NLMorphologyConverter
(latest version is
0.10.0.dev, 10th January 2016 - 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; Imaris, NeuroZoom;
Eutectics and many others ).
- Currently 25 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 30,000 publicly available morphology data files. (Details of automated 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 Links |
Notes |
|---|---|---|
| Windows (x86 32bit) |
latest dev version NLMorphologyConverter_0_10_0_dev_x86.msi last stable version NLMorphologyConverter_0_9_0_x86.msi |
1) Once the MSI file is downloaded, double click to install.
Choose the
installation directory. 2) Invoke the program from a command window (read manual for program usage) |
| Mac
OSX (x86) |
latest dev version Not currently available last stable version NLMorphologyConverter_0_8_1.zip |
|
| Linux |
NOT
CURRENTLY SUPPORTED |
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 - Amaral, AmiraMesh, ArborVitae, Douglas3D, Eutectics, Genesis, Glasgow, GulyasTree, Korogod, MaxSim, NeuroluidaASC, NeurolucidaASCClassic, NeurolucidaDAT, NeurolucidaDATClassic, NeurolucidaXML, NeuroML, NeuronHOC, NeuroZoom, Nevin, NINDS3D, Oxford, PSICS, SWC. Note recent changes: - the NeuronHOC importer and exporter now incorporate support for NTSCable, SWC2HOC, and many other styles. See --style command line option for more details. - LNeuronAmiraMesh has been renamed as simply AmiraMesh - MorphML has been renamed as NeuroML - NeurolucidaClassic has been renamed as NeurolucidaASCClassic Notes - NeuronJ, and ImarisHDF formats are not included in this list, as they are currently import-only |
For
example
-
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: 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.
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
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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.
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.