Unbiased Shape Compactness for Segmentation

We propose to constrain segmentation functionals with a dimensionless, unbiased and position-independent shape compactness prior, which we solve efficiently with an alternating direction method of multipliers (ADMM). Involving a squared sum of pairwise potentials, our prior results in a challenging high-order optimization problem, which involves dense (fully connected) graphs. We split the problem into a sequence of easier sub-problems, each performed efficiently at each iteration: (i) a sparse-matrix inversion based on Woodbury identity, (ii) a closed-form solution of a cubic equation and (iii) a graph-cut update of a sub-modular pairwise sub-problem with a sparse graph. We deploy our prior in an energy minimization, in conjunction with a supervised classifier term based on CNNs and standard regularization constraints. We demonstrate the usefulness of our energy in several medical applications. In particular, we report comprehensive evaluations of our fully automated algorithm over 40 subjects, showing a competitive performance for the challenging task of abdominal aorta segmentation in MRI.Comment: Accepted at MICCAI 201

Affine Registration of label maps in Label Space

Two key aspects of coupled multi-object shape\ud analysis and atlas generation are the choice of representation\ud and subsequent registration methods used to align the sample\ud set. For example, a typical brain image can be labeled into\ud three structures: grey matter, white matter and cerebrospinal\ud fluid. Many manipulations such as interpolation, transformation,\ud smoothing, or registration need to be performed on these images\ud before they can be used in further analysis. Current techniques\ud for such analysis tend to trade off performance between the two\ud tasks, performing well for one task but developing problems when\ud used for the other.\ud This article proposes to use a representation that is both\ud flexible and well suited for both tasks. We propose to map object\ud labels to vertices of a regular simplex, e.g. the unit interval for\ud two labels, a triangle for three labels, a tetrahedron for four\ud labels, etc. This representation, which is routinely used in fuzzy\ud classification, is ideally suited for representing and registering\ud multiple shapes. On closer examination, this representation\ud reveals several desirable properties: algebraic operations may\ud be done directly, label uncertainty is expressed as a weighted\ud mixture of labels (probabilistic interpretation), interpolation is\ud unbiased toward any label or the background, and registration\ud may be performed directly.\ud We demonstrate these properties by using label space in a gradient\ud descent based registration scheme to obtain a probabilistic\ud atlas. While straightforward, this iterative method is very slow,\ud could get stuck in local minima, and depends heavily on the initial\ud conditions. To address these issues, two fast methods are proposed\ud which serve as coarse registration schemes following which the\ud iterative descent method can be used to refine the results. Further,\ud we derive an analytical formulation for direct computation of the\ud "group mean" from the parameters of pairwise registration of all\ud the images in the sample set. We show results on richly labeled\ud 2D and 3D data sets

Automated Global Feature Analyzer - A Driver for Tier-Scalable Reconnaissance

For the purposes of space flight, reconnaissance field geologists have trained to become astronauts. However, the initial forays to Mars and other planetary bodies have been done by purely robotic craft. Therefore, training and equipping a robotic craft with the sensory and cognitive capabilities of a field geologist to form a science craft is a necessary prerequisite. Numerous steps are necessary in order for a science craft to be able to map, analyze, and characterize a geologic field site, as well as effectively formulate working hypotheses. We report on the continued development of the integrated software system AGFA: automated global feature analyzerreg, originated by Fink at Caltech and his collaborators in 2001. AGFA is an automatic and feature-driven target characterization system that operates in an imaged operational area, such as a geologic field site on a remote planetary surface. AGFA performs automated target identification and detection through segmentation, providing for feature extraction, classification, and prioritization within mapped or imaged operational areas at different length scales and resolutions, depending on the vantage point (e.g., spaceborne, airborne, or ground). AGFA extracts features such as target size, color, albedo, vesicularity, and angularity. Based on the extracted features, AGFA summarizes the mapped operational area numerically and flags targets of "interest", i.e., targets that exhibit sufficient anomaly within the feature space. AGFA enables automated science analysis aboard robotic spacecraft, and, embedded in tier-scalable reconnaissance mission architectures, is a driver of future intelligent and autonomous robotic planetary exploration

Adaptive Segmentation of Knee Radiographs for Selecting the Optimal ROI in Texture Analysis

