A proposed framework for consensus-based lung tumour volume auto-segmentation in 4D computed tomography imaging.

This work aims to propose and validate a framework for tumour volume auto-segmentation based on ground-truth estimates derived from multi-physician input contours to expedite 4D-CT based lung tumour volume delineation. 4D-CT datasets of ten non-small cell lung cancer (NSCLC) patients were manually segmented by 6 physicians. Multi-expert ground truth (GT) estimates were constructed using the STAPLE algorithm for the gross tumour volume (GTV) on all respiratory phases. Next, using a deformable model-based method, multi-expert GT on each individual phase of the 4D-CT dataset was propagated to all other phases providing auto-segmented GTVs and motion encompassing internal gross target volumes (IGTVs) based on GT estimates (STAPLE) from each respiratory phase of the 4D-CT dataset. Accuracy assessment of auto-segmentation employed graph cuts for 3D-shape reconstruction and point-set registration-based analysis yielding volumetric and distance-based measures. STAPLE-based auto-segmented GTV accuracy ranged from (81.51  ±  1.92) to (97.27  ±  0.28)% volumetric overlap of the estimated ground truth. IGTV auto-segmentation showed significantly improved accuracies with reduced variance for all patients ranging from 90.87 to 98.57% volumetric overlap of the ground truth volume. Additional metrics supported these observations with statistical significance. Accuracy of auto-segmentation was shown to be largely independent of selection of the initial propagation phase. IGTV construction based on auto-segmented GTVs within the 4D-CT dataset provided accurate and reliable target volumes compared to manual segmentation-based GT estimates. While inter-/intra-observer effects were largely mitigated, the proposed segmentation workflow is more complex than that of current clinical practice and requires further development

Iterative graph cuts for image segmentation with a nonlinear statistical shape prior

Shape-based regularization has proven to be a useful method for delineating objects within noisy images where one has prior knowledge of the shape of the targeted object. When a collection of possible shapes is available, the specification of a shape prior using kernel density estimation is a natural technique. Unfortunately, energy functionals arising from kernel density estimation are of a form that makes them impossible to directly minimize using efficient optimization algorithms such as graph cuts. Our main contribution is to show how one may recast the energy functional into a form that is minimizable iteratively and efficiently using graph cuts.Comment: Revision submitted to JMIV (02/24/13

GRMA: Generalized Range Move Algorithms for the efficient optimization of MRFs

Markov Random Fields (MRF) have become an important tool for many vision applications, and the optimization of MRFs is a problem of fundamental importance. Recently, Veksler and Kumar et al. proposed the range move algorithms, which are some of the most successful optimizers. Instead of considering only two labels as in previous move-making algorithms, they explore a large search space over a range of labels in each iteration, and significantly outperform previous move-making algorithms. However, two problems have greatly limited the applicability of range move algorithms: 1) They are limited in the energy functions they can handle (i.e., only truncated convex functions); 2) They tend to be very slow compared to other move-making algorithms (e.g., �-expansion and ��-swap). In this paper, we propose two generalized range move algorithms (GRMA) for the efficient optimization of MRFs. To address the first problem, we extend the GRMAs to more general energy functions by restricting the chosen labels in each move so that the energy function is submodular on the chosen subset. Furthermore, we provide a feasible sufficient condition for choosing these subsets of labels. To address the second problem, we dynamically obtain the iterative moves by solving set cover problems. This greatly reduces the number of moves during the optimization.We also propose a fast graph construction method for the GRMAs. Experiments show that the GRMAs offer a great speedup over previous range move algorithms, while yielding competitive solutions

Template-free 3D Reconstruction of Poorly-textured Nonrigid Surfaces

Two main classes of approaches have been studied to perform monocular nonrigid 3D reconstruction: Template-based methods and Non-rigid Structure from Motion techniques. While the first ones have been applied to reconstruct poorly-textured surfaces, they assume the availability of a 3D shape model prior to reconstruction. By contrast, the second ones do not require such a shape template, but, instead, rely on points being tracked throughout a video sequence, and are thus illsuited to handle poorly-textured surfaces. In this paper, we introduce a template-free approach to reconstructing a poorly-textured, deformable surface. To this end, we leverage surface isometry and formulate 3D reconstruction as the joint problem of non-rigid image registration and depth estimation. Our experiments demonstrate that our approach yields much more accurate 3D reconstructions than state-of-the-art techniques

3D time series analysis of cell shape using Laplacian approaches

Background: Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possible, but we lack efficient tools for analysing shape deformations in order to understand the real three-dimensional nature of shape changes. Results: We present a framework for 3D+time cell shape analysis. The main contribution is three-fold: First, we develop a fast, automatic random walker method for cell segmentation. Second, a novel topology fixing method is proposed to fix segmented binary volumes without spherical topology. Third, we show that algorithms used for each individual step of the analysis pipeline (cell segmentation, topology fixing, spherical parameterization, and shape representation) are closely related to the Laplacian operator. The framework is applied to the shape analysis of neutrophil cells. Conclusions: The method we propose for cell segmentation is faster than the traditional random walker method or the level set method, and performs better on 3D time-series of neutrophil cells, which are comparatively noisy as stacks have to be acquired fast enough to account for cell motion. Our method for topology fixing outperforms the tools provided by SPHARM-MAT and SPHARM-PDM in terms of their successful fixing rates. The different tasks in the presented pipeline for 3D+time shape analysis of cells can be solved using Laplacian approaches, opening the possibility of eventually combining individual steps in order to speed up computations

A Comparative Study of Modern Inference Techniques for Structured Discrete Energy Minimization Problems

International audienceSzeliski et al. published an influential study in 2006 on energy minimization methods for Markov Random Fields (MRF). This study provided valuable insights in choosing the best optimization technique for certain classes of problems. While these insights remain generally useful today, the phenomenal success of random field models means that the kinds of inference problems that have to be solved changed significantly. Specifically , the models today often include higher order interactions, flexible connectivity structures, large label-spaces of different car-dinalities, or learned energy tables. To reflect these changes, we provide a modernized and enlarged study. We present an empirical comparison of more than 27 state-of-the-art optimization techniques on a corpus of 2,453 energy minimization instances from diverse applications in computer vision. To ensure reproducibility, we evaluate all methods in the OpenGM 2 framework and report extensive results regarding runtime and solution quality. Key insights from our study agree with the results of Szeliski et al. for the types of models they studied. However, on new and challenging types of models our findings disagree and suggest that polyhedral methods and integer programming solvers are competitive in terms of runtime and solution quality over a large range of model types