Here is an example parameter (.prm) input file for LNeuron in which unedited extracted data is used to create virtual cells: unedited.prm
Here is an example parameter file which disregards negative taper values and uses a maximum PK value of 2: edited.prm
See the glossary for descriptions of the parameters used in these files.
This DOS batch file can be used to create and rename virtual cells with sequential random seeds: doswc.bat
Syntax: doswc <.prm input file name without extension> <output file name without extension>
<number of neurons desired> <number of neurons desired> <1>
For example to get 50 cells (seeds 1-50): doswc edited output 50 50 1
To visualize the virtual cells, use the Dendro1, a program which creates dendrograms from SWC files.
Syntax and command line switches for LNeuron.exe:
LNEURON.EXE <options> <input file name>
none (default) output Lviewer VOL file
-v output POV object file
-b output POV blob file
-B output multiple POV blob files
-c output inc files instead of pov files
-d output polyface meshes DXF file
-3 output 3dfaces DXF file
-R output triangles in RAW file
-O output Blob Sculptor BLB file
-V output VRML world file
-X [name] use name.vol as base element
-i link base elements together
-S [num] set string size to num Kbytes
-t [num] set minimum thickness
-r [num] overrule recursion depth
-a [num] overrule angle
-u [num] mutate [num] times
-l show final L-string
-g add ground plane
-L [num] set amount for ~ command
-P [num] set amount for t command
-p [num] limit polygons to [num]
-M use Burke-Marks algorithm
-H use Hillman algorithm
-Y
use Tamori algorithm
-e extend also with Hillman and Tamori algorithm
-T output in Southampton Archive format
-G output in GENESIS format
-N output in NEURON format
-m [name] morphometric measurement of a Southampton Archive file
-2 use Burke's model 2 algorithm
-D use generic developer algorithm
-s [num] set random number generator seed to num
The DOS batch file above runs LNeuron using the –H, -T, and –s switches.