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

High-quality Image Restoration from Partial Mixed Adaptive-Random Measurements

A novel framework to construct an efficient sensing (measurement) matrix, called mixed adaptive-random (MAR) matrix, is introduced for directly acquiring a compressed image representation. The mixed sampling (sensing) procedure hybridizes adaptive edge measurements extracted from a low-resolution image with uniform random measurements predefined for the high-resolution image to be recovered. The mixed sensing matrix seamlessly captures important information of an image, and meanwhile approximately satisfies the restricted isometry property. To recover the high-resolution image from MAR measurements, the total variation algorithm based on the compressive sensing theory is employed for solving the Lagrangian regularization problem. Both peak signal-to-noise ratio and structural similarity results demonstrate the MAR sensing framework shows much better recovery performance than the completely random sensing one. The work is particularly helpful for high-performance and lost-cost data acquisition.Comment: 16 pages, 8 figure

Detection of curved lines with B-COSFIRE filters: A case study on crack delineation

The detection of curvilinear structures is an important step for various computer vision applications, ranging from medical image analysis for segmentation of blood vessels, to remote sensing for the identification of roads and rivers, and to biometrics and robotics, among others. %The visual system of the brain has remarkable abilities to detect curvilinear structures in noisy images. This is a nontrivial task especially for the detection of thin or incomplete curvilinear structures surrounded with noise. We propose a general purpose curvilinear structure detector that uses the brain-inspired trainable B-COSFIRE filters. It consists of four main steps, namely nonlinear filtering with B-COSFIRE, thinning with non-maximum suppression, hysteresis thresholding and morphological closing. We demonstrate its effectiveness on a data set of noisy images with cracked pavements, where we achieve state-of-the-art results (F-measure=0.865). The proposed method can be employed in any computer vision methodology that requires the delineation of curvilinear and elongated structures.Comment: Accepted at Computer Analysis of Images and Patterns (CAIP) 201

Morphological feature extraction for statistical learning with applications to solar image data

Abstract: Many areas of science are generating large volumes of digital image data. In order to take full advantage of the high-resolution and high-cadence images modern technology is producing, methods to automatically process and analyze large batches of such images are needed. This involves reducing complex images to simple representations such as binary sketches or numerical summaries that capture embedded scientific information. Using techniques derived from mathematical morphology, we demonstrate how to reduce solar images into simple ‘sketch ’ representations and numerical summaries that can be used for statistical learning. We demonstrate our general techniques on two specific examples: classifying sunspot groups and recognizing coronal loop structures. Our methodology reproduces manual classifications at an overall rate of 90 % on a set of 119 magnetogram and white light images of sunspot groups. We also show that our methodology is competitive with other automated algorithms at producing coronal loop tracings and demonstrate robustness through noise simulations. 2013 Wile

Bidirectional-Convolutional LSTM Based Spectral-Spatial Feature Learning for Hyperspectral Image Classification

This paper proposes a novel deep learning framework named bidirectional-convolutional long short term memory (Bi-CLSTM) network to automatically learn the spectral-spatial feature from hyperspectral images (HSIs). In the network, the issue of spectral feature extraction is considered as a sequence learning problem, and a recurrent connection operator across the spectral domain is used to address it. Meanwhile, inspired from the widely used convolutional neural network (CNN), a convolution operator across the spatial domain is incorporated into the network to extract the spatial feature. Besides, to sufficiently capture the spectral information, a bidirectional recurrent connection is proposed. In the classification phase, the learned features are concatenated into a vector and fed to a softmax classifier via a fully-connected operator. To validate the effectiveness of the proposed Bi-CLSTM framework, we compare it with several state-of-the-art methods, including the CNN framework, on three widely used HSIs. The obtained results show that Bi-CLSTM can improve the classification performance as compared to other methods

Automated Discrimination of Pathological Regions in Tissue Images: Unsupervised Clustering vs Supervised SVM Classification

Recognizing and isolating cancerous cells from non pathological tissue areas (e.g. connective stroma) is crucial for fast and objective immunohistochemical analysis of tissue images. This operation allows the further application of fully-automated techniques for quantitative evaluation of protein activity, since it avoids the necessity of a preventive manual selection of the representative pathological areas in the image, as well as of taking pictures only in the pure-cancerous portions of the tissue. In this paper we present a fully-automated method based on unsupervised clustering that performs tissue segmentations highly comparable with those provided by a skilled operator, achieving on average an accuracy of 90%. Experimental results on a heterogeneous dataset of immunohistochemical lung cancer tissue images demonstrate that our proposed unsupervised approach overcomes the accuracy of a theoretically superior supervised method such as Support Vector Machine (SVM) by 8%

High-resolution optical and SAR image fusion for building database updating

This paper addresses the issue of cartographic database (DB) creation or updating using high-resolution synthetic aperture radar and optical images. In cartographic applications, objects of interest are mainly buildings and roads. This paper proposes a processing chain to create or update building DBs. The approach is composed of two steps. First, if a DB is available, the presence of each DB object is checked in the images. Then, we verify if objects coming from an image segmentation should be included in the DB. To do those two steps, relevant features are extracted from images in the neighborhood of the considered object. The object removal/inclusion in the DB is based on a score obtained by the fusion of features in the framework of Dempster–Shafer evidence theory