The purposes of this study were to investigate: 1) the effect of placement of region-of-interest (ROI) for texture analysis of subchondral bone in knee radiographs, and 2) the ability of several texture descriptors to distinguish between the knees with and without radiographic osteoarthritis (OA). Bilateral posterior-anterior knee radiographs were analyzed from the baseline of OAI and MOST datasets. A fully automatic method to locate the most informative region from subchondral bone using adaptive segmentation was developed. We used an oversegmentation strategy for partitioning knee images into the compact regions that follow natural texture boundaries. LBP, Fractal Dimension (FD), Haralick features, Shannon entropy, and HOG methods were computed within the standard ROI and within the proposed adaptive ROIs. Subsequently, we built logistic regression models to identify and compare the performances of each texture descriptor and each ROI placement method using 5-fold cross validation setting. Importantly, we also investigated the generalizability of our approach by training the models on OAI and testing them on MOST dataset.We used area under the receiver operating characteristic (ROC) curve (AUC) and average precision (AP) obtained from the precision-recall (PR) curve to compare the results. We found that the adaptive ROI improves the classification performance (OA vs. non-OA) over the commonly used standard ROI (up to 9% percent increase in AUC). We also observed that, from all texture parameters, LBP yielded the best performance in all settings with the best AUC of 0.840 [0.825, 0.852] and associated AP of 0.804 [0.786, 0.820]. Compared to the current state-of-the-art approaches, our results suggest that the proposed adaptive ROI approach in texture analysis of subchondral bone can increase the diagnostic performance for detecting the presence of radiographic OA

An ILP Solver for Multi-label MRFs with Connectivity Constraints

Integer Linear Programming (ILP) formulations of Markov random fields (MRFs) models with global connectivity priors were investigated previously in computer vision, e.g., \cite{globalinter,globalconn}. In these works, only Linear Programing (LP) relaxations \cite{globalinter,globalconn} or simplified versions \cite{graphcutbase} of the problem were solved. This paper investigates the ILP of multi-label MRF with exact connectivity priors via a branch-and-cut method, which provably finds globally optimal solutions. The method enforces connectivity priors iteratively by a cutting plane method, and provides feasible solutions with a guarantee on sub-optimality even if we terminate it earlier. The proposed ILP can be applied as a post-processing method on top of any existing multi-label segmentation approach. As it provides globally optimal solution, it can be used off-line to generate ground-truth labeling, which serves as quality check for any fast on-line algorithm. Furthermore, it can be used to generate ground-truth proposals for weakly supervised segmentation. We demonstrate the power and usefulness of our model by several experiments on the BSDS500 and PASCAL image dataset, as well as on medical images with trained probability maps.Comment: 19 page

Multilevel analysis of nuclear dynamics in lamin perturbed fibroblasts

The nuclear lamina provides structural support to the nucleus and has a central role in defining nuclear organization. Defects in its filamentous constituents, the lamins, lead to a class of diseases collectively referred to as laminopathies. On the cellular level, lamin mutations affect the physical integrity of nuclei and nucleo-cytoskeletal interactions, resulting in increased susceptibility to mechanical stress and altered gene expression [1]. Most studies regarding the mechanical properties of the nucleus in laminopathic conditions are based on the induction of extracellular stress, such as strain or compression, and focus on nuclear integrity and/or nucleo-cytoskeletal interaction [2]. Far less is known about the role of nuclear organization and mobility under basal steady-state conditions. In this study, we quantitatively compared nuclear organization, nuclear deformation and chromatin mobility of fibroblasts from a Hutchinson-Gilford progeria patient with cells from a lamin A/C-deficient patient and wild-type dermal fibroblasts. To this end, we created a toolbox in imageJ for automatically analyzing both nuclear as well as subnuclear dynamics in living cells. Simultaneously, we developed a workflow for comparing cellular morphology and subcellular protein distribution in a high content fashion. We found that the absence of functional lamin A/C leads to increased nuclear plasticity on the hour and minute time scale but also to increased intranuclear mobility down to the seconds time scale. In contrast, progeria cells showed overall reduced nuclear dynamics. In addition, high content analysis revealed marked morphological and topological differences between different culture passages within a cell type and between different pathological variants of culture-age matched laminopathic cell types

