Incorporating prior knowledge in medical image segmentation: a survey

Medical image segmentation, the task of partitioning an image into meaningful parts, is an important step toward automating medical image analysis and is at the crux of a variety of medical imaging applications, such as computer aided diagnosis, therapy planning and delivery, and computer aided interventions. However, the existence of noise, low contrast and objects' complexity in medical images are critical obstacles that stand in the way of achieving an ideal segmentation system. Incorporating prior knowledge into image segmentation algorithms has proven useful for obtaining more accurate and plausible results. This paper surveys the different types of prior knowledge that have been utilized in different segmentation frameworks. We focus our survey on optimization-based methods that incorporate prior information into their frameworks. We review and compare these methods in terms of the types of prior employed, the domain of formulation (continuous vs. discrete), and the optimization techniques (global vs. local). We also created an interactive online database of existing works and categorized them based on the type of prior knowledge they use. Our website is interactive so that researchers can contribute to keep the database up to date. We conclude the survey by discussing different aspects of designing an energy functional for image segmentation, open problems, and future perspectives.Comment: Survey paper, 30 page

Bayesian Semantic Instance Segmentation in Open Set World

This paper addresses the semantic instance segmentation task in the open-set conditions, where input images can contain known and unknown object classes. The training process of existing semantic instance segmentation methods requires annotation masks for all object instances, which is expensive to acquire or even infeasible in some realistic scenarios, where the number of categories may increase boundlessly. In this paper, we present a novel open-set semantic instance segmentation approach capable of segmenting all known and unknown object classes in images, based on the output of an object detector trained on known object classes. We formulate the problem using a Bayesian framework, where the posterior distribution is approximated with a simulated annealing optimization equipped with an efficient image partition sampler. We show empirically that our method is competitive with state-of-the-art supervised methods on known classes, but also performs well on unknown classes when compared with unsupervised methods.Comment: Accepted to ECCV 201

A Continuous Max-Flow Approach to Multi-Labeling Problems under Arbitrary Region Regularization

The incorporation of region regularization into max-flow segmentation has traditionally focused on ordering and part-whole relationships. A side effect of the development of such models is that it constrained regularization only to those cases, rather than allowing for arbitrary region regularization. Directed Acyclic Graphical Max-Flow (DAGMF) segmentation overcomes these limitations by allowing for the algorithm designer to specify an arbitrary directed acyclic graph to structure a max-flow segmentation. This allows for individual 'parts' to be a member of multiple distinct 'wholes.'Comment: 10 pages, 2 figures, 3 algorithms - v2: Fixed typos / grammatical errors and mathematical errors in the primal/dual formulation. Extended methods for weighted DAGs rather than DAGs with edge multiplicit

Just-Enough Interaction Approach to Knee MRI Segmentation: Data from the Osteoarthritis Initiative

State-of-the-art automated segmentation algorithms are not 100\% accurate especially when segmenting difficult to interpret datasets like those with severe osteoarthritis (OA). We present a novel interactive method called just-enough interaction (JEI), which adds a fast correction step to the automated layered optimal graph segmentation of multiple objects and surfaces (LOGISMOS). After LOGISMOS segmentation in knee MRI, the JEI user interaction does not modify boundary surfaces of the bones and cartilages directly. Local costs of underlying graph nodes are modified instead and the graph is re-optimized, providing globally optimal corrected results. Significant performance improvement ($p \ll 0.001$) was observed when comparing JEI-corrected results to the automated. The algorithm was extended from 3D JEI to longitudinal multi-3D (4D) JEI allowing simultaneous visualization and interaction of multiple-time points of the same patient.Comment: Proceedings of the 3rd International Workshop on Interactive Medical Image Computing (IMIC), Held in Conjunction with MICCAI, 201

Adaptable Precomputation for Random Walker Image Segmentation and Registration

The random walker (RW) algorithm is used for both image segmentation and registration, and possesses several useful properties that make it popular in medical imaging, such as being globally optimizable, allowing user interaction, and providing uncertainty information. The RW algorithm defines a weighted graph over an image and uses the graph's Laplacian matrix to regularize its solutions. This regularization reduces to solving a large system of equations, which may be excessively time consuming in some applications, such as when interacting with a human user. Techniques have been developed that precompute eigenvectors of a Laplacian offline, after image acquisition but before any analysis, in order speed up the RW algorithm online, when segmentation or registration is being performed. However, precomputation requires certain algorithm parameters be fixed offline, limiting their flexibility. In this paper, we develop techniques to update the precomputed data online when RW parameters are altered. Specifically, we dynamically determine the number of eigenvectors needed for a desired accuracy based on user input, and derive update equations for the eigenvectors when the edge weights or topology of the image graph are changed. We present results demonstrating that our techniques make RW with precomputation much more robust to offline settings while only sacrificing minimal accuracy.Comment: 9 pages, 8 figure

