Showing papers on "Image processing published in 2016"

Image Style Transfer Using Convolutional Neural Networks

Abstract: Rendering the semantic content of an image in different styles is a difficult image processing task. Arguably, a major limiting factor for previous approaches has been the lack of image representations that explicitly represent semantic information and, thus, allow to separate image content from style. Here we use image representations derived from Convolutional Neural Networks optimised for object recognition, which make high level image information explicit. We introduce A Neural Algorithm of Artistic Style that can separate and recombine the image content and style of natural images. The algorithm allows us to produce new images of high perceptual quality that combine the content of an arbitrary photograph with the appearance of numerous wellknown artworks. Our results provide new insights into the deep image representations learned by Convolutional Neural Networks and demonstrate their potential for high level image synthesis and manipulation.

Gibbs-ringing artifact removal based on local subvoxel-shifts.

Abstract: Purpose To develop a fast and stable method for correcting the gibbs-ringing artifact. Methods Gibbs-ringing is a well-known artifact which manifests itself as spurious oscillations in the vicinity of sharp image gradients at tissue boundaries. The origin can be seen in the truncation of k-space during MRI data-acquisition. Correction techniques like Gegenbauer reconstruction or extrapolation methods aim at recovering these missing data. Here, we present a simple and robust method which exploits a different view on the Gibbs-phenomenon: The truncation in k-space can be interpreted as a convolution of the underlying image with a sinc-function. As the image is reconstructed on a discretized grid, the severity of the ringing artifacts depends on how this grid is located with respect to the edge and the oscillation pattern of the function. We propose to reinterpolate the image based on local, subvoxel-shifts to sample the ringing pattern at the zero-crossings of the oscillating sinc-function. Results With the proposed method, the artifact can simply, effectively, and robustly be removed with a minimal amount of image smoothing. Conclusions The robustness of the method suggests it as a suitable candidate for an implementation in the standard image processing pipeline in clinical routine. Magn Reson Med 76:1574-1581, 2016. © 2015 International Society for Magnetic Resonance in Medicine.

Stacked Sparse Autoencoder (SSAE) for Nuclei Detection on Breast Cancer Histopathology Images

Abstract: Automated nuclear detection is a critical step for a number of computer assisted pathology related image analysis algorithms such as for automated grading of breast cancer tissue specimens. The Nottingham Histologic Score system is highly correlated with the shape and appearance of breast cancer nuclei in histopathological images. However, automated nucleus detection is complicated by 1) the large number of nuclei and the size of high resolution digitized pathology images, and 2) the variability in size, shape, appearance, and texture of the individual nuclei. Recently there has been interest in the application of “Deep Learning” strategies for classification and analysis of big image data. Histopathology, given its size and complexity, represents an excellent use case for application of deep learning strategies. In this paper, a Stacked Sparse Autoencoder (SSAE), an instance of a deep learning strategy, is presented for efficient nuclei detection on high-resolution histopathological images of breast cancer. The SSAE learns high-level features from just pixel intensities alone in order to identify distinguishing features of nuclei. A sliding window operation is applied to each image in order to represent image patches via high-level features obtained via the auto-encoder, which are then subsequently fed to a classifier which categorizes each image patch as nuclear or non-nuclear. Across a cohort of 500 histopathological images (2200 $\times$ 2200) and approximately 3500 manually segmented individual nuclei serving as the groundtruth, SSAE was shown to have an improved F-measure 84.49% and an average area under Precision-Recall curve (AveP) 78.83%. The SSAE approach also out-performed nine other state of the art nuclear detection strategies.

MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis

Abstract: Single-cell analysis of bacteria and subcellular protein localization dynamics has shown that bacteria have elaborate life cycles, cytoskeletal protein networks and complex signal transduction pathways driven by localized proteins. The volume of multidimensional images generated in such experiments and the computation time required to detect, associate and track cells and subcellular features pose considerable challenges, especially for high-throughput experiments. There is therefore a need for a versatile, computationally efficient image analysis tool capable of extracting the desired relationships from images in a meaningful and unbiased way. Here, we present MicrobeJ, a plug-in for the open-source platform ImageJ(1). MicrobeJ provides a comprehensive framework to process images derived from a wide variety of microscopy experiments with special emphasis on large image sets. It performs the most common intensity and morphology measurements as well as customized detection of poles, septa, fluorescent foci and organelles, determines their subcellular localization with subpixel resolution, and tracks them over time. Because a dynamic link is maintained between the images, measurements and all data representations derived from them, the editor and suite of advanced data presentation tools facilitates the image analysis process and provides a robust way to verify the accuracy and veracity of the data.

Traffic-Sign Detection and Classification in the Wild

Abstract: Although promising results have been achieved in the areas of traffic-sign detection and classification, few works have provided simultaneous solutions to these two tasks for realistic real world images. We make two contributions to this problem. Firstly, we have created a large traffic-sign benchmark from 100000 Tencent Street View panoramas, going beyond previous benchmarks. It provides 100000 images containing 30000 traffic-sign instances. These images cover large variations in illuminance and weather conditions. Each traffic-sign in the benchmark is annotated with a class label, its bounding box and pixel mask. We call this benchmark Tsinghua-Tencent 100K. Secondly, we demonstrate how a robust end-to-end convolutional neural network (CNN) can simultaneously detect and classify trafficsigns. Most previous CNN image processing solutions target objects that occupy a large proportion of an image, and such networks do not work well for target objects occupying only a small fraction of an image like the traffic-signs here. Experimental results show the robustness of our network and its superiority to alternatives. The benchmark, source code and the CNN model introduced in this paper is publicly available1.

Dynamic Image Networks for Action Recognition

Abstract: We introduce the concept of dynamic image, a novel compact representation of videos useful for video analysis especially when convolutional neural networks (CNNs) are used. The dynamic image is based on the rank pooling concept and is obtained through the parameters of a ranking machine that encodes the temporal evolution of the frames of the video. Dynamic images are obtained by directly applying rank pooling on the raw image pixels of a video producing a single RGB image per video. This idea is simple but powerful as it enables the use of existing CNN models directly on video data with fine-tuning. We present an efficient and effective approximate rank pooling operator, speeding it up orders of magnitude compared to rank pooling. Our new approximate rank pooling CNN layer allows us to generalize dynamic images to dynamic feature maps and we demonstrate the power of our new representations on standard benchmarks in action recognition achieving state-of-the-art performance.

A review on image segmentation techniques

Abstract: Digital image processing plays a vital role in many applications to retrieve required information from the given image in a way that it has not affect the other features of the image. Image segmentation is one of the most important tasks in image processing which is used to partition an image into several disjoint subsets such that each subset corresponds to a meaningful part of the image. The goal of image segmentation is to cluster pixels into salient image regions corresponding to individual surfaces, objects, or natural parts of objects. With the growing research on image segmentation many segmentation methods have been developed and interpreted differently towards content analysis and image understanding for different applications. Thus an organized review on image segmentation methods is essential and this paper provides a review on the various image segmentation techniques proposed in the literature.

Video Super-Resolution With Convolutional Neural Networks

Abstract: Convolutional neural networks (CNN) are a special type of deep neural networks (DNN). They have so far been successfully applied to image super-resolution (SR) as well as other image restoration tasks. In this paper, we consider the problem of video super-resolution. We propose a CNN that is trained on both the spatial and the temporal dimensions of videos to enhance their spatial resolution. Consecutive frames are motion compensated and used as input to a CNN that provides super-resolved video frames as output. We investigate different options of combining the video frames within one CNN architecture. While large image databases are available to train deep neural networks, it is more challenging to create a large video database of sufficient quality to train neural nets for video restoration. We show that by using images to pretrain our model, a relatively small video database is sufficient for the training of our model to achieve and even improve upon the current state-of-the-art. We compare our proposed approach to current video as well as image SR algorithms.

