Supported file formats¶

NeuroM currently supports the SWC format, the BBP HDF5 formats, and offers experimental support for NeuroLucida .asc files.

SWC¶

The SWC format represents a neuron as a set of trees that are connected to a soma. The neuronal morphology is encoded as a rooted tree of 3D points and the corresponding radii. More information can be found here.

Note

The following information about SWC format concern the standard representation as it has been established in the neuromorpho.org database. This file format is not yet supported by NeuroM, but it may be modified to do so in the future. Currently, NeuroM does not enforce all the semantic restrictions for the different soma representations, and is therefore more permissive.

The points of type “1” that represent the soma, have to be in the beginning of the file. The soma can be represented in one of the following formats:

TypeA: One point soma¶

The soma is represented by its center and a radius that corresponds to the sphere that preserves the surface area of the soma. The center of the soma has as parent ID -1 and all the initial points of the neuronal trees are connected to the soma.

TypeB: Three point soma¶

The soma is represented by three points that correspond to the center of the soma (x, y, z), with parent ID -1, and two diametrically opposite points (x, y-r, z) and (x, y+r, z), where r is the radius of the sphere that preserves the surface area of the soma. The radii of the soma points are not necessarily meaningful, so they can be set to zero. As such, they should not be taken into account in further calculations. The other two of the soma points are connected to the center of the soma, as well as the first points of all the neuronal trees.

TypeC: N - points soma¶

The soma is represented by a set of points. The first point of the soma has as parent ID -1. The other points define a contour of the soma in the maximum cross-section of the x-y plane. The radii of the soma points are not necessarily meaningful, so they can be set to zero. As such, they should not be taken into account in further calculations. The radius of the soma is computed from the equivalent sphere that preserves the surface area of the soma. The first points of all the neuronal trees have as parent one of the soma points.

Tree sections¶

It is not considered a good practice to represent the same section of the tree in different places within a file, but it is not forbidden. The parent ID should always be smaller that the current ID of a point.

Todo

Add reference to SWC paper and more semantic constraints.

Todo

Add semantic constraints on different soma types once these have been determined. For more info on what is to be considered, see neuromorpho.org’s.

HDF5¶

The HDF5 morphology formats developed by the BBP represent the neuron as a tree of sections. The specifications for the two versions of the format cn be found in the HBP morphology format documentation page.

NeuroLucida (experimental)¶

The NeuroLucida .asc file format is commonly used but lacking in an open format specification. NeuroM provides a best-effort experimental reader that parses information equivalent to the two formats above, that is to say, it does not deal with annotations or other meta-data, and is restricted purely to the topological and geometrical features of a neuron, as well as the neurite type information.

Warning

The NeuroLucida parser is experimental. Use at own risk when extracting numerical information. We make no statement as to the correctness of numerical output.

Todo

References and more information?