Neuronland

NLMorphologyConverter   (current version is  0.9.0,   17th October 2010   - release notes HERE -)

A simple command-line utility for converting between most biological neuron 3D morphology formats (including: all Neurolucida formats; SWC; MorphML; NeuronHOC; Genesis; NeuroZoom; Eutectics and many others ).

  • Currently 21 different morphology file formats fully or partially supported. (Details of file format support status HERE.)
  • 50+ file format variations (different format versions or data layout styles) supported.
  • Automatic detection of input file format.
  • Faithful reproduction of output file formatting.
  • Many command line options for manipulating data prior to export.  (User manual can be found HERE.)
  • Intensively tested using over 13,000 publicly available morphology data files. (Details of testing regime HERE.)
All users are advised to check the generated output data before making further use of it (the NLMorphologyViewer is usually a suitable tool). Although import and export algorithms are well tested and generally reliable, there might be special cases which are not imported correctly - e.g. for certain file formats original data occasionally contains errors which the importer may not recognize, or be able to deal with correctly; other formats are not sufficiently strictly specified that correct import can be guaranteed under all circumstances.


Download and Install
OS
 Download Link
 Size
 Notes
Windows
(x86 32bit)
 		NLMorphologyConverter_0_9_0_x86.msi



 		~2.1MB
 1) Once the MSI file is downloaded, double click to install. Choose the installation directory.
2) IMPORTANT: the installation path is no longer appended to the system PATH environment variable. You will have to add it manually, or invoke the command using its full path.  (This will be fixed in a future version.)
Mac OSX
 (PPC, x86) 		NLMorphologyConverter_0_9_0_osx.zip
(available shortly)
1) Mac OSX version.  Universal binary (compiled on OSX 10.5.6. x86). Targetting 10.4 SDK
2) To install, just unzip and copy the executable file to a suitable location.
Linux





NOT CURRENTLY SUPPORTED


Usage

The simplest way to use the converter is like this -

NLMorphologyConverter  <input_file_name> <output_file_name> <output_format_name>

<input_file_name> the file you wish to convert (the format will be automatically detected, if it is supported)
<output_file_name> the output file you wish to generate
<output_format_name>
 one of the following format identifiers to specify the output file format -

ArborVitae, Douglas3D, Eutectics, Genesis, Glasgow, GulyasTree, LNeuronAmiraMesh, MaxSim, MorphML, NeuroluidaASC, NeurolucidaClassic, NeurolucidaDAT, NeurolucidaXML, NeuronHOC, NeuroZoom, Nevin, NINDS3D, Oxford, PSICS, SWC.

(Note: the NeuronHOC importer and exporter now incorporate support for NTSCable, SWC2HOC, and many other styles. See --style command line option for more details.)

For example -

NLMorphologyConverter neuron01.swc neuron01.asc NeurolucidaASC

will convert an SWC format file into a NeurolucidaASC format file.

Since version 0.6.0, additional command line options have been introduced to enable the user to (1) view more information about the imported file, and (2) give more control over the exported data.


More information:

Contact and Feedback

Although heavy automated testing has resulted in quite a stable application, there are undoubtably some bugs left. In particular, the quantity of publicly available data is quite limited for many morphology formats, and various special cases of data layout may not have been tested.

Any feedback would be appreciated. The following would be particularly useful:

  • Details of any installation problems.
  • Suggestions for improvements.
  • Information about (and specifications for) any morphology formats which are not yet supported.
  • Sample data files (any format) which cause the application to crash.
  • Sample data files (any format) which fail to load (i.e. are not automatically detected properly).
  • Sample data files (any format) which are not converted correctly.
  • Any other bugs encountered.

If you have any questions or wish to give some feedback then please contact:     feedback AT neuronland.org  (replace  " AT " with "@")

Alternatively, use the NLMorphologyConverter mailing list:

To Subscribe:            nlmorphologyconverter-subscribe@yahoogroups.co.uk
To Unsubscribe:        nlmorphologyconverter-unsubscribe@yahoogroups.co.uk
To Send a message:   nlmorphologyconverter@yahoogroups.co.uk

This mailing list is fully moderated.

Thanks

Many thanks to the creators of, and contributors to, all the morphology data archives which have been used to test this software.
Many thanks also to those who have reported bugs, and to those who have provided additional data for testing.

Software License
This software is licensed for non-commercial use only. Permission is granted for this software to be freely copied and redistributed provided that the files contained in the distribution are not modified in any way.  All copyright and license information must be retained.

No Warranty

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. THERE IS NO WARRANTY FOR THE SOFTWARE.