Supported file formats

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

See also

The morphology definitions page for definitions of concepts such as point, section, soma and neurite in NeuroM.

Todo

Complete this section with additional NeuroM specific restrictions on the formats below.

SWC

The SWC format represents a neuron as a tree of 3D points with additional information. More information can be found here.

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?