A Cross-Modality Learning Approach for Vessel Segmentation in Retinal Images

Abstract: This paper presents a new supervised method for vessel segmentation in retinal images. This method remolds the task of segmentation as a problem of cross-modality data transformation from retinal image to vessel map. A wide and deep neural network with strong induction ability is proposed to model the transformation, and an efficient training strategy is presented. Instead of a single label of the center pixel, the network can output the label map of all pixels for a given image patch. Our approach outperforms reported state-of-the-art methods in terms of sensitivity, specificity and accuracy. The result of cross-training evaluation indicates its robustness to the training set. The approach needs no artificially designed feature and no preprocessing step, reducing the impact of subjective factors. The proposed method has the potential for application in image diagnosis of ophthalmologic diseases, and it may provide a new, general, high-performance computing framework for image segmentation.

FIT2D: a multi-purpose data reduction, analysis and visualization program

Abstract: FIT2D is one of the principal area detector data reduction, analysis and visualization programs used at the European Synchrotron Radiation Facility and is also used by more than 400 research groups worldwide, including many other synchrotron radiation facilities. It has been developed for X-ray science, but is applicable to other structural techniques and is used in analysing electron diffraction data and microscopy, and neutron diffraction and scattering data. FIT2D works for both interactive and `batch'-style data processing. Calibration and correction of detector distortions, integration of two-dimensional data to a variety of one-dimensional scans, and one- and two-dimensional model fitting are the main uses. Many other general-purpose image processing and image visualization operations are available. Commands are available through a `graphical user interface' and operations common to certain types of analysis are grouped within `interfaces'. Executable versions for most workstation and personal computer systems, and web page documentation, are available at http://www.esrf.eu/computing/scientific/FIT2D.

A Perspective on Deep Imaging

Abstract: The combination of tomographic imaging and deep learning, or machine learning in general, promises to empower not only image analysis but also image reconstruction. The latter aspect is considered in this perspective article with an emphasis on medical imaging to develop a new generation of image reconstruction theories and techniques. This direction might lead to intelligent utilization of domain knowledge from big data, innovative approaches for image reconstruction, and superior performance in clinical and preclinical applications. To realize the full impact of machine learning for tomographic imaging, major theoretical, technical and translational efforts are immediately needed.

Efficient Algorithms for Convolutional Sparse Representations

Abstract: When applying sparse representation techniques to images, the standard approach is to independently compute the representations for a set of overlapping image patches. This method performs very well in a variety of applications, but results in a representation that is multi-valued and not optimized with respect to the entire image. An alternative representation structure is provided by a convolutional sparse representation, in which a sparse representation of an entire image is computed by replacing the linear combination of a set of dictionary vectors by the sum of a set of convolutions with dictionary filters. The resulting representation is both single-valued and jointly optimized over the entire image. While this form of a sparse representation has been applied to a variety of problems in signal and image processing and computer vision, the computational expense of the corresponding optimization problems has restricted application to relatively small signals and images. This paper presents new, efficient algorithms that substantially improve on the performance of other recent methods, contributing to the development of this type of representation as a practical tool for a wider range of problems.

