L-Neuron Help

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.