title: Dendritic spine classification using shape and appearance features based on two-photon microscopy.
abstract: Neuronal morphology and function are highly coupled. In particular, dendritic spine morphology is strongly governed by the incoming neuronal activity. The first step towards understanding the structure-function relationships is to classify spine shapes into the main spine types suggested in the literature. Due to the lack of reliable automated analysis tools, classification is mostly performed manually, which is a time-intensive task and prone to subjectivity.
  
  
  
  We propose an automated method to classify dendritic spines using shape and appearance features based on challenging two-photon laser scanning microscopy (2PLSM) data. Disjunctive Normal Shape Models (DNSM) is a recently proposed parametric shape representation. We perform segmentation of spine images by applying DNSM and use the resulting representation as shape features. Furthermore, we use Histogram of oriented gradients (HOG) to extract appearance features. In this context, we propose a kernel density estimation (KDE) based framework for dendritic spine classification, which uses these shape and appearance features.
  
  
  
  Our shape and appearance features based approach combined with Neural Network (NN) correctly classifies 87.06% of spines on a dataset of 456 spines.
  
  
  
  Our proposed method outperforms standard morphological feature based approaches. Our KDE based framework also enables neuroscientists to analyze the separability of spine shape classes in the likelihood ratio space, which leads to further insights about nature of the spine shape analysis problem.
  
  
  
  Results validate that performance of our proposed approach is comparable to a human expert. It also enable neuroscientists to study shape statistics in the likelihood ratio space.
authors.affiliation: Signal Processing and Information Systems Lab., Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. Electronic address: mughani@bu.edu.
authors.forename: Muhammad Usman
authors.initials: MU
authors.lastname: Ghani
authors.affiliation: Electrical and Computer Engineering Department, University of Utah, Salt Lake City, UT, USA.
authors.forename: Fitsum
authors.initials: F
authors.lastname: Mesadi
authors.affiliation: Signal Processing and Information Systems Lab., Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
authors.forename: Sümeyra Demir
authors.initials: SD
authors.lastname: Kanık
authors.affiliation: Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal. Electronic address: argunsah@hifo.uzh.ch.
authors.forename: Ali Özgür
authors.initials: AÖ
authors.lastname: Argunşah
authors.affiliation: Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal.
authors.forename: Anna Felicity
authors.initials: AF
authors.lastname: Hobbiss
authors.affiliation: Champalimaud Neuroscience Programme, Champalimaud Centre for the Unknown, Lisbon, Portugal. Electronic address: ii2176@cumc.columbia.edu.
authors.forename: Inbal
authors.initials: I
authors.lastname: Israely
authors.affiliation: Biomedical Engineering Department, Faculty of Engineering, Izmir University of Economics, Izmir, Turkey.
authors.forename: Devrim
authors.initials: D
authors.lastname: Ünay
authors.affiliation: Electrical and Computer Engineering Department, University of Utah, Salt Lake City, UT, USA.
authors.forename: Tolga
authors.initials: T
authors.lastname: Taşdizen
authors.affiliation: Signal Processing and Information Systems Lab., Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey.
authors.forename: Müjdat
authors.initials: M
authors.lastname: Çetin
mesh_terms: D000818:Animals; D003627:Data Interpretation, Statistical; D049229:Dendritic Spines / Q000145:classification*; D006624:Hippocampus / Q000166:cytology; D021621:Imaging, Three-Dimensional / Q000379:methods*; D000069550:Machine Learning; D051379:Mice; D018613:Microscopy, Confocal / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D046509:Tissue Culture Techniques
keywords: Classification; Dendritic spines; Disjunctive Normal Shape Model; Histogram of oriented gradients; Kernel density estimation; Microscopy; Shape analysis