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Neuromorpho : Graphical Database neuronal morphologies in SWC format

Is Neuromorpho scientific repository that offers the possibility to download more of 6.000 3D digital reconstructions, neuronal morphologies.

Has inputs 58 laboratories who bring their models 45 brain regions different.

The models can be downloaded in two different formats that contain the information necessary for the reconstruction three-dimensional morphologies species (Human, mouse, elephant, …)

NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications. It contains contributions from over 50 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. To date, NeuroMorpho.Org is the largest collection of publicly accessible 3D neuronal reconstructions and associated metadata.

Neuromorpho / neuroMorpho / index.jsp

The search in the database can be performed under different criteria, as the species, brain region, the type of neuron or the laboratory that has been digitized.

Incorporates a viewer that performs a three-dimensional reconstruction of the neuron selected.

Downloading files

You can download the files in SWF format from the pages of the repository. To do this we select the search criteria you wish (Laboratory, brain region, neuron type of the species).

The search result will give us a list of the morphologies that meet the specified criteria.

Morphologies will select those we want to download. If you select the root of the tree, automatically be marked all that are below.

After the selection, on the same page at the bottom, we start the download by clicking on the button “Get SWC files“.

Formato SWC

The formato SWC we offer a plain text file with different fields.

The three dimensional structure of a neuron can be represented in a SWC format (Cannon et al., 1998). SWC is a simple Standardized format. Each line has 7 fields encoding data for a single neuronal compartment:

The file contains three-dimensional information allows reconstructing 3D polygons (coupling the cylinder cones) that diagram the spatial position of the nucleus of the neuron (sum). the axon and dendrites (basal and apical). Besides the spatial position of these points, for each of them is the average radius of the branch neuronal, together with information that allows “order” or establish continuity of the vertices of the polygon.

The first part of the file contains a header with general information of the authors, laboratory conditions for obtaining digitized. The lines of the text file that begin with the symbol “#” Entries MUST be understood as.

Here we find the description of the morphology. For each point a line of text use (numbered sequentially increasing) and then some numeric fields.

The order of the fields in each line is:

  • An integer that identifies the vertex (labeled with different numbers for each point)
  • Vertex Type (indicates which type of structure belongs)
    0 – Indefinite
    1 – Sum
    2 – Axon
    3 – Dendrite basal
    4 – Apical dendrite
  • Vertex coordinate it
  • Coordinate of the vertex
  • Z coordinate of the vertex
  • Radio via section
  • Previous vertex in the structure (node priest)

Each node of the structure has a single parent node, the first node has a value “-1” in the field. The index of the parent node is always less than the index of the child node.

The core can be a single point, or may consist of more than one.