Automated neuron tracing using probability hypothesis density filtering

ImageJ plugin

Radojević, M., & Meijering, E. (2017). Automated neuron tracing using probability hypothesis density filtering. Bioinformatics, 33(7), 1073-1080.

doi.org/10.1093/bioinformatics/btw751

Usage

• copy phd_.jar and vess_.jar to ImageJ's plugins directory
• Open ImageJ > Plugins > BrainCadet > PHD
• select file (works with 8bit images and image stacks, dark background)
• enter values in the parameter menu

ImageJ macro for batch processing

• parameter grid
• possibility to use the parameter grid to process all existing *.tif 8bit images in given directory
• ij macro: ij-macro/run_phd.ijm
• test case (~/test/ directory with run_phd.ijm and img.tif), example call:

#!java

java -Xmx4g -jar ~/ImageJ/ij.jar -ijpath ~/ImageJ/plugins/ -batch ~/test/run_phd.ijm ~/test/