEm2.swc
  • The following new Slicing thickness values have been added: 0.045µm, 0.5µm, 45µm, 450µm, 7µm
  • The following new Stain values have been added: betaIV-spectrin, streptavidin-488, Streptavidin-Alexa 405, Fluorescence Cytochrome Oxidase, Streptavidin-conjugated Alexa 647, tandem dimer green fluorescent protein (tdGFP), Texas red
  • The following new Reconstruction Software have been added: neuTu, TrakEm2



Version 7.2 released on 07/19/2017 contained 70025 neurons

What's new in version 7.2 ?
  • The following new Species have been added: Blind mole-rat
  • The following new Strains of species have been added:
    • Blind mole-rat: Spalax Judaei
    • C. elegans: wdIs52, mnr-1(dz175), lect-2(rz2), lect-2(rz2):dma-1(tm5159), lect-2(rz2):mnr-1(dz175), lect-2(rz2):sax-7(nj48), dma-1(tm5159), sax-7(nj48)
    • domestic pig: Yorkshire
    • drosophila melanogaster: ppkCD4tdTomato heterozygous
    • monkey: Cynomolgus
    • mouse: VIPcre/tdTomato heterozygous, B6.129S4-Pten /J homozygous, Ebf2- Cre, MMP-9 -/-, B6;C3-Opa1, Tg2576, B6.Cg-Tg(Thy1-YFPH)2Jrs/J, eGFP-DRD4/Chat-Cre/TdTomato, Thy-GFP-M, FVB-NJ (wild type), CBA/C57BL6 Hybrid, Thy1-YFP-H, R26R:Nex-Cre, Reeler (rlr), Htr3a-GFP, B6c3Fe(+/-)a/a-Reln, GlyT2-GFP, Ctgf-2A-dgCre, Thy-1-EGFP line M, Wildtype, Ts16, C57BL6J/129SvJae, Mash1CreER:RCE, AT-1 S113R/+
    • rabbit: pigmented
    • zebrafish: wild type, pou4f3:GAL4 X UAS:GAP-GFP, GE4a, RIKEN Wako
  • The following new Brain Regions have been added:
    • Primary brain region: accessory olfactory bulb
    • Secondary brain region: cingulate, glomeruli, somatosensory thalamus, ventral tegmental area
    • Tertiary brain region: 0 degree receptive field, 1 degree receptive field, 20 degree receptive field, Brodmann area 21, G glomerular cluster, Locus Coeruleus, basal nucleus, bed nucleus of the stria terminalis, central, lG glomerular cluster, lG3 glomerulus, lG4 glomerulus, lateral nucleus, layer 6a, left, maG glomerular cluster, mdG1 glomerulus, mdG2 glomerulus, mdG3 glomerulus, mdG4 glomerulus, mdG5 glomerulus, mdG6 glomerulus, sublamina a, sublamina b, vaG glomerular cluster, ventrolateral preoptic nucleus, vmG glomerular cluster, vpG glomerulus, vpG1 glomerulus
  • The following new Cell Types have been added:
    • Secondary cell type: dLGN-projecting, low-threshold calcium spiking, microglia, modified bipolar, non low-threshold calcium spiking, noradrenaline-excited, noradrenaline-inhibited, noradrenaline-inhibited, noradrenergic, output neuron, propriospinal, serotonin-excited, serotonin-inhibited, tilted, unusual projection neurons
    • Tertiary cell type: A17, A2, a/b bistratified, beta-hydroxylase-positive, C-type, Cerebellar-projecting, Class 1, Class 2, Class 3, cone, Connective Tissue Growth Factor positive, corticofugal, corticogeniculate, early-born, edge detector, IN-like, Iba1-positive, lhx2a tg+, Long wavelength-depolarized, medium-field, melanopsin-positive, narrow-field, ON-OFF type, Off response, On response, On-Off direction selective ganglion cell, orientation selective, polyaxonal, PVD, rod, serotonin-excited, serotonin-inhibited, sleep promoting neuron, stem cell-derived (ES:Hb9), Sustained, tbx21 tg+, Thoracic, Transient, translocating, triphasic, UV-depolarized, Vg3, W3b, wide-field
  • The following new Experimental Conditions have been added: 1-methyl-4-phenylpyridinium ion (MPP), 1-methyl-4-phenylpyridinium ion (MPP) + Neuroprotectin D1 (NDP1), Activity-based anorexia, Alfy/Wdfy3 Knockout, BDNF+CNTF, Beta-hydroxy-beta-methylbutyrate (HMB), BRAF, Cisplatin, Crmp2 knockout, Disc1, DISC1 N terminus (1-301 expressing), DISC1-Boymaw fusion protein expressing, dma-1, dma-1/lect-2 double mutant, DMSO, Down Syndrome trisomic, DYNC1I1 knockdown, DYNC1I1 knockdown+BRAF, FGF7, FGFb, Frizzled1-knockdown, gamma-tubulin shRNA, GDNF, GI 254025X, GI 254025X + rNegr1, Glra2KO, heterozygote, high fat diet, high frequency infralimbic stimulation, high multiplicity of infection (MOI), human AT-1 overexpression, idebenone, IDPN treated, IGF, in utero glucocorticoid (iuGC), Katnal2 Knockout, lect-2, lect-2/mnr-1 double mutant, lect-2/sax-7 double mutant, Lithium-pilocarpine injection, Metformin, Metformin + Cisplatin, mnr-1, traumatic brain injury
  • The following new Original Format of reconstruction files have been added: Custom.hoc, Knossos.swc, NeuroGPS-Tree.swc, PyKNOSSOS.nmx
  • The following new Slicing thickness values have been added: 0.025µm, 135µm
  • The following new Stain values have been added: "Alexa Flour 488, immunostaining", "Biocytin, Alexa 568", Alexa Fluor 460, membrane-tetherd YFP, OGB-1, osmium and lead citrate, Texas Red dextran
  • The following new Reconstruction Software have been added: Knossos, NeuroGPS-Tree, PyKNOSSOS
  • The About page includes three new interactive plots for number of reconstructions, data categories, and, downloads and hits, respectively.



