ImageJ plugin: performs morphometric analyses of structures with branching morphologies (e.g., neuronal dendritic spines, vascular morphology, and primary cilia) using BranchAnalysis2D/3D and adds functionality for Sholl Analysis with AutoSholl.
The compiled version of this algorithm is located under the folder Fiji.app. Sample data sets are also provided in a separate folder labelled dataSets. Instructions on how to use the algorithm is present in the file readme.pdf. Both BranchAnalysis2D/3D and AutoSholl are available for download in this version.
Source code is in the folder sourceCode.
If using AutoSholl, please cite: Srinivasan A, Srinivasan A, Ferland RJ. AutoSholl allows for automation of Sholl analysis independent of user tracing. Journal of Neuroscience Methods 331. doi:10.1016/j.jneumeth.2019.108529
If using BranchAnalysis2D/3D, please cite: Srinivasan A, Muñoz Estrada J, Bourgeois JR, Nalwalk J, Pumiglia K, Sheen V, Ferland RJ. BranchAnalysis2D/3D automates morphometry analyses of branching structures. J Neurosci Methods, 294:1-6, 2018. If using AutoSholl, please cite:
Pubmed: https://www.ncbi.nlm.nih.gov/pubmed/29061345 (BranchAnalysis2D/3D)
Pubmed: https://www.ncbi.nlm.nih.gov/pubmed/31760060 (AutoSholl)