Branch-Generator

Generates 2-way dendritic branches with variable branching angle and branch lengths as well as linear branches. A simple single point soma wull be included as well.

Build

• Clone this repository
• Open in IntelliJ IDEA
• Build->Build Project in IntelliJ IDEA

Alternative Build (Ant)

• Navigate to $CWD
• Type ant in $CWD Note that it might be necessary to edit build.properties in $CWD.

Alternative Build (Kotlinc)

• Navigaegt to $CWD
• Type kotlinc src/BranchGenerator.kt -include-runtime -d Branch-Generator.jar

Usage (constant radii)

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.

Usage (tapering)

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

Usage (Rall)

According to Rall and Rinzel 1973 the sum of radii of child branches at each branching point raised to the power of 3/2 must equal the parent branch radius also raised to the power of 3/2 (Rall's 3/2 power rule). The user can specify these radii with method Rall.

Usage (linear)

The following command will generate an unbranched cable with length 10, start radius of 2 and end radius of 1. There will be inserted 10 points leading to 9 segments respectively edges:

java -jar Branch-Generator.jar --method linear --filename unbranched --l0 10 --r0 2 --r1 1 --n 10.

Usage (bended)

Create bended linear cable with length 10 and bending angle 60 degrees java -jar Branch-Generator.jar --method bende --angle 60 --length 10.

Options

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

      3. RALL: --r0 RADIUS_PARENT_BRANCHR --r1 RADIUS_LEFT_CHILD --r2 RADIUS_RIGHT_CHILD

      4. LINEAR: --r0 START_RADIUS --r1 END_RADIUS --l0 LINEAR_CABLE_LENGTH --n NUM_POINTS 

Postprocessing

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)"

Geometries

Two way branch geometries are stored here and linear cables there.

References

• Rall W, Rinzel J. Branch input resistance and steady attenuation for input to one branch of a dendritic neuron model. Biophys J. 1973;13(7):648-687. doi:10.1016/S0006-3495(73)86014-X
• Article in Scholarpedia