Version 7.1 released on 03/30/2017 contained 62304 neurons

What's new in version 7.1 ?
  • The following new Species have been added: Baboon, Hamster, Leopard, Tiger, Xenopus laevis
  • The following new Strains of species have been added:
    • Baboon: Chacma
    • drosophila melanogaster: NP0282-Gal4, R13F02-GAL4>UAS-C3PA-GFP; UAS-dicer2
    • Hamster: Syrian Hamster
    • monkey: Vervet
    • mouse: C57BL/6N, BALB/c, C57BL/6 - NgR1, C57BL6/J x CBA, Thy1-GFP-M, C57BL/6-Tg-(CAM2a-BDNF)A9stl/J, Cux2-CreERT2, TgCRND8, C57BL/6-(BAC)-transgenic mouse, C56BL/6J, C57BL/6-C3H/HeJ, SynRas transgenic, OMP-GFP (129 x C57BL/6), C57BL/6J Lgi1-/-, Thy1-GFP M-line, Sst-IRES-Cre (Jax 013044) x Ai14 Cre reporter line (Jax 007914), Pvalb-Cre (Jax 008069) x Ai14 Cre reporter line (Jax 007914), Thy1-YFP-G, M72-GFP, Pvalb-2A-Cre/Ai3, X98 SST (Jax 006340), OF1, B6SJLTgN(SOD1-G93A)/1Gur/J
    • rabbit: New Zealand white
    • rat: WAG/Rij
    • zebrafish: Nacre
  • The following new Brain Regions have been added:
    • Primary brain region: corpus callosum
    • Secondary brain region: Posterior Cingulate, inferotemporal, presubiculum
    • Tertiary brain region: A1, A4, B2, B3, Brodmann area 5, Brodmann area 7, C2, C4, C5, Cluster cortex, Contralateral, Core, D1, D2, D5, E2, E4, E5, Hindlimb representation, Ipsilateral, Secondary gyrus brevis, Septa, Subplate, area 4, area 6, caudal fin, dorsolateral cortex, dorsolateral cortex 1, dorsolateral cortex 4, hand representation, inferior temporal gyrus, infrapyramidal blade, inner, intermediate capsule, lateral edge, lateral spinal nucleus, mid-septo-temporal, middle temporal gyrus, middle third, optic, outer, posterior third, posterior/dorsal, precentral gyrus
  • The following new Cell Types have been added:
    • Primary cell type: glia
    • Secondary cell type: CT1, Dm, Dm10, Dm3, Dm6, Dm7, Excitatory, Inhibitory, Lawf2, Mi, Mi2, Mi4, Mi9, Oligodendrocyte, Pm, Pm2, Regulator of calcineurin 2 (Rcan2)-postive, Serotonin receptor type 3A (5-HT3)-positive, T4a, T4b, T4c, T4d, T4out, astrocyte, deep projecting cell, horizontally elongated, oriens-bistratified, shrub cell, single bouquet, tritufted
    • Tertiary cell type: 16 days old, AII, Caudoputamen-projecting, GIN, GIN-like, Homeobox Protein Cux-2-positive, Intercalated, Intrinsically photosensitive, Midbrain-projecting, NG2-expressing, Non-neurogliaform, Precursor cell, X94-like, afferent fiber collateral, alpha-beta, atypical SOM-like, delayed, direct pathway, elongated, equatorial, fast motor unit, giant bistratified, high-threshold, indirect pathway, initial doublet, interplexiform, northern, quasi fast spiking, recoverin-positive, repetitive, slow motor unit
  • The following new Experimental Conditions have been added: Arousal, Blocked wheel, caSRF-expressing, CELSR3 shRNAi, Chrna5 knockout, ciSRF-expressing, Cocaine, cocaine self-administration, conditional Knock-Out, Corticosterone, corticosterone/Fluoxetine, Daidzein, Disc 1 Homozygous Knockout, Disc1 Heterozygous, Doxycycline + NRG2 overexpression, Early training, Endotoxin, Eutherm, GYKI, Habituated control, Late training, Limited wheel access, mSOD1 mutant, Nestin-Mfp2 knockout, NGF, Non-habituated control, Paclitaxel, PIWIL1 siRNA, Resolvin D1, scar-like reactive astrocytes, scar-like reactive astrocytes & Olfactory ensheathing cell transplantation, Spared nerve injury, Stimulated, Torpor, Transgenic, Tumor, unlimited wheel access, Va112-Ha-Ras, Wheel running, yoked saline, yoked-cocaine
  • The following new Original Format of reconstruction files have been added: Amira.swc, Imaris.hoc, Imaris.imx, Imaris.swc, Janelia Workstation-Large Volume Viewer.swc, Orion.swc, Simple Neurite Tracer.swc, Simple Neurite Tracer.traces, Trees Toolbox.mtr
  • The following new Slicing thickness values have been added: 0.01µm, 1.00µm, 2.00µm, 5.00µm, 25.00µm, 35.00µm, 160.00µm, 230.00µm, 310.00µm
  • The following new Stain values have been added: Alexa 647-dextrane, Alexa Fluor 555, enhanced yellow fluorescent protein, Streptavidin-Alexa 488
  • The following new Age Classification values have been added: tadpole
  • The following new Reconstruction Software have been added: Janelia Workstation-Large Volume Viewer, ORION, TREES toolbox
  • Current known issues to be fixed will be listed and described in a specific page from this version on. For more details, see the Known Issues page.
  • Terminology of several metadata categories has been updated in the repository (details available for download here).



Version 7.0 released on 09/01/2016 contained 50356 neurons

What's new in version 7.0 ?
  • The following new Species have been added: Siberian hamster
  • The following new Strains of species have been added:
    • drosophila melanogaster: Canton S G1 x w1118
    • giraffe: Masai
    • mouse: C57BL/6JxBALB/cJ, Vip-eGFP, Gad2-IRES-Cre, C57BL6/delta3'UTRalphaCamKII, C57BL6/nestin::CreERT2XFmr1, E0585-Gal4, 5-HT1A-Gal4, nestin-Cre ERT2-αCaMKIIf/f/Rosa26-LacZ+/-, GlyT2-EGFP, Htr3a-Cre_NO152, nestin-Cre ERT2+αCaMKIIf/f/Rosa26-LacZ+/-, Nr5a1-Cre, Ntsr1-Cre_GN220, Pv-cre x RosaYFP, Pvalb-IRES-Cre, Rbp4-Cre_KL100, Rorb-IRES2-Cre, ROSA26tdTomato, B6.129S4-Pten/J, Cr-iCre, C57BL/6-Tg(Grik4-cre)G32-4Stl/J, Scnn1a-Tg2-Cre, Scnn1a-Tg3-Cre, Sst-IRES-Cre, VIP-cre x RosaYFP
    • turtle: Trachemys scripta elegans
  • The following new Brain Regions have been added:
    • Secondary brain region: D10, D8, D9, L2, L5, L5-L6, S1, S2
    • Tertiary brain region: L2i, L2o, L3, dorsal border, dorsal horn border, forelimb representation, lamina VII, parieto-occipital contour, ventral border, ventral horn border
  • The following new Cell Types have been added:
    • Secondary cell type: A00b, A00b2, A00c, A02m/A02n, A02o, A03o, A05e, A05q, A08d, A08m, A08x, A08y, A10a, A10f, A10j, A10l, A12m, A12q, A19c, A23g, A29b, Basin-1, Basin-2, Basin-3, Basin-4, Back-Projecting, Gustatory, Goro, Ipsigoro, Ipsiphone, lch5-1, lch5-3, lch5-5, lch5-2/lch5-4, MOPP, non-renshaw, oriens-alveus, oriens-oriens, prion protein (PrP) promoter-positive, scratch-activated, SEZ DN 1, T05t, T08x, Telegoro, Telephone, TePn04, transverse, v'ch, vchA/vchB
    • Tertiary cell type: Chicken ovalbumin upstream promoter transcription factor 2 (CoupTFII)-negative, Neuronal Nitric Oxide Synthase (nNOS)-negative, Neurotensin Receptor 1-positive, Plasma Retinol-Binding Protein-Positive, Retinoid-Related Orphan Receptor-Beta-positive, Non Voltage Gated 1 Alpha Subunit-positive, Sodium Channel, Non Voltage Gated 1 Alpha Subunit-Negative, Serotonin receptor type 3A (5-HT3)-negative, Steroid Hormone Receptor Ad4BP-positive, Translaminar, Vesicular glutamate transporter type 3 (VGluT3)-positive, fusiform, galanin-expressing, gigantopyramidal, glycinergic, mossy fiber associated, starfish
  • The following new Experimental Conditions have been added: Acute melatonin treatment, ATP6AP2-knockdown, CELSR1-knockdown, CELSR3-knockdown, Early withdrawal: 1 day post saline/nicotine, Early withdrawal: 1 day post saline/saline, Early withdrawal: 1 day post SCH23390/nicotine, Early withdrawal: 1 day post SCH23390/saline, Electroconvulsive shock, Fmr1 knockout, Late withrawal: 21 days post saline/nicotine, Late withdrawal: 21 days post saline/saline, Late withdrawal: 21 days post SCH23390/nicotine, Late withdrawal: 21 days post SCH23390/saline, Learning, Learning + Fmr1 knockout, Learning + Fmr1 knockout + MPEP Treatment, lipopolysaccharide injection, Myosin 2B knockout, Phosphatase and Tensin Homolog on Chromosome Ten knockout, Tamalin knockout, TARP Gamma-1, TARP Gamma-2, TARP Gamma-3, TARP Gamma-4, TARP Gamma-5, TARP Gamma-7, TARP Gamma-8, TARP Gamma-8 & APV-treated (5-10 DIV), TARP Gamma-8 & CNQX-treated (5-10 DIV), TARP Gamma-8 shRNA, TARP Gamma-8-ct-gamma-1, TARP Gamma-8-ex-gamma-1, Tetanus neurotoxin
  • The following new Original Format of reconstruction files have been added: Trees.swc
  • The following new Slicing thickness values have been added: 0.05µm, 125µm, 375µm
  • The following new Stain values have been added: Alexa 555, Sato's lead
  • The following new Reconstruction Software have been added: Catmaid
  • OntoSearch 2.0
    Brain region, cell types, and experimental condition metadata have now been incorporated into OntoSearch. See FAQ for information on underlying conceptual hierarchies and ontologies.
  • The species ontology was updated (OntoSearch v2.0) to include new turtle, giraffe, and rodent species as well as several new mice and fruit fly strains (27 terms mapped to 33 new concepts). See FAQ for details about Brain regions, cell types and other metadata.
  • A total of 54 duplicated entries were merged into single entries. We have indicated this in individual entries, and the previous additional reconstructions are still available for download.
  • Some previously released reconstructions from Chiang archive had been incompletely processed. These issues have been fixed and noted in individual entries. The pre-v.7.0 versions of the processed files are available for download here.
  • The literature coverage includes a new Data usage entry that lists: (1) references using data downloaded from the repository; (2) references describing data that have been deposited (or in process) in the repository; (3) references about NeuroMorpho.Org; and, (4) references citing NeuroMorpho.Org.
  • Terminology of several metadata categories has been updated in the repository (details available for download here).



