A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

Fuzzy-based Propagation of Prior Knowledge to Improve Large-Scale Image Analysis Pipelines

Many automatically analyzable scientific questions are well-posed and offer a variety of information about the expected outcome a priori. Although often being neglected, this prior knowledge can be systematically exploited to make automated analysis operations sensitive to a desired phenomenon or to evaluate extracted content with respect to this prior knowledge. For instance, the performance of processing operators can be greatly enhanced by a more focused detection strategy and the direct information about the ambiguity inherent in the extracted data. We present a new concept for the estimation and propagation of uncertainty involved in image analysis operators. This allows using simple processing operators that are suitable for analyzing large-scale 3D+t microscopy images without compromising the result quality. On the foundation of fuzzy set theory, we transform available prior knowledge into a mathematical representation and extensively use it enhance the result quality of various processing operators. All presented concepts are illustrated on a typical bioimage analysis pipeline comprised of seed point detection, segmentation, multiview fusion and tracking. Furthermore, the functionality of the proposed approach is validated on a comprehensive simulated 3D+t benchmark data set that mimics embryonic development and on large-scale light-sheet microscopy data of a zebrafish embryo. The general concept introduced in this contribution represents a new approach to efficiently exploit prior knowledge to improve the result quality of image analysis pipelines. Especially, the automated analysis of terabyte-scale microscopy data will benefit from sophisticated and efficient algorithms that enable a quantitative and fast readout. The generality of the concept, however, makes it also applicable to practically any other field with processing strategies that are arranged as linear pipelines.Comment: 39 pages, 12 figure

Reconstructive Sparse Code Transfer for Contour Detection and Semantic Labeling

We frame the task of predicting a semantic labeling as a sparse reconstruction procedure that applies a target-specific learned transfer function to a generic deep sparse code representation of an image. This strategy partitions training into two distinct stages. First, in an unsupervised manner, we learn a set of generic dictionaries optimized for sparse coding of image patches. We train a multilayer representation via recursive sparse dictionary learning on pooled codes output by earlier layers. Second, we encode all training images with the generic dictionaries and learn a transfer function that optimizes reconstruction of patches extracted from annotated ground-truth given the sparse codes of their corresponding image patches. At test time, we encode a novel image using the generic dictionaries and then reconstruct using the transfer function. The output reconstruction is a semantic labeling of the test image. Applying this strategy to the task of contour detection, we demonstrate performance competitive with state-of-the-art systems. Unlike almost all prior work, our approach obviates the need for any form of hand-designed features or filters. To illustrate general applicability, we also show initial results on semantic part labeling of human faces. The effectiveness of our approach opens new avenues for research on deep sparse representations. Our classifiers utilize this representation in a novel manner. Rather than acting on nodes in the deepest layer, they attach to nodes along a slice through multiple layers of the network in order to make predictions about local patches. Our flexible combination of a generatively learned sparse representation with discriminatively trained transfer classifiers extends the notion of sparse reconstruction to encompass arbitrary semantic labeling tasks.Comment: to appear in Asian Conference on Computer Vision (ACCV), 201

A High-Order Scheme for Image Segmentation via a modified Level-Set method

In this paper we propose a high-order accurate scheme for image segmentation based on the level-set method. In this approach, the curve evolution is described as the 0-level set of a representation function but we modify the velocity that drives the curve to the boundary of the object in order to obtain a new velocity with additional properties that are extremely useful to develop a more stable high-order approximation with a small additional cost. The approximation scheme proposed here is the first 2D version of an adaptive "filtered" scheme recently introduced and analyzed by the authors in 1D. This approach is interesting since the implementation of the filtered scheme is rather efficient and easy. The scheme combines two building blocks (a monotone scheme and a high-order scheme) via a filter function and smoothness indicators that allow to detect the regularity of the approximate solution adapting the scheme in an automatic way. Some numerical tests on synthetic and real images confirm the accuracy of the proposed method and the advantages given by the new velocity.Comment: Accepted version for publication in SIAM Journal on Imaging Sciences, 86 figure

Locally Adaptive Frames in the Roto-Translation Group and their Applications in Medical Imaging

Locally adaptive differential frames (gauge frames) are a well-known effective tool in image analysis, used in differential invariants and PDE-flows. However, at complex structures such as crossings or junctions, these frames are not well-defined. Therefore, we generalize the notion of gauge frames on images to gauge frames on data representations $U:\mathbb{R}^{d} \rtimes S^{d-1} \to \mathbb{R}$ defined on the extended space of positions and orientations, which we relate to data on the roto-translation group $SE(d)$, $d=2,3$. This allows to define multiple frames per position, one per orientation. We compute these frames via exponential curve fits in the extended data representations in $SE(d)$. These curve fits minimize first or second order variational problems which are solved by spectral decomposition of, respectively, a structure tensor or Hessian of data on $SE(d)$. We include these gauge frames in differential invariants and crossing preserving PDE-flows acting on extended data representation $U$ and we show their advantage compared to the standard left-invariant frame on $SE(d)$. Applications include crossing-preserving filtering and improved segmentations of the vascular tree in retinal images, and new 3D extensions of coherence-enhancing diffusion via invertible orientation scores

Steered mixture-of-experts for light field images and video : representation and coding

Research in light field (LF) processing has heavily increased over the last decade. This is largely driven by the desire to achieve the same level of immersion and navigational freedom for camera-captured scenes as it is currently available for CGI content. Standardization organizations such as MPEG and JPEG continue to follow conventional coding paradigms in which viewpoints are discretely represented on 2-D regular grids. These grids are then further decorrelated through hybrid DPCM/transform techniques. However, these 2-D regular grids are less suited for high-dimensional data, such as LFs. We propose a novel coding framework for higher-dimensional image modalities, called Steered Mixture-of-Experts (SMoE). Coherent areas in the higher-dimensional space are represented by single higher-dimensional entities, called kernels. These kernels hold spatially localized information about light rays at any angle arriving at a certain region. The global model consists thus of a set of kernels which define a continuous approximation of the underlying plenoptic function. We introduce the theory of SMoE and illustrate its application for 2-D images, 4-D LF images, and 5-D LF video. We also propose an efficient coding strategy to convert the model parameters into a bitstream. Even without provisions for high-frequency information, the proposed method performs comparable to the state of the art for low-to-mid range bitrates with respect to subjective visual quality of 4-D LF images. In case of 5-D LF video, we observe superior decorrelation and coding performance with coding gains of a factor of 4x in bitrate for the same quality. At least equally important is the fact that our method inherently has desired functionality for LF rendering which is lacking in other state-of-the-art techniques: (1) full zero-delay random access, (2) light-weight pixel-parallel view reconstruction, and (3) intrinsic view interpolation and super-resolution