NLMorphologyConverter
Supported Formats and Current Status
Import/Export Key
| Works
with
all tested data |
|
| Disabled/Unimplemented |
3D Formats
| Format
Name |
Import |
Export |
Notes
(see user manual for full list of format-specific command line options) |
Format
Details |
Import & Export Structure Name Control (see.opts) |
Variations
Supported
(styles
or
versions) |
Stores
(D)iameter
or (R)adius |
Structure
which
format
is
capable
of
supporting:
(Y)es/(N)o |
|||||
| Soma?
|
Axon?
|
Dend?
|
Marks? |
Spines? |
Non-Bin? |
||||||||
| Amaral |
|
SPECIFICATION |
- |
1 |
D |
Y |
Y |
Y |
N |
N |
Y |
||
| AmiraMesh |
See "--style"
option. Default: HxLineSet, LNeuron style. |
SPECIFICATION | - |
3 |
R |
N |
N |
Y |
N |
N |
Y |
||
| ArborVitae |
|
SPECIFICATION |
- |
1 |
D |
N |
N |
Y |
N |
N |
N |
||
| Douglas3D |
SPECIFICATION | - |
1 |
D |
Y |
N |
Y |
N |
N |
N |
|||
| Eutectics |
See
"--hintXXX"
options.
Default
axon
substring
is
"ax". |
SPECIFICATION | Y |
1 |
D |
Y |
Y |
Y |
N |
Y* (T) |
N |
||
| Genesis |
|
SPECIFICATION | - |
2 |
D |
Y |
Y |
Y |
N |
N |
Y |
||
| Glasgow |
SPECIFICATION |
- |
1 |
D |
Y |
Y |
Y |
N |
N |
Y |
|||
| GulyasTree |
SPECIFICATION | - |
1 |
D |
N |
N |
Y |
N |
N |
N |
|||
| ImarisHDF |
Export may be
implemented in the future, if practical.. |
SPECIFICATION | - |
1 |
D |
N |
N |
Y |
N |
Y |
Y |
||
| Korogod |
SPECIFICATION | - |
1 |
D |
Y |
Y |
Y |
N |
N |
Y |
|||
| MaxSim |
|
SPECIFICATION | - |
1 |
D |
Y |
Y |
N |
N |
N |
N |
||
| NeurolucidaASC |
See
"--hintXXX"
and
"--style"
options.
Default: Contours with (CellBody) property or named "Cell Body" or "CellBody", or with a name that contains "Soma" will be treated as soma data. |
SPECIFICATION | Y |
6 |
D | Y | Y | Y | Y (G,T,S) |
Y (T) |
Y | ||
| NeurolucidaASCClassic |
old ASC format |
SPECIFICATION | - |
1 |
D |
Y |
Y |
Y |
Y (T) |
N |
N |
||
| NeurolucidaDAT |
See
"--hintXXX"
and
"--style"
options.
Default: Contours with (CellBody) property or named "Cell Body" or "CellBody", or with a name that contains "Soma" will be treated as soma data. |
SPECIFICATION | Y |
2 |
D |
Y | Y | Y | Y (G,T,S) |
Y (T) |
Y | ||
| NeurolucidaDATClassic |
old DAT format |
SPECIFICATION | - |
1 |
D |
Y |
Y |
Y |
Y (T) |
N |
N |
||
| NeurolucidaXML |
See
"--hintXXX"
and
"--style"
options.
Default: Contours with (CellBody) property or named "Cell Body" or "CellBody", or with a name that contains "Soma" will be treated as soma data. |
SPECIFICATION |
Y |
2 |
D | Y | Y | Y | Y (G,T,S) |
Y (T) |
Y | ||
| NeuroML |
Supports
all
versions
from
1.0
to
2.0.
Default
export
version
is
latest
official
release
(1.8.2).
Export
version
using
e.g.
"--versionNumber
1.6" |
SPECIFICATION | Y |
15 |
D |
Y |
Y | Y | Y (G) |
Y (G,T) |
Y |
||
| NeuronHOC |
supports
common
HOC
styles
for
representing
neuron
geometry.
Also
see
"--hintNeuronHOCEntryProc"
option.