Version 6.3 released on 03/04/2016 contained 37712 neurons

What's new in version 6.3 ?
  • The following new Species have been added: domestic pig
  • The following new Strains of species have been added:
    • drosophila melanogaster: transgenic melanogaster
    • guinea pig: Dunkin-Hartley
    • mouse: TH-eGFP, Cdh3, ICR, GFP-YFP, W3, FVB/129, B6;129S6-Chattm2(cre)Lowl/J, GAD67-eGFP, JAM-B, BD, K, C57BL6/GFP-line15, Nkx2.1Cre-RCE, C57BL6/GFP-M, Olfr73-GFP, rTg4510 P301-L mutant, CB2, CB6-Tg(Gad1-EGFP)G42Zjh/J [GAD67-GFP (line G42)], CBA/J rd1, Ddo -/-, W7, Bassoon (bsn) mutant, NMRI, C57BL/6H
  • The following new Brain Regions have been added:
    • Secondary brain region: diagonal band, external plexiform layer, facial nucleus, lateral geniculate nucleus, M1-M6, mitral layer, posterior thalamic nucleus, spinal trigeminal nucleus, substantia innominata
    • Tertiary brain region: Brodmann area 3b, D8-S1, L9, dorsal, hand representation, hindlimb representation, horizontal limb of diagonal band of broca, inner, inner surface, lateral, layer 10, layer 2/3 & 5, left, mid-temporal, middle, oriens/pyramidale border, outer, postcentral gyrus, precentral gyrus, radiatum/lacunosum-moleculare border, secondary visual, subnucleus caudalis, suprapyramidal blade, ventral
  • The following new Cell Types have been added:
    • Secondary cell type: Choline acetyltransferase (ChAT)-positive, Intersubnuclear neuron, Neuroblast, Shepherd's crook neuron, internal tufted, mitral, tufted, tyrosine-hydroxylase-positive
    • Tertiary cell type: Calbindin (CB)-negative, Caudal Ganglionic Eminence (CGE)-derived, Chicken ovalbumin upstream promoter transcription factor 2 (CoupTFII)-positive, Cholecystokinin (CCK)-negative, Depolarizing, Doublecortin (DCX)-containing, Enkephalin (Enk)-positive, ErbB4-positive, Eugenol-glomerulus projecting (EG), F type, Hyperpolarizing, Immature, Ivy, Medial Ganglionic Eminence (MGE)-derived, Multilaminar, Neuronal Nitric Oxide Synthase (nNOS)-positive, Neuropeptide Y (NPY)-negative, Non-Eugenol-glomerulus projecting (non-EG), S type, Serotonin insensitive, Serotonin receptor type 3A (5-HT3)-positive, Serotonin sensitive, Somatostatin (SOM)-negative, Sp5c-Pr5 ascending, Vesicular glutamate transporter type 3 (VGluT3)-positive, amygdala-projecting, biphasic, cluster A, cluster B, cluster C, cluster D, cluster E, cluster F, cluster G, cluster H, cluster I, cluster U, cluster V, cluster W, cluster X, cluster Y, cluster Z, corticocortical, early bifurcating, genioglossus, geniohyoid, hyoglossus, inner tongue muscle, late bifurcating, mGluR1alpha-negative, mGluR1alpha-positive, medial-entorhinal-cortex-projecting, medial-prefrontal-cortex-projecting, migratory, omohyoid, post-migratory, sternohyoid, stuttering
  • The following new Experimental Conditions have been added: Calsyntenin-1 knockout, Chronic stress, D-aspartate oxidase (Ddo) knockout, D-aspartate oxidase (Ddo) wildtype (Control), D-aspartate treatment, DA Lesion, Doxycycline (DOX), facial-facial anastomosis, fluoxetine, Mitochondrial Rho GTPase 1 (Miro1)-binding domain of trafficking kinesin protein 2 (TRAK2-MBD), mitofusin 1, porcine reproductive and respiratory syndrome virus
  • The following new Original Format of reconstruction files have been added: FIJI.traces, Imaris.iv, Neurolucida.swc
  • The following new Slicing thickness values have been added: 140.00µm, 275.00µm, 325.00µm
  • The following new Stain values have been added: Streptavidin-Alexa 546, Farnesylated enhanced green fluorescent protein (eGFP-F), Rapid Golgi, Sindbis XFP virus, turboRFP
  • The following new Protocol values have been added: in ovo, in utero
  • The following new Reconstruction Software have been added: Simple Neurite Tracer
  • The species ontology was updated (OntoSearch v1.3) to include Pig (1 newly term mapped to 4 new concepts) and 26 new strains for mouse, rat, guinea pig, and zebrafish.
  • A total of 8 duplicated entries were merged into single entries. Out of them, 5 were clones and 3 were spliced from independent reconstructions of the dendritic and axonal arbors from the same specimen. We have indicated this in individual entries, and the previous additional reconstructions are still available for download.
  • The SWC units for the neurons in Chiang archive are not expressed in micrometers. The exact scaling factors, which are different for each neuron, are not known, but our approximate estimate is 0.32 in XY and 0.26 in Z. A warning note has been added to all neurons in this archive.
  • Metadata of some reconstructions/archives were corrected and updated in the repository (details available for download here). Terminology of several metadata categories has also been updated in the repository (details available for download here).



