title: MDL constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images.
abstract: 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.
authors.affiliation: Jonsson Engineering Center, Center for Subsurface Sensing & Imaging Systems, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
authors.forename: Xiaosong
authors.initials: X
authors.lastname: Yuan
authors.forename: Joshua T
authors.initials: JT
authors.lastname: Trachtenberg
authors.forename: Steve M
authors.initials: SM
authors.lastname: Potter
authors.forename: Badrinath
authors.initials: B
authors.lastname: Roysam
mesh_terms: D022126:Access to Information; D000465:Algorithms; D001331:Automation; D003116:Color; D016208:Databases, Factual; D003712:Dendrites; D049229:Dendritic Spines; D005188:False Negative Reactions; D005453:Fluorescence; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal / Q000379:methods*; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods*; D009474:Neurons / Q000166:cytology*; D012984:Software; D012985:Software Design