Ertunc Erdil

Combining multiple clusterings using similarity graph

Multiple clusterings are produced for various needs and reasons in both distributed and local environments. Combining multiple clusterings into a final clustering which has better overall quality has gained importance recently. It is also expected that the final clustering is novel, robust, and scalable. In order to solve this challenging problem we introduce a new graph-based method. Our method uses the evidence accumulated in the previously obtained clusterings, and produces a very good quality final clustering. The number of clusters in the final clustering is obtained automatically; this is another important advantage of our technique. Experimental test results on real and synthetically generated data sets demonstrate the effectiveness of our new method.

Obtaining better quality final clustering by merging a collection of clusterings

MOTIVATION Clustering methods including k-means, SOM, UPGMA, DAA, CLICK, GENECLUSTER, CAST, DHC, PMETIS and KMETIS have been widely used in biological studies for gene expression, protein localization, sequence recognition and more. All these clustering methods have some benefits and drawbacks. We propose a novel graph-based clustering software called COMUSA for combining the benefits of a collection of clusterings into a final clustering having better overall quality. RESULTS COMUSA implementation is compared with PMETIS, KMETIS and k-means. Experimental results on artificial, real and biological datasets demonstrate the effectiveness of our method. COMUSA produces very good quality clusters in a short amount of time. AVAILABILITY http://www.cs.umb.edu/∼smimarog/comusa CONTACT selim.mimaroglu@bahcesehir.edu.tr

A joint classification and segmentation approach for dendritic spine segmentation in 2-photon microscopy images

Shape priors have been successfully used in challenging biomedical imaging problems. However when the shape distribution involves multiple shape classes, leading to a multimodal shape density, effective use of shape priors in segmentation becomes more challenging. In such scenarios, knowing the class of the shape can aid the segmentation process, which is of course unknown a priori. In this paper, we propose a joint classification and segmentation approach for dendritic spine segmentation which infers the class of the spine during segmentation and adapts the remaining segmentation process accordingly. We evaluate our proposed approach on 2-photon microscopy images containing dendritic spines and compare its performance quantitatively to an existing approach based on nonparametric shape priors. Both visual and quantitative results demonstrate the effectiveness of our approach in dendritic spine segmentation.

ASOD: Arbitrary shape object detection

Arbitrary shape object detection, which is mostly related to computer vision and image processing, deals with detecting objects from an image. In this paper, we consider the problem of detecting arbitrary shape objects as a clustering application by decomposing images into representative data points, and then performing clustering on these points. Our method for arbitrary shape object detection is based on COMUSA which is an efficient algorithm for combining multiple clusterings. Extensive experimental evaluations on real and synthetically generated data sets demonstrate that our method is very accurate and efficient.

An efficient and scalable family of algorithms for combining clusterings

Clustering is the process of grouping objects that are similar, where similarity between objects is usually measured by a distance metric. The groups formed by a clustering method are referred as clusters. Clustering is a widely used activity with multiple applications ranging from biology to economics. Each clustering technique has some advantages and disadvantages. Some clustering algorithms may even require input parameters which strongly affect the result. In most cases, it is not possible to choose the best distance metric, the best clustering method, and the best input argument values for an input data set. Therefore, multiple clusterings can be obtained by several distance metrics, several clustering methods, and several input argument values. And, multiple clusterings can be combined into a new and better quality final clustering. We propose a family of combining multiple clustering algorithms that are memory efficient, scalable, robust, and intuitive. Our new algorithms offer tremendous speed gain and low memory requirements by working at cluster level, while producing very good quality final clusters. Extensive experimental evaluations on some very challenging artificially generated and real data sets from a diverse set of domains establish the usefulness of our methods.

A tool for automatic dendritic spine detection and analysis. Part I: Dendritic spine detection using multi-level region-based segmentation

We propose an image processing pipeline for dendritic spine detection in two-photon fluorescence microscopy images. Spines of interest to neuroscientists often contain high intensity regions with respect to their surroundings. We find such maxima regions using morphological image reconstruction. These regions facilitate a multi-level segmentation algorithm to detect spines. First, watershed algorithm is applied to extract initial rough regions of spines. Then, these results are further refined using a graph-theoretic region-growing algorithm which incorporates segmentation on a sparse representation of image data and hierarchical clustering as a post-processing step. We compare our final results to segmentation results of the domain expert. Our pipeline produces promising segmentation results with practical run times for monitoring streaming data.

Automatic dendritic spine detection using multiscale dot enhancement filters and SIFT features

Statistical characterization of morphological changes of dendritic spines is becoming of crucial interest in the field of neurobiology. Automatic detection and segmentation of dendritic spines promises significant reductions on the time spent by the scientists and reduces the subjectivity concerns. In this paper, we present two approaches for automated detection of dendritic spines in 2-photon laser scanning microscopy (2pLSM) images. The first method combines the idea of dot enhancement filters with information from the dendritic skeleton. The second method learns an SVM classifier by utilizing some pre-labeled SIFT feature descriptors and uses the classifier to detect dendritic spines in new images. For the segmentation of detected spines, we employ a watershed-variational segmentation algorithm. We evaluate the proposed approaches by comparing with manual segmentations of domain experts and the results of a noncommercial software, NeuronIQ. Our methods produce promising detection rate with high segmentation accuracy thus can serve as a useful tool for spine analysis.

Nonparametric joint shape and feature priors for segmentation of dendritic spines

Multimodal shape density estimation is a challenging task in many biomedical image segmentation problems. Existing techniques in the literature estimate the underlying shape distribution by extending Parzen density estimator to the space of shapes. Such density estimates are only expressed in terms of distances between shapes which may not be sufficient for ensuring accurate segmentation when the observed intensities provide very little information about the object boundaries. In such scenarios, employing additional shape-dependent discriminative features as priors and exploiting both shape and feature priors can aid to the segmentation process. In this paper, we propose a segmentation algorithm that uses nonparametric joint shape and feature priors using Parzen density estimator. The joint prior density estimate is expressed in terms of distances between shapes and distances between features. We incorporate the learned joint shape and feature prior distribution into a maximum a posteriori estimation framework for segmentation. The resulting optimization problem is solved using active contours. We present experimental results on dendritic spine segmentation in 2-photon microscopy images which involve a multimodal shape density.

MCMC Shape Sampling for Image Segmentation with Nonparametric Shape Priors

Segmenting images of low quality or with missing data is a challenging problem. Integrating statistical prior information about the shapes to be segmented can improve the segmentation results significantly. Most shape-based segmentation algorithms optimize an energy functional and find a point estimate for the object to be segmented. This does not provide a measure of the degree of confidence in that result, neither does it provide a picture of other probable solutions based on the data and the priors. With a statistical view, addressing these issues would involve the problem of characterizing the posterior densities of the shapes of the objects to be segmented. For such characterization, we propose a Markov chain Monte Carlo (MCMC) sampling-based image segmentation algorithm that uses statistical shape priors. In addition to better characterization of the statistical structure of the problem, such an approach would also have the potential to address issues with getting stuck at local optima, suffered by existing shape-based segmentation methods. Our approach is able to characterize the posterior probability density in the space of shapes through its samples, and to return multiple solutions, potentially from different modes of a multimodal probability density, which would be encountered, e.g., in segmenting objects from multiple shape classes. We present promising results on a variety of data sets. We also provide an extension for segmenting shapes of objects with parts that can go through independent shape variations. This extension involves the use of local shape priors on object parts and provides robustness to limitations in shape training data size.

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.