Version 6.2 released on 10/06/2015 contained 34082 neurons

What's new in version 6.2 ?
  • The following new Species have been added:
    • Bottlenose dolphin, Chimpanzee, Clouded leopard, Giraffe, Humpback whale, Locust, Manatee, Minke whale, Pouched lamprey, Siberian tiger
  • The following new Strains of species have been added:
    • Mouse: Atoh1/nGFP transgenic mice, BDNF Met/Met, BDNF WT, C57BL/6J POMC-Cre EGFP (+), ICR White, L0579 (BDNF WT) X L0582 (BDNF Met/Met), L0579 (BDNF WT) X L0623 (BDNF Met/Met)
    • Manatee: Florida manatee
    • Chimpanzee: Common chimpanzee
  • The following new Brain Regions have been added:
    • Primary brain region: Endocrine system
    • Secondary brain region: Adrenal gland, Lobula, Reticular formation, Tectum
    • Tertiary brain region: Anterior, C2, C3, C4, Central nucleus, Clarke's column, Dorsal left, Dorsal right, Inferior colliculus, L3-L4, L4-L5, Lamina I, Lateral cortex Layer 3, M1, Nucleus magnocellularis, Posterior, Primary motor (M1), Rectus capitus anterior (RCA) motor nucleus, Right, Ventral horn
  • The following new Cell Types have been added:
    • Secondary cell type: Local circuit neuron, Lugaro cell, Nonpyramidal, Parachromaffin cell, Perforant pathway-associated, Trilaminar, Ventral spinocerebellar tract cell
    • Tertiary cell type: Anterolateral-targeting (ALT) neuron, Atypical, Betz-like, Extraverted, Flexor, HICAP cell, HIPP cell, Lobula giant movement detector (LGMD) neuron, Newborn, Pheochromocytoma line 12, Slowly adapting, Somatic, Sternzelle, Touch receptor, Typical, Waldeyer neuron
  • The following new Experimental Conditions have been added: Acetylcholine and Kynurenic acid, Akt-ko, Bile duct litigation (BDL), Bile duct litigation combining ammonia acetate (BDLHD), Bungarotoxin and Pertussis toxin, Choline treatment, Chronic variable stress (CVS), Middle cerebral artery occlusion (MCAO), Nerve growth factor, Nerve growth factor and Acetylcholine, Nerve growth factor and Kynurenic acid, Nerve growth factor and Nicotine, Nerve growth factor and Pertussis toxin, Nerve transection, Nicotine and FK506, Old heterochronic parabiosis, Old isochronic parabiosis, Sham
  • The following new Original Format of reconstruction files have been added: neuTube.swc
  • The following new Slicing thickness value has been added: 12 µm
  • The following new Stain values have been added: Anti-alpha-Tubulin Antibodies, Bodian stain, Phalloidin, Red fluorescent protein (RFP), Sindbis palGFP virus
  • The following new Protocol has been added: Ex vivo
  • The following new Reconstruction Software has been added: neuTube
  • The species ontology was updated (OntoSearch v1.2) to include giraffe, chimpanzee, manatee, lamprey, dolphin, whale, tiger and leopard (50 newly added terms mapped to sixteen new concepts).
  • Reference articles on the neuron detail information pages include a link to the original journal publication through the associated DOI (when available).
  • Completeness information for all reconstructions deposited in NeuroMorpho.Org have been annotated at the neuron-level. For more details, see the FAQs page.
  • A total of 34 duplicated entries are merged into single entries. Out of them, 14 were clones and 20 were additional reconstructions of the same neuron. We have indicated this in individual entries, and the previous additional reconstructions are still available for download.
  • We updated our data inclusion criteria (see FAQ page), and as a consequence 26 old cells have been deleted. The reconstructions are still available for download here.
  • Other updates to the database include:
    • Metadata of some reconstructions/archives were corrected and updated in the repository (details available for download here). Consequently, the following new cell type has been added:
      • Tertiary: Alpha
    • Experiment protocol in Kellendonk and Flores has been updated to in vitro
    • Secondary brain region entry Primary visual cortex is updated to Primary visual (V1)



Version 6.1 released on 05/13/2015 contained 31982 neurons

What's new in version 6.1 ?
  • Please note: In every neuron page from these new archives, the soma appears thinner than it should in the static neuron images. This is purely a rendering issue, and the downloadable data (SWC files) have the correct somatic values. New images with the correct soma appearance will be released as soon as we solve the rendering problem.
  • The following new Cell Types have been added:
    • Secondary cell type: Nitrergic neuron
  • The following new Experimental Conditions have been added: AMPAR GluA1(Q)-flip, AMPAR GluA1(Q)-flop, AMPAR GluA1(R)-flip, AMPAR GluA2(Q)-flip, AMPAR GluA2(Q)-flop, AMPAR GluA2(R)-flip, AMPAR GluA2(R)-flop, AMPAR GluA3(Q)-flip, AMPAR GluA3(Q)-flop, AMPAR GluR1(Q)-flip, AMPAR GluR2(Q)-flip, AMPAR GluR2(Q)-flop, AMPAR GluR2(R)-flip, AMPAR GluR2(R)-flop, AMPAR GluR3(Q)-flip
  • We are aware that the database contains 24 cases of duplicate neurons. We have indicated this in individual entries. In future release of NMO, the duplicates will be merged into single entries, where both reconstructions will be made available.
  • Some previously released reconstructions had been incompletely processed. These issues have been fixed and noted in individual entries. The pre-v.6.1 versions of the processed files are available for download here.
  • Brain regions included in BrainInfo portal and also present in NeuroMorpho.Org are now cross-linked by hyperlinks when displayed in the various results pages. For more details, see the FAQs page.
  • The Metadata_Form has been updated to include a more detailed description and examples of the metadata categories.
  • Literature Coverage has been updated to include publications through April 2015. When available, Digital Object Identifiers (DOI) are now included within the literature Complete Details sheet.
  • Other updates to the database include:
    • Metadata of some reconstructions/archives were corrected and updated in the repository (details available for download here). Consequently, the following new Brain regions have been added:
      • Secondary: Cercal
      • Tertiary: Cercal mechanosensory periphery



