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MDL Constrained 3-D Grayscale Skeletonization Algorithm for Automated Extraction of Dendrites and Spines from Fluorescence Confocal Images
| Content Provider | PubMed Central |
|---|---|
| Author | Yuan, Xiaosong Trachtenberg, Joshua T. Potter, Steve M. Badrinath, Roysam |
| 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. |
| Related Links | http://dx.doi.org/10.1007/s12021-009-9057-y |
| Ending Page | 232 |
| Page Count | 20 |
| Starting Page | 213 |
| File Format | |
| ISSN | 15392791 |
| e-ISSN | 15590089 |
| Journal | Neuroinformatics |
| Issue Number | 4 |
| Volume Number | 7 |
| Language | English |
| Publisher Date | 2009-12-01 |
| Access Restriction | Open |
| Subject Keyword | Software Neuroscience(all) Information Systems Research in Higher Education |
| Content Type | Text |
| Resource Type | Article |
| Subject | Neuroscience Information Systems Software |
