Dendritic Spine Shape Analysis: A Clustering Perspective

Functional properties of neurons are strongly coupled with their morphology. Changes in neuronal activity alter morphological characteristics of dendritic spines. First step towards understanding the structure-function relationship is to group spines into main spine classes reported in the literature. Shape analysis of dendritic spines can help neuroscientists understand the underlying relationships. Due to unavailability of reliable automated tools, this analysis is currently performed manually which is a time-intensive and subjective task. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. In this paper, we aim to address these issues by presenting a clustering perspective. In this context, clustering may serve both confirmation of known patterns and discovery of new ones. We perform cluster analysis on two-photon microscopic images of spines using morphological, shape, and appearance based features and gain insights into the spine shape analysis problem. We use histogram of oriented gradients (HOG), disjunctive normal shape models (DNSM), morphological features, and intensity profile based features for cluster analysis. We use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). For all features, this analysis produces 4 clusters and we observe the formation of at least one cluster consisting of spines which are difficult to be assigned to a known class. This observation supports the argument of intermediate shape types.Comment: Accepted for BioImageComputing workshop at ECCV 201

Dendritic spine shape analysis based on two-photon microscopy images

Neuronal morphology and function are highly coupled. In particular, dendritic spine morphology is strongly governed by the incoming neuronal activity. Previously, volumes of dendritic spines have been considered as a primary parameter to study spine morphology and gain insight into structure-function coupling. However, this reductionist approach fails to incorporate the broad spine structure repertoire. First step towards integrating the rich spine morphology information into functional coupling is to classify spine shapes into main spine types suggested in the literature. Due to the lack of reliable automated analysis tools, classification is currently performed manually, which is a time-intensive task and prone to subjectivity. Availability of automated spine shape analysis tools can accelerate this process and help neuroscientists understand underlying structure and function relationship. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. This thesis focuses on morphological, shape, and appearance features based methods to perform dendritic spine shape analysis using both clustering and classification approaches. We apply manifold learning methods for dendritic spine classification and observe that ISOMAP implicitly computes prominent features suitable for classification purposes. We also apply linear representation based approach for spine classification and conclude that sparse representation provides slightly better classification performance. We propose 2D and 3D morphological features based approach for spine shape analysis and demonstrate the advantage of 3D morphological features. We also use a deep learning based approach for spine classification and show that mid-level features extracted from Convolutional Neural Networks (CNNs) perform as well as hand-crafted features. We propose a kernel density estimation (KDE) based framework for dendritic spine classification. We evaluate our proposed approaches by comparing labels assigned by a neuroscience expert. Our KDE based framework also enables neuroscientists to analyze separability of spine shape classes in the likelihood ratio space, which leads to further insights about the nature of the spine shape analysis problem. Furthermore, we also propose a methodology for unsupervised learning and clustering of spine shapes. In particular, we use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). The objective of clustering in this context is two-fold: confirm the hypothesis of some distinct shape classes and discover new natural groups. We observe that although there are many spines which easily fit into the definition of standard shape types (confirming the hypothesis), there are also a significant number of others which do not comply with standard shape types and demonstrate intermediate properties

Visual Clutter Study for Pedestrian Using Large Scale Naturalistic Driving Data

Some of the pedestrian crashes are due to driver’s late or difficult perception of pedestrian’s appearance. Recognition of pedestrians during driving is a complex cognitive activity. Visual clutter analysis can be used to study the factors that affect human visual search efficiency and help design advanced driver assistant system for better decision making and user experience. In this thesis, we propose the pedestrian perception evaluation model which can quantitatively analyze the pedestrian perception difficulty using naturalistic driving data. An efficient detection framework was developed to locate pedestrians within large scale naturalistic driving data. Visual clutter analysis was used to study the factors that may affect the driver’s ability to perceive pedestrian appearance. The candidate factors were explored by the designed exploratory study using naturalistic driving data and a bottom-up image-based pedestrian clutter metric was proposed to quantify the pedestrian perception difficulty in naturalistic driving data. Based on the proposed bottom-up clutter metrics and top-down pedestrian appearance based estimator, a Bayesian probabilistic pedestrian perception evaluation model was further constructed to simulate the pedestrian perception process

Organising a photograph collection based on human appearance

This thesis describes a complete framework for organising digital photographs in an unsupervised manner, based on the appearance of people captured in the photographs. Organising a collection of photographs manually, especially providing the identities of people captured in photographs, is a time consuming task. Unsupervised grouping of images containing similar persons makes annotating names easier (as a group of images can be named at once) and enables quick search based on query by example. The full process of unsupervised clustering is discussed in this thesis. Methods for locating facial components are discussed and a technique based on colour image segmentation is proposed and tested. Additionally a method based on the Principal Component Analysis template is tested, too. These provide eye locations required for acquiring a normalised facial image. This image is then preprocessed by a histogram equalisation and feathering, and the features of MPEG-7 face recognition descriptor are extracted. A distance measure proposed in the MPEG-7 standard is used as a similarity measure. Three approaches to grouping that use only face recognition features for clustering are analysed. These are modified k-means, single-link and a method based on a nearest neighbour classifier. The nearest neighbour-based technique is chosen for further experiments with fusing information from several sources. These sources are context-based such as events (party, trip, holidays), the ownership of photographs, and content-based such as information about the colour and texture of the bodies of humans appearing in photographs. Two techniques are proposed for fusing event and ownership (user) information with the face recognition features: a Transferable Belief Model (TBM) and three level clustering. The three level clustering is carried out at “event” level, “user” level and “collection” level. The latter technique proves to be most efficient. For combining body information with the face recognition features, three probabilistic fusion methods are tested. These are the average sum, the generalised product and the maximum rule. Combinations are tested within events and within user collections. This work concludes with a brief discussion on extraction of key images for a representation of each cluster