Version 6.0 released on 12/11/2014 contained 27385 neurons

What's new in version 6.0 ?
  • The following new Strains of species have been added:
    • Drosophila melanogaster: 5-HT1B-Gal4, Cha-Gal4, FRT40A wild-type control MARCM clone, fru-Gal4, G0239-Gal4, Gad1-Gal4, GH146, GH146-Gal4, NP5194, NP6099, npf-GAL4, Tdc2-Gal4, TH-Gal4, Trh-Gal4, tutlc00018 FRT40A mutant MARCM clone, UAS-Actin-GFP constructs, VGlut-Gal4, wild-type Oregon R
  • The following new Brain Regions have been added:
    • Primary brain region: Left Adult Central Complex, Left Adult Subesophageal Zone, Left Antennal Lobe, Left lateral Complex, Left Lateral Horn, Left Mushroom Body, Left Optic Lobe, Left Protocerebrum, Left Subesophageal Ganglion, Left Ventrolateral Neuropils, Right Adult Central Complex, Right Adult Subesophageal Zone, Right Antennal Lobe, Right lateral Complex, Right Lateral Horn, Right Mushroom Body, Right Optic Lobe, Right Protocerebrum, Right Subesophageal Ganglion, Right Ventrolateral Neuropils
    • Secondary brain region: Left Antennal Lobe Glomerulus, Left Calyx, Left Caudal Ventrolateral Protocerebrum, Left Caudalcentral Protocerebrum, Left Caudalmedial Protocerebrum, Left Central Body, Left Dorsomedial Protocerebrum, Left Dosrsolateral Protocerebrum, Left Frontal Superpeduncular Protocerebrum, Left Inferior Dorsofrontal Protocerebrum, Left Inner Dorsolateral Protocerebrum, Left Lateral Triangle, Left Lobula Complex, Left Medulla, Left Noduli, Left Optic Glomerulus, Left Optic Tubercle, Left Protocerebral Bridge, Left Saddle, Left Superior Dorsofrontal Protocerebrum, Left Superpeduncular Protocerebrum, Left Ventrolateral Protocerebrum, Left Ventromedial Protocerebrum, Lumbosacral, Right Antennal Lobe Glomerulus, Right Calyx, Right Caudal Ventrolateral Protocerebrum, Right Caudalcentral Protocerebrum, Right Caudalmedial Protocerebrum, Right Central Body, Right Dorsomedial Protocerebrum, Right Dosrsolateral Protocerebrum, Right Frontal Superpeduncular Protocerebrum, Right Inferior Dorsofrontal Protocerebrum, Right Inner Dorsolateral Protocerebrum, Right Lateral Triangle, Right Lobula Complex, Right Medulla, Right Optic Glomerulus, Right Optic Tubercle, Right Protocerebral Bridge, Right Saddle, Right Superior Dorsofrontal Protocerebrum, Right Superpeduncular Protocerebrum, Right Ventrolateral Protocerebrum, Right Ventromedial Protocerebrum
    • Tertiary brain region: Bordering Left Adult Central Complex, Bordering Left Antennal Lobe, Bordering Left Antennal Mechanosensory and Motor Centre, Bordering Left Fanshaped Body, Bordering Left Lateral Horn, Bordering Left Lobula, Bordering Left Lobula Plate, Bordering Left Mushroom Body, Bordering Left Optic Lobe, Bordering Left Protocerebrum, Bordering Left Subesophageal Ganglion, Bordering Left Superior Dorsofrontal Protocerebrum, Bordering Left Ventrolateral Neuropils, Bordering Right Adult Central Complex, Bordering Right Antennal Lobe, Bordering Right Antennal Mechanosensory and Motor Centre, Bordering Right Calyx, Bordering Right Dorsomedial Protocerebrum, Bordering Right Fanshaped Body, Bordering Right Lateral Horn, Bordering Right Lobula, Bordering Right Lobula Plate, Bordering Right Medulla, Bordering Right Mushroom Body, Bordering Right Optic Lobe, Bordering Right Protocerebral Bridge, Bordering Right Protocerebrum, Bordering Right Subesophageal Ganglion, Bordering Right Superior Dorsofrontal Protocerebrum, Bordering Right Superpeduncular Protocerebrum, Bordering Right Ventrolateral Neuropils, Left Antennal Mechanosensory and Motor Centre, Left Ellipsoid Body, Left Fanshaped Body, Left Lobula, Left Lobula Plate, Left Proximal Antennal Protocerebrum, Right Antennal Mechanosensory and Motor Centre, Right Ellipsoid Body,Right Fanshaped Body, Right Lobula, Right Lobula Plate, Right Proximal Antennal Protocerebrum
  • The following new Cell Types have been added:
    • Secondary cell type: Unknown neurotransmitter, GABAergic neuron, Octopaminergic neuron, Serotonergic neuron
    • Tertiary cell type: embryo Born, day1 Born, day2 Born, day3 Born, day4 Born, day5 Born, day6 Born, day7 Born, day8 Born, day9 Born, unknown Born
  • The NeuroMorpho.Org species ontology was updated in release 6.0 with the transgenic fly strains (OntoSearch v1.1). The Chiang archive included thirteen different GAL4 strains targeting neurotransmitter specific cell types. These strains were mapped to flybase.org allowing to search by names and synonyms while preserving their external concept IDs. The previously released fly archives by Jefferis and Chklovskii were also similarly mapped to flybase as reflected in the updated species ontology. The fly data can now be searched using over 170 terms, with strains such as Cha-GAL4 mapping to 43 alternative names.
  • NeuroMorpho.Org data are now directly accessible from BrainInfo and NeuronDB based on brain region details and neuron types.
  • The Summary display of selected neurons has been modified to include brain sub-regions and cell sub-types for each neuron.
  • A new metadata annotation system and search functionality has been introduced to allow users to retrieve reconstructions from the database based on their level of completeness. All publications whose data are deposited in NeuroMorpho.Org have been annotated; neuron-level annotation will continue in future releases. For more details, see the FAQs page.
  • The Metadata_Form has been updated to include details on the completeness of reconstructions.
  • Other updates to the database include:
    • The Species Drosophila has been updated to Drosophila melanogaster.
    • The Strain for Chklovskii, Cirelli, Cox, Jefferis, Landgraf and Ye archives have been updated to indicate their genotype (previously listed as melanogaster).
    • Tertiary cell class for 10 reconstructions in Cox archive have been updated.
    • Development in Jefferis archive has been updated to Adult (previously listed as Larva).
    • Staining method in Allman archive has been updated to Golgi (previously listed as Nissl).



