Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images

We study the problem of segmenting, reconstructing, and analyzing the structure growth of thrombi (clots) in blood vessels in vivo based on 2-photon microscopic image data. First, we develop an algorithm for segmenting clots in 3D microscopic images based on density-based clustering and methods for dealing with imaging artifacts. Next, we apply the union-of-balls (or alpha-shape) algorithm to reconstruct the boundary of clots in 3D. Finally, we perform experimental studies and analysis on the reconstructed clots and obtain quantitative data of thrombus growth and structures. We conduct experiments on laser-induced injuries in vessels of two types of mice (the wild type and the type with low levels of coagulation factor VII) and analyze and compare the developing clot structures based on their reconstructed clots from image data. The results we obtain are of biomedical significance. Our quantitative analysis of the clot composition leads to better understanding of the thrombus development, and is valuable to the modeling and verification of computational simulation of thrombogenesis

Unsupervised morphological segmentation for images

This paper deals with a morphological approach to unsupervised image segmentation. The proposed technique relies on a multiscale Top-Down approach allowing a hierarchical processing of the data ranging from the most global scale to the most detailed one. At each scale, the algorithm consists of four steps: image simplification, feature extraction, contour localization and quality estimation. The main emphasis of this paper is to discuss the selection of a simplification filter for segmentation. Morphological filters based on reconstruction proved to be very efficient for this purpose. The resulting unsupervised algorithm is very robust and can deal with very different type of images.Peer ReviewedPostprint (published version

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

Graph Spectral Image Processing

Recent advent of graph signal processing (GSP) has spurred intensive studies of signals that live naturally on irregular data kernels described by graphs (e.g., social networks, wireless sensor networks). Though a digital image contains pixels that reside on a regularly sampled 2D grid, if one can design an appropriate underlying graph connecting pixels with weights that reflect the image structure, then one can interpret the image (or image patch) as a signal on a graph, and apply GSP tools for processing and analysis of the signal in graph spectral domain. In this article, we overview recent graph spectral techniques in GSP specifically for image / video processing. The topics covered include image compression, image restoration, image filtering and image segmentation

Combining Contrast Invariant L1 Data Fidelities with Nonlinear Spectral Image Decomposition

This paper focuses on multi-scale approaches for variational methods and corresponding gradient flows. Recently, for convex regularization functionals such as total variation, new theory and algorithms for nonlinear eigenvalue problems via nonlinear spectral decompositions have been developed. Those methods open new directions for advanced image filtering. However, for an effective use in image segmentation and shape decomposition, a clear interpretation of the spectral response regarding size and intensity scales is needed but lacking in current approaches. In this context, $L^1$ data fidelities are particularly helpful due to their interesting multi-scale properties such as contrast invariance. Hence, the novelty of this work is the combination of $L^1$-based multi-scale methods with nonlinear spectral decompositions. We compare $L^1$ with $L^2$ scale-space methods in view of spectral image representation and decomposition. We show that the contrast invariant multi-scale behavior of $L^1-TV$ promotes sparsity in the spectral response providing more informative decompositions. We provide a numerical method and analyze synthetic and biomedical images at which decomposition leads to improved segmentation.Comment: 13 pages, 7 figures, conference SSVM 201

A Multiscale Approach for Statistical Characterization of Functional Images

Increasingly, scientific studies yield functional image data, in which the observed data consist of sets of curves recorded on the pixels of the image. Examples include temporal brain response intensities measured by fMRI and NMR frequency spectra measured at each pixel. This article presents a new methodology for improving the characterization of pixels in functional imaging, formulated as a spatial curve clustering problem. Our method operates on curves as a unit. It is nonparametric and involves multiple stages: (i) wavelet thresholding, aggregation, and Neyman truncation to effectively reduce dimensionality; (ii) clustering based on an extended EM algorithm; and (iii) multiscale penalized dyadic partitioning to create a spatial segmentation. We motivate the different stages with theoretical considerations and arguments, and illustrate the overall procedure on simulated and real datasets. Our method appears to offer substantial improvements over monoscale pixel-wise methods. An Appendix which gives some theoretical justifications of the methodology, computer code, documentation and dataset are available in the online supplements