MDL Constrained 3-D Grayscale Skeletonization Algorithm for Automated Extraction of Dendrites and Spines from Fluorescence Confocal Images

This paper presents a method for improved automatic delineation of dendrites and spines from three-dimensional (3-D) images of neurons acquired by confocal or multi-photon fluorescence microscopy. The core advance presented here is a direct grayscale skeletonization algorithm that is constrained by a structural complexity penalty using the minimum description length (MDL) principle, and additional neuroanatomy-specific constraints. The 3-D skeleton is extracted directly from the grayscale image data, avoiding errors introduced by image binarization. The MDL method achieves a practical tradeoff between the complexity of the skeleton and its coverage of the fluorescence signal. Additional advances include the use of 3-D spline smoothing of dendrites to improve spine detection, and graph-theoretic algorithms to explore and extract the dendritic structure from the grayscale skeleton using an intensity-weighted minimum spanning tree (IW-MST) algorithm. This algorithm was evaluated on 30 datasets organized in 8 groups from multiple laboratories. Spines were detected with false negative rates less than 10% on most datasets (the average is 7.1%), and the average false positive rate was 11.8%. The software is available in open source form.