Version 5.7 released on 05/30/2014 contained 11335 neurons

What's new in version 5.7 ?
  • Twenty-nine data sets (1341 reconstructions) have been added:
  • The following new Species have been added:
    • Dragonfly, Moth, Sheep
  • The following new Strains of species have been added:
    • Mouse: C56BL/6, C57Bl6/129Sv, C57BL6/GABAAR a2H101R, FVB/AntFx, GAD67-GFP, Transgenic
    • Rat: VGAT-Venus
    • Sheep: Western
  • The following new Brain Regions have been added:
    • Primary brain region: Central nervous system (this refers to the fly larva and should not be confused with the usage of the same term in vertebrate anatomy), Lateral line organ, Optic lobe, Pons, Ventral nerve cord
    • Secondary brain region: Dorsal intermediate tract 1 (DIT1), Dorsal intermediate tract 2 (DIT2), Dorsal intermediate tract 3 (DIT3), Dorsal root ganglion, Median dorsal tract 1 (MDT1), Median dorsal tract 2 (MDT2), Median dorsal tract 3 (MDT3), Median dorsal tract 4 (MDT4), Median dorsal tract 5 (MDT5), Medulla (this refers to the insect sub-region of the optic lobes, not to be confused with the vertebrate region of the central nervous system, from which reconstructions are also available), Pedunculopontine nucleus (PPN), Pontine tegmentum, Pre-Botzinger complex
    • Tertiary brain region: Abdominal segment 2-4, Dorsalis/deep, Dorsalis/middle, Dorsalis/superficial, Lateralis/deep, Lateralis/middle, Lateralis/superficial, Layer 5/6, Medialis/deep, Molecular layer, Nucleus incertus, S1, S3, S4, Ventroposterior/middle, Ventroposterior/superficial
  • The following new Cell Types have been added:
    • Secondary cell type: C2, C3, Cholinergic cell, Dm1/6-like, Dm10, Dm1-like, Dm2, Dm3-like, Dm4, Dm5-like, Dm7-like, Dm8, Dm9, Dm-type unknown-1, Dm-type unknown-2, Dorsal root ganglion neuron, Fast-spiking, Inspiratory neuron, Ivy/Neurogliaform cell, L1, L2, L3, L4, L5, LaWF1, Mi1, Mi10, Mi11-like, Mi13, Mi14, Mi15, Mi3-like, Mi4, Mi9, Mi-type unknown-1, Mt11-like, Mt3-like, Mt4-like, Mt5-like, Non-cholinergic cell, Olfactory neuron, Olt-like, Pm1, Pm2-like, Pm-type unknown-1, Pm-type unknown-2, R7, R8, Relaxin-3 (RLN3) containing cell, T1, T2, T2a, T3, T4, Tangential, Target-selective descending neuron (TSDN), Tm1, Tm12/25, Tm16, Tm2, Tm20, Tm23/24, Tm28/TmY9, Tm3, Tm4, Tm5a, Tm5b, Tm5c-like, Tm5Y, Tm6/14, Tm9, TmY10, TmY13, TmY14, TmY3, TmY4, TmY5a, TmY5-like, Tm-type unknown-1, Tm-type unknown-10, Tm-type unknown-11, Tm-type unknown-12, Tm-type unknown-13, Tm-type unknown-14, Tm-type unknown-15, Tm-type unknown-16, Tm-type unknown-17, Tm-type unknown-2, Tm-type unknown-3, Tm-type unknown-4, Tm-type unknown-5, Tm-type unknown-6, Tm-type unknown-7, Tm-type unknown-8, Tm-type unknown-9, TmY-type unknown-1, Y4, Y6
    • Tertiary cell type: Anterior corner cell (aCC), Corticospinal, Lateralis afferent neuron, VS1
  • The following new Experimental Conditions have been added: Brn3a-expression, Brn3b-expression, Brn3c-expression, Highwire (Hiw) mutant, Hypoxia-ischemia (HI), Tmie mutant (deaf)
  • The following new Original Format of reconstruction files have been added: Imaris.ims, Neuronstudio.swc
  • The following new Slicing thickness value has been added: 0.04 µm
  • The following new Magnification value has been added: 5000x
  • OntoSearch (v1.0) performs a search of species and strains in NeuroMorpho.Org through a formal species taxonomy. This new functionality enables powerful features, such as hierarchical logic (e.g. a search for �rodents� retrieves data from rats, mice, guinea pigs, proechimys, and agouti), seamless synonym translation (e.g. a search for �fruit fly� retrieves Drosophila data), and keyword auto-completion (e.g. typing �Spr� proposes a search for Sprague-Dawley rat data, but user has the option to disregard and override this suggestion).
  • Due to increased security constraints in the Java environment, the 3D Neuron Viewer in the neuron details page may fail to launch. Please see FAQs to help with troubleshooting this error.
  • Literature Coverage has been updated to include publications through March 2014.



Version 5.6 released on 05/06/2013 contained 10004 neurons

What's new in version 5.6 ?
  • Sixteen data sets (1146 reconstructions) have been added:
  • The following new Species have been added:
    • C. elegans, Chicken
  • The following new Strains of species have been added:
    • C. elegans: N2
    • Chicken: White leghorn
    • Mouse: C57BL6/CLM-1, C57BL6/CLM-11, C57BL6/Etv1, C57BL6/Glt25d2, GAD65-GFP
    • Zebrafish: Wild type AB
  • The following new Brain Regions have been added:
    • Primary brain region: Hypothalamus, Midbrain, Pharyngeal nervous system, Somatic nervous system
    • Secondary brain region: Anterior bulb, Dorsal ganglion, Dorsal motor nucleus of the vagus, Dorsolateral prefrontal cortex, Dorsorectal ganglion, Frontal cortex, Inner labial sensilla, Lateral ganglia, Lateral hypothalamic area, Lumbar, Lumbar ganglia, Lumbar ganglion, Nucleus laminaris (NL), Posterior bulb, Preanal ganglion, PreB�tzinger complex, Primary visual cortex, Retrovesicular ganglion, Solitary nucleus, Ventral ganglion, Ventral nerve cord
    • Tertiary brain region: Brodmann area 9, Broadmann area 46, Dorsal horn, Dorsolateral, Lamina III, Layer 5A, Layer 5B, Layer 6B, Nucleus magnocellularis (NM), Postcruciate gyrus, Precentral gyrus, Secondary motor cortex (M2)
  • The following new Cell Types have been added:
    • Secondary cell type: Amphid, GAD65 neuron, Horizontal, Integrative ring, Inverted cell, Non-fast spiking, Non-glutamatergic neuron, Pharyngeal, Projection neuron, Ring, Ring/Pharynx
    • Tertiary cell type: Alpha-actinin 2 (AAc) - positive, Calretinin (CR) containing cell, Caudal primary, Chemosensory, Corticothalamic, Corticotropin releasing factor (CRF) - positive, Dbx1-negative, Dbx1-positive, Descending, intracolumnar Pyramidal cell, Low threshold spiking, Mechanosensory, Motoneuron, Multisensory, Neurokinin 1 receptor (NK1r) - immunoreactive, Neurosecretory (Serotonin), Odorsensory, Perirhinal cortex-projecting, Putative mechanosensory neuron, Putative sensory neuron, Ring, Stretch-sensitive sensory neuron, transcolumnar Pyramidal cell
  • The following new Experimental Conditions have been added: Dbx1-expression, F363L kv3.3 mutation, R335H kv3.3 mutation, rAAV2-BDNF-GFP, rAAV2-CNTF-GFP, rAAV2-GAP43-GFP, rAAV2-GFP, wtkv3.3 EGFP
  • The following new Original Format of reconstruction files has been added: MorphML.morph.xml
  • The following new Slicing thickness values have been added: 550 µm, 1000 µm.
  • A new search functionality in the Detailed Statistics page allows users to quickly retrieve the site's unique visits from specific countries and the download activity of specific cell types, brain regions, species, and archives.
  • A quick 1 minute video introducing NeuroMorpho.Org has been added to the Quickstart page.
  • On 24 June, 2013 morphometrics for all 10,004 reconstructions in the database were updated using the latest version of L-Measure (v5.0). See details of the updates and please email us at nmadmin@gmu.edu or neuromorpho@gmail.com with any questions.



Version 5.5 released on 01/15/2013 contained 8858 neurons

What's new in version 5.5?
  • Twenty-six data sets (872 reconstructions) have been added:
  • The following new Mouse strains have been added:
    • rd10/Thy1-GFP, CXCR4-EGFP, C57Bl6/129SvEv, B13, C57BL6J/Dync1li1N235Y, C57BL, Arx(GCG)7-1 KI (B6), SV126/BL6.
  • The following new Experimental Conditions have been added:
    • L100P/GSK3alpha mutant, L100P/GSK3alpha knockout, GSK3alpha knockout, Disc1-L100P mutant, Disc1-Q31L mutant, Nicotine-treated, Fluid percussion injury, RICS expression, Myo9b expression, Intermittent stress, Brief stress, D2R-overexpression, D2R-overexpression + AAV2/1-GFP virus, dcc heterozygous, Point mutation in Dync1li1, Knock-in, WASP-interacting protein (WIP) knockout.
  • The following new Brain Regions have been added:
    • Primary brain region: Medulla
    • Secondary brain region: Cerebellar cortex, Inferior olive, Inner plexiform layer (IPL), Insular cortex, Main intercalated nucleus.
    • Tertiary brain region: Dorsomedial, Inner molecular layer (IML), Outer molecular layer (OML), Pregenual, Pars compacta, Purkinje cell layer, Rostral agranular insular cortex, Subnucleus c, Vermis.
  • The following new Cell Types have been added:
    • Secondary cell type: Dendritic-targeting, GABAergic projection cell, Perisomatic-targeting, Semilunar granule cell.
    • Tertiary cell type: A1 type, A2 inner type, A2 outer type, B1 type, B3 outer type, C2 inner type, C2 outer type, Climbing fiber, OFF type, ON type.
  • The following new Reconstruction Software has been added: AutoNeuron.
  • The following new Slice thickness values have been added: 30µm, 225µm.
  • The following reconstructions have been renamed and reassigned archives:
  • 11 reconstruction files, formerly in the Barrionuevo archive are now under the (Ascoli, Barrionuevo archives).
  • Graphs of data trends have been added in the About page.
  • Literature Coverage has been updated to include publications through December 2012.
  • An error in the number of reconstructions within the Literature Coverage has been corrected.
  • Other updates to the database include:
    • Reconstruction software for 3 reconstructions in the Luebke archive have been updated to AutoNeuron (previously listed as Neurolucida).
    • Staining method in Kubota and Spruston archives has been updated to Biocytin (previously listed as DAB reaction).
    • DAB reaction has been deleted as an entry in the Staining method category.