(Incorporates
NeuronNTSCable
and
NeuronSWC2HOC
format
support). |
SPECIFICATION |
Y |
8+ |
D |
Y |
Y |
Y |
N |
N |
Y |
||
| NeuroZoom |
See
"--hintXXX"
and
"--style"
options.
Default
structure
substrings:
"axon",
"dend",
"soma"
|
SPECIFICATION |
Y |
2 |
D |
Y |
Y |
Y |
Y (G) |
Y (G) |
Y |
||
| Nevin |
|
SPECIFICATION |
- |
1 |
D |
Y |
N |
Y |
N |
N |
N |
||
| NINDS3D |
|
SPECIFICATION |
- |
1 |
D |
N |
N |
Y |
N |
N |
N |
||
| OntoMorphTabXML |
Not supported.
Could be in
the future, if requested. Based on Neurolucida files, and very similar
to NeurolucidaXML. |
SPECIFICATION | Y |
1 |
D |
Y |
Y |
Y |
Y (G,T,S) |
Y (T) |
Y |
||
| Oxford |
SPECIFICATION | - |
1 |
D |
Y |
N |
Y |
N |
N |
N |
|||
| PSICS |
See "--hintXXX" options. Default structure substrings: "axon", "dend", "soma". XML, but many similarities with SWC format. | SPECIFICATION | Y |
1 |
R |
Y |
Y |
Y |
N |
N |
Y |
||
| SWC |
If necessary, use
"--hintSWCStyle
<style>" option to help importer with non-standardised SWC
import.
See also "--style" option |
SPECIFICATION |
- |
2 |
R |
Y |
Y |
Y |
N |
N |
Y |
||
Notes:
(1) Soma support:
(2) Marker and spine support is classified in to (G)lobal, (T)ree,
and (S)oma. *Eutectics import will identify spine
bases.
2D
Formats
In addition, currently one 2D format is
partially supported (import only, export will not be
implemented).
| Format
Name |
Import |
Export |
Notes |
Format
Details |
Import & Export Structure Name Control (see.opts) |
Variations Supported (styles or versions) | Stores
(D)iameter or (R)adius |
Structure which format is capable of supporting: (Y)es/(N)o | |||||
| Soma?
|
Axon?
|
Dend?
|
Marks? |
Spines? |
Non-Bin? |
||||||||
| NeuronJ
|
Versions
1.0,
1.01,
1.4.0
tested
so
far
(probably
other
versions
will
work
too). |
SPECIFICATION |
Y |
3+ |
-- |
N |
N |
Y |
N |
N |
Y |
||
Note: Correct import of
NeuronJ requires usage of command line options for scaling
position, to convert from pixels to microns (this scaling data is not
included in the original file). The importer sets all z-coordinates to
0.0, and all diameter values to 1.0.
1D Formats
Several older 3D formats have an
associated 1D
format, which retain diameter, length and connectivity data, while
discarding 3D spatial data.
Import algorithms require assignment of
arbitrary spatial properties to the imported
data,
Except for the Bannister format, no
import/export algorithms are currently
implemented. and will only be implemented on request,
or on appearance in the NeuroMorpho.org archive.
| Format
Name |
Import |
Export |
Notes |
Format
Details |
Stores
(D)iameter or (R)adius |
Structure which format is capable of supporting: (Y)es/(N)o | |||||
| Soma?
|
Axon?
|
Dend?
|
Marks? |
Spines? |
Non-Bin? |
||||||
| Bannister |
See
NeuroMorpho:
larkman
archive |
SPECIFICATION | D |
N |
N |
Y |
N |
N (*) |
N |
||
| Douglas1D |
Import and/or export algorithms will be implemented on request. | SPECIFICATION | D |
N |
N |
Y |
N |
N |
N |
||
| GulyasSeg1D |
Import and/or export algorithms will be implemented on request. | SPECIFICATION | D |
N |
N |
Y |
N |
N |
N |
||
| NINDS1D |
Import and/or export algorithms will be implemented on request. | SPECIFICATION | D |
N |
N |
Y |
N |
N |
N |
||
* Bannister format provides a spine
density value for each segment, but not particularly useful from a
morphology point of view.