Quantitative assessment for detection and monitoring of coastline dynamics with temporal RADARSAT images

© 2018 by the authors. This study aims to detect coastline changes using temporal synthetic aperture radar (SAR) images for the state of Kelantan, Malaysia. Two active images, namely, RADARSAT-1 captured in 2003 and RADARSAT-2 captured in 2014, were used to monitor such changes. We applied noise removal and edge detection filtering on RADARSAT images for preprocessing to remove salt and pepper distortion. Different segmentation analyses were also applied to the filtered images. Firstly, multiresolution segmentation, maximum spectral difference and chessboard segmentation were performed to separate land pixels from ocean ones. Next, the Taguchi method was used to optimise segmentation parameters. Subsequently, a support vector machine algorithm was applied on the optimised segments to classify shorelines with an accuracy of 98% for both temporal images. Results were validated using a thematic map from the Department of Survey and Mapping of Malaysia. The change detection showed an average difference in the shoreline of 12.5 m between 2003 and 2014. The methods developed in this study demonstrate the ability of active SAR sensors to map and detect shoreline changes, especially during low or high tides in tropical regions where passive sensor imagery is often masked by clouds

Articulated Statistical Shape Modelling of the Shoulder Joint

The shoulder joint is the most mobile and unstable joint in the human body. This makes it vulnerable to soft tissue pathologies and dislocation. Insight into the kinematics of the joint may enable improved diagnosis and treatment of different shoulder pathologies. Shoulder joint kinematics can be influenced by the articular geometry of the joint. The aim of this project was to develop an analysis framework for shoulder joint kinematics via the use of articulated statistical shape models (ASSMs). Articulated statistical shape models extend conventional statistical shape models by combining the shape variability of anatomical objects collected from different subjects (statistical shape models), with the physical variation of pose between the same objects (articulation). The developed pipeline involved manual annotation of anatomical landmarks selected on 3D surface meshes of scapulae and humeri and establishing dense surface correspondence across these data through a registration process. The registration was performed using a Gaussian process morphable model fitting approach. In order to register two objects separately, while keeping their shape and kinematics relationship intact, one of the objects (scapula) was fixed leaving the other (humerus) to be mobile. All the pairs of registered humeri and scapulae were brought back to their native imaged position using the inverse of the associated registration transformation. The glenohumeral rotational center and local anatomic coordinate system of the humeri and scapulae were determined using the definitions suggested by the International Society of Biomechanics. Three motions (flexion, abduction, and internal rotation) were generated using Euler angle sequences. The ASSM of the model was built using principal component analysis and validated. The validation results show that the model adequately estimated the shape and pose encoded in the training data. Developing ASSM of the shoulder joint helps to define the statistical shape and pose parameters of the gleno humeral articulating surfaces. An ASSM of the shoulder joint has potential applications in the analysis and investigation of population-wide joint posture variation and kinematics. Such analyses may include determining and quantifying abnormal articulation of the joint based on the range of motion; understanding of detailed glenohumeral joint function and internal joint measurement; and diagnosis of shoulder pathologies. Future work will involve developing a protocol for encoding the shoulder ASSM with real, rather than handcrafted, pose variation

Performance evaluation of object based greenhouse detection from Sentinel-2 MSI and Landsat 8 OLI data: A case study from Almería (Spain)

tThis paper shows the first comparison between data from Sentinel-2 (S2) Multi Spectral Instrument (MSI)and Landsat 8 (L8) Operational Land Imager (OLI) headed up to greenhouse detection. Two closely relatedin time scenes, one for each sensor, were classified by using Object Based Image Analysis and RandomForest (RF). The RF input consisted of several object-based features computed from spectral bands andincluding mean values, spectral indices and textural features. S2 and L8 data comparisons were alsoextended using a common segmentation dataset extracted form VHR World-View 2 (WV2) imagery totest differences only due to their specific spectral contribution. The best band combinations to performsegmentation were found through a modified version of the Euclidian Distance 2 index. Four differentRF classifications schemes were considered achieving 89.1%, 91.3%, 90.9% and 93.4% as the best overallaccuracies respectively, evaluated over the whole study area