Version 5.4 released on 5/17/2012 contained 7986 neurons
What's new in version 5.4?
  • Twenty-eight data sets (754 reconstructions) have been added:
  • The following new Species have been added:
    • Agouti
    • Frog
    • Proechimys
    • Turtle
  • The following new Strains have been added:
    • 5HT3-EGFP, B6/C57J, C57BL/6J, C57BL6/TrkB.T1 deficient mouse,
      Calretinin-EGFP, Dbx1cre; ROSA26YFP, Rana ridibunda, Testudo horsfieldi, and thy-1-YFP-16.
  • The following new Brain Regions have been added:
    • Secondary brain region: Cervical spinal cord, Inferior olive, Interscutularis muscle (in the Peripheral Nervous System), Lumbar enlargement, Medial prefrontal cortex, Orbital cortex, Ventroposterolateral (VPL) nucleus.
    • Tertiary brain region: C2-C3 (segments of the cervical spinal cord), Infralimbic cortex, Layer 1 (parietal cortex), S2 (secondary somatosensory cortex).
  • The following new Cell Types have been added:
    • Secondary cell type: Cajal-Retzius cell, Dorsal root afferent fiber collateral, Non-basket cell, Olivocerebellar fiber, Pyramidal-like neuron, Reticulospinal fiber, Schaffer-collateral associated cell, Small axonless neuron, Type III ISI (interneuron-specific interneuron), Oriens-lacunosum moleculare cell.
    • Tertiary cell type: CB1R-positive, CB1R-negative, CCK-positive, Fast-spiking, Late-spiking, Non-fast spiking, Simple cell, Slender-tufted, Thick-tufted, YFP-positive, YFP-negative.
  • The following new Experimental Conditions have been added:
    • Cerebellar lesion, Environmental enrichment, KCl treatment, Knockout, and short hairpin PFN2a expression.
  • The following new Reconstruction Method has been added:
    • NeuronJ.
  • The following new Stains have been added:
    • Alexa 568 hydrazide, Enhanced green fluorescent protein (EGFP), and FluoroRuby.
  • The following new Slicing directions have been added:
    • Frontal, Oblique horizontal, and Tangential.
  • The following new functionalities have been added:
    • Random neurons - will display a random selection of neurons from the database giving users a one-click access to samples of reconstructions (Browse>Random neurons).
    • Multiple archives - reconstructions resulting from collaborations between multiple laboratories can now be assigned to more than one Archive.
    • The alpha version of Neuron Atlas is now released on NeuroMorpho.Org. For additional details on the application and how to download it, see Neuron Atlas.
    • Keyword search (Search>Keywords) now includes NeuroMorpho.Org ID in the search query. See How can I use "Search by Keywords"? and What is a NeuroMorpho.Org ID? for more details.
  • Reconstructions contributed to the DIADEM Challenge are also listed under DIADEM archive.
  • The FAQs page has 3 new updates:
  • Literature Coverage has been updated to include publications through April 2012. The literature database is now being updated monthly thus providing the most current coverage.
  • The About page has been updated and includes Quick Facts and Quick Stats about NeuroMorpho.Org.
  • Terms of Use has been updated and moved to a more prominent position in the main toolbar. Please email us at nmadmin@gmu.edu or neuromorpho@gmail.com if you have any questions.



Version 5.3 released on 11/08/2011 contained 7232 neurons
What's new in version 5.3?
  • Nine new data sets (618 reconstructions) have been added:
  • The following new species have been added:
    • Goldfish
    • Zebrafish
  • The following new brain regions have been added:
    • Primary brain region: Optic nerve, Peripheral nervous system.
    • Secondary brain region: Cuticle, Ventral lateral nucleus.
    • Tertiary brain region: Abdominal segment 4-7, Lateral, Anterior lateral, Posterior lateral.
  • The following new cell types have been added:
    • Secondary cell type: Sensory neuron, Thalamocortical neuron.
    • Tertiary cell type: Multidendritic-dendritic arborization neuron, Retinotectal.
  • Soma representation in all standardized (CNG.swc) files have been modified from a sphere to a cylinder. See Soma Format for additional details.
  • The FAQs page has 1 new update:
  • We are currently in the process of identifying reconstructions in the repository that contain errors. The erroneous reconstructions will be corrected and updated at subsequent releases and details will be provided here. If you are aware of specific reconstructions with any errors, please email us at nmadmin@gmu.edu or neuromorpho@gmail.com.



Version 5.2 released on 06/01/2011 contained 6614 neurons
What's new in version 5.2?
  • Four new data sets (400 reconstructions) have been added:
  • The following new species have been added:
    • Elephant
    • Spiny lobster
  • The following new brain regions have been added:
    • Primary brain region: Stomatogastric ganglion.
    • Secondary brain region: Suprasylvian gyrus.
  • The following new cell types have been added:
    • Tertiary cell type: bipolar, crab-like, flattened, fork, inverted, matriarch, monopolar, multiapical, pyloric dilator (PD) neuron, superficial.
  • Each neuron in the database is now associated with a "NeuroMorpho.Org ID" (See FAQs for details).
  • Reconstructions can now be saved in NeuroML format from the 3D Neuron Viewer, in addition to NEURON and GENESIS formats.
  • Literature Coverage has been updated to include publications through 2010.
  • Terms of use page has been updated.
  • The FAQs page has 2 new updates:



Version 5.1 released on 03/10/2011 contained 6214 neurons
What's new in version 5.1?
  • Nine new data sets (421 reconstructions) have been added:
  • The following new brain regions have been added:
    • Primary brain region: anterior olfactory nucleus.
    • Secondary brain region: pars externa, pars principalis, primary auditory, cochlear nucleus, main olfactory bulb.
    • Tertiary brain region: superior frontal gyrus, infragranular layer, deep, middle, superficial, inner plexiform layer, outer granule cell layer, mid granule cell layer, granule cell layer/white matter border, glomerular layer, layer 3/4.
  • The following new cell types have been added:
    • Secondary cell type: vertical cell, external tufted cell (ETC), deep short axon cell (dSAC), type I, type II.
    • Tertiary cell type: non-bursting, bursting, glomerular layer-dSAC, granule cell layer-dSAC, external plexiform layer-dSAC, projection-dSAC, adapting, oblique.
  • A new experimental condition has been added:
    • Down syndrome.
  • Multiple tertiary levels have been added for both brain region and cell type to accommodate additional information, when available. These are displayed in the details page separated by commas.
  • 13 reconstructions that were wrongly categorized under the Ascoli archive have been moved to the Barrionuevo archive.
  • The FAQs page has 3 new updates:
  • Other minor cosmetic changes have been made to the Morphometry, FAQs and Quickstart pages.



