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? |
||||||||
| 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 |
|||
| LNeuronAmiraMesh |
SPECIFICATION | - |
1 |
R |
N |
N |
Y |
N |
N |
Y |
|||
| MaxSim |
|
SPECIFICATION | - |
1 |
D |
Y |
Y |
N |
N |
N |
N |
||
| MorphML |
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 |
||
| 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 | ||
| NeurolucidaClassic |
|
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 | ||
| 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 |
1 |
D | Y | Y | Y | Y (G,T,S) |
Y (T) |
Y | ||
| NeuronHOC |
Generic
HOC
parser disabled pending fixes. Still supports 'swc2hoc' and 'ntscable' |
supports
common
HOC
styles
for
representing
neuron
geometry. Also see
"--hintNeuronHOCEntryProc" option. (Incorporates NeuronNTSCable and NeuronSWC2HOC
format
support). NEW IMPORT FUNCTIONALITY DISABLED PENDING FIXES |
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 |
||
| 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,
NeuronJ, is partially supported (import only, export will not be
implemented). Correct import of
this format 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.
| 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 |
||
1D Formats
Several 3D formats have an associated 1D
format, which retains diameter, length and connectivity data, while
discarding 3D spatial data. No import/export algorithms are currently
implemented. Import algorithms will
require assignment of arbitrary spatial properties to the imported
data, and will only be implemented on request. Export could be easily implemented as a
simplification of
the corresponding 3D export algorithm, and will also only be
implemented on
request.
| 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? |
||||||
| 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 |
||