Co-Sparse Textural Similarity for Image Segmentation

We propose an algorithm for segmenting natural images based on texture and color information, which leverages the co-sparse analysis model for image segmentation within a convex multilabel optimization framework. As a key ingredient of this method, we introduce a novel textural similarity measure, which builds upon the co-sparse representation of image patches. We propose a Bayesian approach to merge textural similarity with information about color and location. Combined with recently developed convex multilabel optimization methods this leads to an efficient algorithm for both supervised and unsupervised segmentation, which is easily parallelized on graphics hardware. The approach provides competitive results in unsupervised segmentation and outperforms state-of-the-art interactive segmentation methods on the Graz Benchmark

Active Mean Fields for Probabilistic Image Segmentation: Connections with Chan-Vese and Rudin-Osher-Fatemi Models

Segmentation is a fundamental task for extracting semantically meaningful regions from an image. The goal of segmentation algorithms is to accurately assign object labels to each image location. However, image-noise, shortcomings of algorithms, and image ambiguities cause uncertainty in label assignment. Estimating the uncertainty in label assignment is important in multiple application domains, such as segmenting tumors from medical images for radiation treatment planning. One way to estimate these uncertainties is through the computation of posteriors of Bayesian models, which is computationally prohibitive for many practical applications. On the other hand, most computationally efficient methods fail to estimate label uncertainty. We therefore propose in this paper the Active Mean Fields (AMF) approach, a technique based on Bayesian modeling that uses a mean-field approximation to efficiently compute a segmentation and its corresponding uncertainty. Based on a variational formulation, the resulting convex model combines any label-likelihood measure with a prior on the length of the segmentation boundary. A specific implementation of that model is the Chan-Vese segmentation model (CV), in which the binary segmentation task is defined by a Gaussian likelihood and a prior regularizing the length of the segmentation boundary. Furthermore, the Euler-Lagrange equations derived from the AMF model are equivalent to those of the popular Rudin-Osher-Fatemi (ROF) model for image denoising. Solutions to the AMF model can thus be implemented by directly utilizing highly-efficient ROF solvers on log-likelihood ratio fields. We qualitatively assess the approach on synthetic data as well as on real natural and medical images. For a quantitative evaluation, we apply our approach to the icgbench dataset

The Candidate Multi-Cut for Cell Segmentation

Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by solving a Multi-Cut problem. In this paper, we introduce a model that unifies both approaches. Our model, the Candidate Multi-Cut (CMC), allows joint selection and clustering of segment candidates from a merge-tree. This way, we overcome the respective limitations of the individual methods: (1) the space of possible segmentations is not constrained to candidates of a merge-tree, and (2) the decision for clustering can be made on candidates larger than superpixels, using features over larger contexts. We solve the optimization problem of selecting and clustering of candidates using an integer linear program. On datasets of 2D light microscopy of cell populations and 3D electron microscopy of neurons, we show that our method generalizes well and generates more accurate segmentations than merge-tree or Multi-Cut methods alone

A Multi-Agents Architecture to Learn Vision Operators and their Parameters

In a vision system, every task needs that the operators to apply should be {\guillemotleft} well chosen {\guillemotright} and their parameters should be also {\guillemotleft} well adjusted {\guillemotright}. The diversity of operators and the multitude of their parameters constitute a big challenge for users. As it is very difficult to make the {\guillemotleft} right {\guillemotright} choice, lack of a specific rule, many disadvantages appear and affect the computation time and especially the quality of results. In this paper we present a multi-agent architecture to learn the best operators to apply and their best parameters for a class of images. Our architecture consists of three types of agents: User Agent, Operator Agent and Parameter Agent. The User Agent determines the phases of treatment, a library of operators and the possible values of their parameters. The Operator Agent constructs all possible combinations of operators and the Parameter Agent, the core of the architecture, adjusts the parameters of each combination by treating a large number of images. Through the reinforcement learning mechanism, our architecture does not consider only the system opportunities but also the user preferences.Comment: IJCSI, May 201

Pixel-Level Matching for Video Object Segmentation using Convolutional Neural Networks

We propose a novel video object segmentation algorithm based on pixel-level matching using Convolutional Neural Networks (CNN). Our network aims to distinguish the target area from the background on the basis of the pixel-level similarity between two object units. The proposed network represents a target object using features from different depth layers in order to take advantage of both the spatial details and the category-level semantic information. Furthermore, we propose a feature compression technique that drastically reduces the memory requirements while maintaining the capability of feature representation. Two-stage training (pre-training and fine-tuning) allows our network to handle any target object regardless of its category (even if the object's type does not belong to the pre-training data) or of variations in its appearance through a video sequence. Experiments on large datasets demonstrate the effectiveness of our model - against related methods - in terms of accuracy, speed, and stability. Finally, we introduce the transferability of our network to different domains, such as the infrared data domain.Comment: To appear on ICCV 201