Version 5.0 released on 11/05/2010 contained 5793 neurons
What's new in Version 5.0?
  • Nine new data sets (122 reconstructions) have been added:
  • The website has been completely redesigned to facilitate user's access to data. The new functionalities include:
    • Metadata - multiple options can be selected from the drop down menu.
    • Downloads - files can be selected to be downloaded at end of the session.
    • Browse - browse pages have been modified to reduce upload time.
    • Pie charts - both the pie chart and tags are clickable.
    • Neuron thumbnail images are displayed when the user browses through the list of neuron names.
    • Neuron details - units have been added to each measurement.
    • Detailed statistics - a live map of users from around the world has been added
    • Site map - has been added to facilitate navigation of the website.
  • 2 new categories have been added to the Metadata list: Experimental Condition and Tissue Shrinkage.
  • NeuroMorpho.Org has a new Homepage displaying the morphometrics included in the website.
  • An About page has been added which contains details about the website.
  • The Quickstart page, FAQs page and Literature coverage have each been modified and updated.
  • Reconstructions in the Borst archive have been updated as requested by the data owners.
  • Morphological measurements have been updated for 8 archives (Ascoli, Bikson, Bob Jacobs, Chalupa, DeFelipe, Gwen Jacobs, Helmstaedter, Luebke).
  • Reconstructions of Bikson (28), Chalupa (181), Helmstaedter (5) were re-processed and updated.
  • Notes for Ascoli archive were updated
  • The South China Univeristy of Technology in Guagzhou, China held a national modeling contest and NeuroMorpho.Org was the online resource for digital reconstructions. Click here for more details.



Version 4.0 released on 02/16/2010 contained 5673 neurons
What's new in Version 4.0?
  • Two new data sets (159 reconstructions) have been added:
  • A new link has been added to access the results of our extensive literature search for publications describing digital neuronal reconstructions. Results can be viewed by 1) complete details, 2) publication information, 3) reconstruction information, and 4) availability status.
  • A new search option has been added to enable users to enter a PMID and check the status of that publication in the data addition pipeline of NeuroMorpho.Org.
  • A new link has been added to invite users to preview the "Location Visualizer" tool and to send us suggestions and feedback to improve and expand this application.
  • An option has been added to our download functionality enabling users to download the accompanying GPG signature for each file. This ensures the exact identity and version of each file.
  • The FAQ and Quickstart sections have been expanded to provide more information regarding new literature coverage effort and its results.



Version 3.3 released on 09/04/2009 contained 5514 neurons.
What's new in Version 3.3?
  • Three new data sets (222 reconstructions) have been added:
  • The Neuroscience Information Framework (NIF) indicates NeuroMorpho.Org as one of the original resources 'deeply registered' with NIF.
  • Four cells from Dendritica archive (602c, 503c, 913c and 822) removed from the repository. These cells were misclassified duplicates of four cells in Claiborne archive.
  • A new link has been added to homepage to invite users to inform us of available data not yet included in NeuroMorpho.Org.



Version 3.2 released on 3/26/2009 contained 5292 neurons.
What's new in Version 3.2?
  • Three new data sets (788 reconstructions) have been added:
  • Search by "Metadata" modified to include an option for selecting neurons based on a reference's PubMed identification (PMID) number.
  • An additional publication provided in "Terms of use" page to serve as an alternative citation reference for data downloaded from NeuroMorpho.Org.
  • Tools & Links page reorganized and new links to NIF, NeuronLand.Org, and NeuronStudio have been added.
  • The FAQ section has been expanded to provide more information regarding SWC format and soma information in reconstruction files.



Version 3.1 released on 10/01/2008 contained 4508 neurons.
What's new in Version 3.1?
  • Two new data sets (46 reconstructions) have been added:
  • As requested by users "Age scale" has been added to Details page.
  • Browse page re-organized and minor bugs fixed.



Version 3.0 released on 07/15/2008 contained 4462 neurons.
What's new in Version 3.0?
  • Four new data sets (2277 reconstructions) have been added:
  • Search by morphometry modified to include advanced options for selecting neuronal tree types. This addition gives users a choice to specify which neuronal tree(s) they want to target in their search criteria.
  • The information in the "Detailed use stats" page now includes the average daily downloads per cell.



Version 2.1 released on 12/20/2007 contained 1906 neurons.
What's new in Version 2.1?


Version 2.0 released on 10/15/2007 contained 1826 neurons.
What's new in Version 2.0?
  • One new data set (414 reconstructions) has been added:
    • 414 reconstructions (Lewis archive - 262 from Monkey, 152 from Human)
  • "Keyword Search" has been added to allow typing of free text as search criteria.
  • The FAQ and Quickstart sections expanded to reflect new "Keyword Search" functionality - including quick tips and examples.
  • A new option implemented to allow external queries to retrieve data from NeuroMorpho.Org automatically. This feature enables powerful searches through resources designed to mine and integrate neuroscience data.
If you are interested in this function please email us at nmadmin@gmu.edu or neuromorpho@gmail.com.


Version 1.2 released on 08/29/2007 contained 1412 neurons.
What's new in Version 1.2?
  • One new data set (252 reconstruction) has been added:
  • New button has been added in browse page allowing modification of selections and deselecting all previous selections.
  • The FAQ section expanded.
  • Minor editing of the terminology implemented throughout NeuroMorpho.Org to increase semantic consistency.
  • Launch of a new email-based support group for users of L-Measure and related resources, including NeuroMorpho.Org.
If you would like to join, please register for the free email-based support group by sending your e-mail address to nmadmin@gmu.edu or neuromorpho@gmail.com.


Version 1.1 released on 05/04/2007 contained 1160 neurons.
What's new in Version 1.1?
  • Two new data sets (131 reconstructions) have been added:
  • Detailed "Usage Statistics" available in a dedicated page.
The 3D neuron viewer modified to save neurons in NEURON "named segments" format instead of "structure only".


Version 1.0 released on 12/22/2006 contained 1029 neurons.
What's new in Version 1.0?
  • One new data set (29 reconstructions) has been added:
  • 3D neuron viewer has been added. Each neuron can be now be viewed in 3D, rotated, resized and in area projection.
  • 3D neuron viewer also allows to save the neuron in NEURON or GENESIS formats.
  • An animation (growing and rotating image) for each reconstruction has been added.
  • Direct links to the reconstructions and standardization files of each neuron have been added.
  • Search results open in a new window allowing you to go back and refine your search criteria.
  • Images to illustrate common irregularities detected and/or edited in the standardization process have been added.
QuickStart and FAQ pages edited to improve navigation of the site.


Version Beta released on 9/20/2006 contained 1000 neurons.
What's new in Beta Version?
  • One new data set (68 reconstructions) have been added:
  • A new functionality allows the display of the number of hits matching the selected search criteria before retrieving the reconstructions (see details).
  • Addition of links to individual entries in the original (source) labs from the detail pages of single neurons.
  • Addition of "deposition date" and "upload date" for each reconstruction.
  • QuickStart page edited to help better navigation of the site.
  • Available "notes" from data owners have been added for each reconstruction to provide extra information in the detail pages of single neurons.
  • Addition of Usage statistical information.
Additional information on academic affiliation of data owners provided in the Acknowledgements page.


Version Alpha released on 08/01/06 contained 932 neurons. If you have any questions (not answered in the FAQ), or if you have any suggestions, please email us at nmadmin@gmu.edu or neuromorpho@gmail.com.
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