Radojević, M., & Meijering, E. (2017). Automated neuron tracing using probability hypothesis density filtering. Bioinformatics, 33(7), 1073-1080.
doi.org/10.1093/bioinformatics/btw751
- 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
- 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/