Version 5.7 - Released: 05/30/2014 - Content: 11335 neurons
   Home > What's new?

What's new in version 5.7 ?
  • 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.



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

What's new in version 5.6 ?
  • 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, PreBötzinger 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 Objective type has been added: Air.
  • 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.
© Copyright 2006-2014   George Mason University All Rights Reserved.   Link Graphic to NIF website