Multi-object segmentation using coupled nonparametric shape and relative pose priors

We present a new method for multi-object segmentation in a maximum a posteriori estimation framework. Our method is motivated by the observation that neighboring or coupling objects in images generate configurations and co-dependencies which could potentially aid in segmentation if properly exploited. Our approach employs coupled shape and inter-shape pose priors that are computed using training images in a nonparametric multi-variate kernel density estimation framework. The coupled shape prior is obtained by estimating the joint shape distribution of multiple objects and the inter-shape pose priors are modeled via standard moments. Based on such statistical models, we formulate an optimization problem for segmentation, which we solve by an algorithm based on active contours. Our technique provides significant improvements in the segmentation of weakly contrasted objects in a number of applications. In particular for medical image analysis, we use our method to extract brain Basal Ganglia structures, which are members of a complex multi-object system posing a challenging segmentation problem. We also apply our technique to the problem of handwritten character segmentation. Finally, we use our method to segment cars in urban scenes

Integration of multimodal data based on surface registration

The paper proposes and evaluates a strategy for the alignment of anatomical and functional data of the brain. The method takes as an input two different sets of images of a same patient: MR data and SPECT. It proceeds in four steps: first, it constructs two voxel models from the two image sets; next, it extracts from the two voxel models the surfaces of regions of interest; in the third step, the surfaces are interactively aligned by corresponding pairs; finally a unique volume model is constructed by selectively applying the geometrical transformations associated to the regions and weighting their contributions. The main advantages of this strategy are (i) that it can be applied retrospectively, (ii) that it is tri-dimensional, and (iii) that it is local. Its main disadvantage with regard to previously published methods it that it requires the extraction of surfaces. However, this step is often required for other stages of the multimodal analysis such as the visualization and therefore its cost can be accounted in the global cost of the process.Postprint (published version

Coupled non-parametric shape and moment-based inter-shape pose priors for multiple basal ganglia structure segmentation

This paper presents a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. In biological tissues, such as the human brain, neighboring structures exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and inter-shape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance (MR) images. We present a set of 2D and 3D experiments as well as a quantitative performance analysis. In addition, we perform a comparison to several existent segmentation methods and demonstrate the improvements provided by our approach in terms of segmentation accuracy

Automated detection of brain abnormalities in neonatal hypoxia ischemic injury from MR images.

We compared the efficacy of three automated brain injury detection methods, namely symmetry-integrated region growing (SIRG), hierarchical region splitting (HRS) and modified watershed segmentation (MWS) in human and animal magnetic resonance imaging (MRI) datasets for the detection of hypoxic ischemic injuries (HIIs). Diffusion weighted imaging (DWI, 1.5T) data from neonatal arterial ischemic stroke (AIS) patients, as well as T2-weighted imaging (T2WI, 11.7T, 4.7T) at seven different time-points (1, 4, 7, 10, 17, 24 and 31 days post HII) in rat-pup model of hypoxic ischemic injury were used to assess the temporal efficacy of our computational approaches. Sensitivity, specificity, and similarity were used as performance metrics based on manual ('gold standard') injury detection to quantify comparisons. When compared to the manual gold standard, automated injury location results from SIRG performed the best in 62% of the data, while 29% for HRS and 9% for MWS. Injury severity detection revealed that SIRG performed the best in 67% cases while 33% for HRS. Prior information is required by HRS and MWS, but not by SIRG. However, SIRG is sensitive to parameter-tuning, while HRS and MWS are not. Among these methods, SIRG performs the best in detecting lesion volumes; HRS is the most robust, while MWS lags behind in both respects

Thermo-visual feature fusion for object tracking using multiple spatiogram trackers

In this paper, we propose a framework that can efficiently combine features for robust tracking based on fusing the outputs of multiple spatiogram trackers. This is achieved without the exponential increase in storage and processing that other multimodal tracking approaches suffer from. The framework allows the features to be split arbitrarily between the trackers, as well as providing the flexibility to add, remove or dynamically weight features. We derive a mean-shift type algorithm for the framework that allows efficient object tracking with very low computational overhead. We especially target the fusion of thermal infrared and visible spectrum features as the most useful features for automated surveillance applications. Results are shown on multimodal video sequences clearly illustrating the benefits of combining multiple features using our framework

Model and Appearance Based Analysis of Neuronal Morphology from Different Microscopy Imaging Modalities

