title: Dendritic tree extraction from noisy maximum intensity projection images in C. elegans.
abstract: BACKGROUND
  Maximum Intensity Projections (MIP) of neuronal dendritic trees obtained from confocal microscopy are frequently used to study the relationship between tree morphology and mechanosensory function in the model organism C. elegans. Extracting dendritic trees from noisy images remains however a strenuous process that has traditionally relied on manual approaches. Here, we focus on automated and reliable 2D segmentations of dendritic trees following a statistical learning framework.
  
  
  METHODS
  Our dendritic tree extraction (DTE) method uses small amounts of labelled training data on MIPs to learn noise models of texture-based features from the responses of tree structures and image background. Our strategy lies in evaluating statistical models of noise that account for both the variability generated from the imaging process and from the aggregation of information in the MIP images. These noisy models are then used within a probabilistic, or Bayesian framework to provide a coarse 2D dendritic tree segmentation. Finally, some post-processing is applied to refine the segmentations and provide skeletonized trees using a morphological thinning process.
  
  
  RESULTS
  Following a Leave-One-Out Cross Validation (LOOCV) method for an MIP databse with available "ground truth" images, we demonstrate that our approach provides significant improvements in tree-structure segmentations over traditional intensity-based methods. Improvements for MIPs under various imaging conditions are both qualitative and quantitative, as measured from Receiver Operator Characteristic (ROC) curves and the yield and error rates in the final segmentations. In a final step, we demonstrate our DTE approach on previously unseen MIP samples including the extraction of skeletonized structures, and compare our method to a state-of-the art dendritic tree tracing software.
  
  
  CONCLUSIONS
  Overall, our DTE method allows for robust dendritic tree segmentations in noisy MIPs, outperforming traditional intensity-based methods. Such approach provides a useable segmentation framework, ultimately delivering a speed-up for dendritic tree identification on the user end and a reliable first step towards further morphological characterizations of tree arborization.
authors.forename: Ayala
authors.initials: A
authors.lastname: Greenblum
authors.forename: Raphael
authors.initials: R
authors.lastname: Sznitman
authors.forename: Pascal
authors.initials: P
authors.lastname: Fua
authors.forename: Paulo E
authors.initials: PE
authors.lastname: Arratia
authors.forename: Meital
authors.initials: M
authors.lastname: Oren
authors.forename: Benjamin
authors.initials: B
authors.lastname: Podbilewicz
authors.affiliation: Department of Biomedical Engineering, Technion - Israel Institute of Technology, 32000, Haifa, Israel. sznitman@bm.technion.ac.il.
authors.forename: Josué
authors.initials: J
authors.lastname: Sznitman
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans / Q000166:cytology*; D003712:Dendrites; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D040542:Mechanotransduction, Cellular; D018613:Microscopy, Confocal / Q000379:methods*