Generates 2-way dendritic branches with variable branching angle and branch lengths starting from a simple point soma. Note: If you had previously a local copy (clone) of this repository, this is not further maintained. The repository now reflects a clean from scratch code base.
- Clone this repository
- Open in IntelliJ IDEA
Build->Build Projectin IntelliJ IDEA
- Navigate to
$CWD - Type
antin$CWDNote that it might be necessary to edit build.properties in$CWD.
java -jar Branch-Generator.jar --method constant --filename test --l0 100 --l1 100 --l2 100 --d0 10 --angle 90 --n 2
This will generate a SWC file: Y-branch_angle=90.swc with parent or root branch
of length 100, child branches (left and right) of length 100. Branching angle is 90°.
Parent branch's diameter is set to 10 corresponding length units and the branches
taper off at the branching point by a factor of 2 and the dendrites by a factor of
5 with two points per branch. Additionally parameters to adjust can be displaye via:
java -jar Y-Generator.jar.
java -jar Branch-Generator.jar --method tapering --filename test --l0 100 --l1 100 --l2 100 --d0 10 --angle 90 --n 2 --d1 5 --d2 5
For explanation of command line arguments, execute: java -jar Y-Generator.jar:
Usage:
Branch_Generator_jar/Branch-Generator --method CONSTANT,TAPERING --filename FILENAME --angle ANGLE --n NUM_POINTS
Additional options for the methods:
1. CONSTANT: --d0 DIAMETER, --l0 PARENT_LENGTH -l1 RIGHT_CHILD_LENGTH -l2 LEFT_CHILD_LENGTH
2. TAPERING: --d1 DIAMETER_RIGHT_CHILD_END_POINT --d2 DIAMETER_LEFT_CHILD_END_POINT
The generated SWC file contains the 1D line graph geometry and can be
converted to a full 3D geometry with embedded ER (scale factor 0.5 for example and 2 refinements)
in the UGX file format by invoking the following ugshell call:
../bin/ugshell -call ../bin/ugshell -call "create_two_way_branch_from_swc(\"test_angle=90.0.swc\", 0.5, 2)"