The neuronal morphology analysis is key for understanding how a brain works. This process requires the neuron imaging system with single-cell resolution; however, there is no feasible system for the human brain. Fortunately, the knowledge can be inferred from the model organism, Drosophila melanogaster, to the human system. This dissertation explores the morphology analysis of Drosophila larvae at single-cell resolution in static images and image sequences, as well as multiple microscopy imaging modalities. Our contributions are on both computational methods for morphology quantification and analysis of the influence of the anatomical aspect. We develop novel model-and-appearance-based methods for morphology quantification and illustrate their significance in three neuroscience studies. Modeling of the structure and dynamics of neuronal circuits creates understanding about how connectivity patterns are formed within a motor circuit and determining whether the connectivity map of neurons can be deduced by estimations of neuronal morphology. To address this problem, we study both boundary-based and centerline-based approaches for neuron reconstruction in static volumes. Neuronal mechanisms are related to the morphology dynamics; so the patterns of neuronal morphology changes are analyzed along with other aspects. In this case, the relationship between neuronal activity and morphology dynamics is explored to analyze locomotion procedures. Our tracking method models the morphology dynamics in the calcium image sequence designed for detecting neuronal activity. It follows the local-to-global design to handle calcium imaging issues and neuronal movement characteristics. Lastly, modeling the link between structural and functional development depicts the correlation between neuron growth and protein interactions. This requires the morphology analysis of different imaging modalities. It can be solved using the part-wise volume segmentation with artificial templates, the standardized representation of neurons. Our method follows the global-to-local approach to solve both part-wise segmentation and registration across modalities. Our methods address common issues in automated morphology analysis from extracting morphological features to tracking neurons, as well as mapping neurons across imaging modalities. The quantitative analysis delivered by our techniques enables a number of new applications and visualizations for advancing the investigation of phenomena in the nervous system

Constrained snake vs. conventional snake for carotid ultrasound automated IMT measurements on multi-center data sets

Accurate intima-media thickness (IMT) measurement of the carotid artery from minimal plaque ultrasound images is a relevant clinical need, since IMT increase is related to the progression of atherosclerosis. In this paper, we describe a novel dual snake-based model for the high-performance carotid IMT measurement, called Carotid Measurement Using Dual Snakes (CMUDS). Snakes (which are deformable contours) adapt to the lumen-intima (LI) and media-adventitia (MA) interfaces, thus enabling the IMT computation as distance between the LI and MA snakes. However, traditional snakes might be unable to maintain a correct distance and in some spatial location along the artery, it might even collapse between them or diverge. The technical improvement of this work is the definition of a dual snake-based constrained system, which prevents the LI and MA snakes from collapsing or bleeding, thus optimizing the IMT estimation. The CMUDS system consists of two parametric models automatically initialized using the far adventitia border which we automatically traced by using a previously developed multi-resolution approach. The dual snakes evolve simultaneously and are constrained by the distances between them, ensuring the regularization of LI/MA topology. We benchmarked our automated CMUDS with the previous conventional semi-automated snake system called Carotid Measurement Using Single Snake (CMUSS). Two independent readers manually traced the LIMA boundaries of a multi-institutional, multi-ethnic, and multi-scanner database of 665 CCA longitudinal 2D images. We evaluated our system performance by comparing it with the gold standard as traced by clinical readers. CMUDS and CMUSS correctly processed 100% of the 665 images. Comparing the performance with respect to the two readers, our automatically measured IMT was on average very close to that of the two readers (IMT measurement biases for CMUSS was equal to −0.011 ± 0.329 mm and −0.045 ± 0.317 mm, respectively, while for CMUDS, it was 0.030 ± 0.284 mm and −0.004 ± 0.273 mm, respectively). The Figure-of-Merit of the system was 98.5% and 94.4% for CMUSS, while 96.0% and 99.6% for CMUDS, respectively. Results showed that the dual-snake system CMUDS reduced the IMT measurement error accuracy (Wilcoxon, p < 0.02) and the IMT error variability (Fisher, p < 3 × 10−2). We propose the CMUDS technique for use in large multi-centric studies, where the need for a standard, accurate, and automated IMT measurement technique is require

Coercive Region-level Registration for Multi-modal Images

We propose a coercive approach to simultaneously register and segment multi-modal images which share similar spatial structure. Registration is done at the region level to facilitate data fusion while avoiding the need for interpolation. The algorithm performs alternating minimization of an objective function informed by statistical models for pixel values in different modalities. Hypothesis tests are developed to determine whether to refine segmentations by splitting regions. We demonstrate that our approach has significantly better performance than the state-of-the-art registration and segmentation methods on microscopy images.Comment: This work has been accepted to International Conference on Image Processing (ICIP) 201