New 3D neuron morphology data format conversion utility....

[marmite]

Hello,

In the interests of making use of some old code, I have recently put together a little command-line utility which is designed to convert between most of the existing 3D neuron morphology formats. Including Neurolucida (both formats), SWC, Eutectics, Nevin, Neuron (2 varieties so far - SWC2HOC, and NTSCable output), Genesis, plus a good selection of more obscure formats.

Format support is bi-directional, i.e. can both import and export in any of the supported formats (subject to the limitations of the type of data supported by the format).

Initial public release is Version 0.1.0. and available from http://www.neuronland.org

Features
* 16 different formats are currently supported (though some have isssues, limitations).
* Automatic detection of the input file format.
* Faithful reproduction of output formats (including various formatting quirks).

Issues
* MorphML support is completely disabled while I iron out some bugs.
* Several formats have conversion problems for some of the tested files, but often work ok (please refer to website for details)
* For several formats, there is a very limited (sometimes zero) amount of publicly available data, and the converter has not been as well-tested as i would like.

Please note that is is a very early release of the software. Although i will hopefuly soon provide both linux and mac distributions, for the moment the release is windows only.

Any feedback (preferably via the email address given on the website) would be welcome, especially examples of data files which do not work, installation problems, and any other bug reports!

Regards

James

[ted]

If you want others to try your software, it might be a good idea to give them some explicit
reasons for trust. Thoughtful individuals will have reservations about installing compiled code
from an unknown source on any machine, let alone on a machine that runs a version of MS
Windows, "the hacker's favorite target OS."

[marmite]

Perfectly reasonable point

Of course, if anyone does feel that they would like to use the software, and do have any concerns about doing so, they can contact me directly at the email address given on the website. I am quite happy to answer any questions in private email, and quite happy to convert a file or two (into a format of their choice), as proof of functionality. If anyone can see a worthwhile use for the software in their work, I hope that they will contact me.


Regards,

James

[marmite]

Just an update for those who found the converter via this forum...

The NLMorphologyConverter has now made it to version 0.4.0.

A lot of bugs have been fixed over the last month, though there is still some work to do to get all formats equally well supported, and to fix the remaining known bugs.

Full details of the current status can be found at http://www.neuronland.org, but the main points to note are -

* Both Windows and Mac OSX versions are now available.
* A Linux (x86) version is actively being worked on, and should be available with version 0.5.0 (hopefully by the end of the April, time permitting).
* The converter is now subjected to an intensive automated testing regime using thousands of morphology data files obtained from various publicly available morphology archives (in particular the excellent neuromorpho archive - http://www.neuromorpho.org).

Thanks to those from whom i have received suggestions/feedback. Any more would be welcome.

James

[marmite]

A new version of the morphology file format converter has been released.

This is a full windows/mac/linux release.

Main changes since version 0.4.0 -
* MorphML support re-activated.
* NeuronJ support added.
* New command line options to view neuron statistics and control exported data.
* Many bug fixes (all but 1 of 5000+ tested files now pass the automated testing regime).
* Still some import issues for certain non-standardized SWC files. Will hopefully be resolved for the next release.

See the full release notes here -> http://www.neuronland.org/versionHistory.html

I would like to encourage all interested parties to subscribe to the mailing list in order to receive future notification of new releases (details given here -> http://www.neuronland.org/).

James