EMPIAR: a public archive for raw electron microscopy image data

Abstract: Raw 2D image data sets are often considerably larger than the final 3D reconstructions (gigabytes to terabytes versus megabytes to gigabytes), and their incorporation into EMDB is not currently feasible. In an effort to address the needs of the EM community and assess the challenges involved in data transfer and archiving, PDBe has developed EMPIAR, which is designed to handle data sets with sizes in the terabyte range. The EMPIAR website is the main portal to EMPIAR data. It includes a web-based deposition system and functionality to search, browse, view and download EMPIAR data sets (Fig. 1). Data can be transferred using Aspera (http://asperasoft. com) and Globus (https://www.globus.org) software or, if the amount of data is small, using standard FTP and HTTP protocols. EMPIAR currently contains 45 released entries averaging ~700 GB in size, with five entries exceeding 1 TB. On average, 13 TB of data are downloaded every month. There has been a recent increase in the number of downloads, as EMPIAR is the source of raw image data for the EMDataBank Map Validation Challenge (http://challenges.emdatabank.org/?q=2015_map_challenge). Although the basic infrastructure for EMPIAR is in place, we plan to improve the integration of EMDB and EMPIAR data in the PDBe web services and to provide API (application programming interface) access to EMPIAR metadata to facilitate integration with thirdparty web resources. Acting on input from the community2, we are also extending EMPIAR to support related imaging modalities including 3D scanning electron microscopy, soft X-ray tomography and CLEM (correlative light and electron microscopy). EMPIAR is being developed as a pilot archive with funding to September 2017. We envision that the archived raw data will be used to support the validation of selected structures; development, comparison and testing of new data-processing methods; development of new validation software; data provision for community challenges; peer review by anonymous referees; and teaching and training efforts for scientists who are new to EM. If the archive is successful in satisfying the needs of the community, we expect it to become an established resource in cellular and molecular structural biology.

Robust Retinal Vessel Segmentation via Locally Adaptive Derivative Frames in Orientation Scores

Abstract: This paper presents a robust and fully automatic filter-based approach for retinal vessel segmentation. We propose new filters based on 3D rotating frames in so-called orientation scores, which are functions on the Lie-group domain of positions and orientations $\mathbb {R}^{2} \rtimes S^{1}$ . By means of a wavelet-type transform, a 2D image is lifted to a 3D orientation score, where elongated structures are disentangled into their corresponding orientation planes. In the lifted domain $\mathbb {R}^{2} \rtimes S^{1}$ , vessels are enhanced by means of multi-scale second-order Gaussian derivatives perpendicular to the line structures. More precisely, we use a left-invariant rotating derivative (LID) frame, and a locally adaptive derivative (LAD) frame. The LAD is adaptive to the local line structures and is found by eigensystem analysis of the left-invariant Hessian matrix (computed with the LID). After multi-scale filtering via the LID or LAD in the orientation score domain, the results are projected back to the 2D image plane giving us the enhanced vessels. Then a binary segmentation is obtained through thresholding. The proposed methods are validated on six retinal image datasets with different image types, on which competitive segmentation performances are achieved. In particular, the proposed algorithm of applying the LAD filter on orientation scores (LAD-OS) outperforms most of the state-of-the-art methods. The LAD-OS is capable of dealing with typically difficult cases like crossings, central arterial reflex, closely parallel and tiny vessels. The high computational speed of the proposed methods allows processing of large datasets in a screening setting.

Microscopy Image Browser: A Platform for Segmentation and Analysis of Multidimensional Datasets.

Abstract: Understanding the structure–function relationship of cells and organelles in their natural context requires multidimensional imaging. As techniques for multimodal 3-D imaging have become more accessible, effective processing, visualization, and analysis of large datasets are posing a bottleneck for the workflow. Here, we present a new software package for high-performance segmentation and image processing of multidimensional datasets that improves and facilitates the full utilization and quantitative analysis of acquired data, which is freely available from a dedicated website. The open-source environment enables modification and insertion of new plug-ins to customize the program for specific needs. We provide practical examples of program features used for processing, segmentation and analysis of light and electron microscopy datasets, and detailed tutorials to enable users to rapidly and thoroughly learn how to use the program.

New Light Field Image Dataset

Abstract: Recently, an emerging light field imaging technology, which enables capturing full light information in a scene, has gained a lot of interest. To design, develop, implement, and test novel algorithms in light field image processing and compression, the availability of suitable light field image datasets is essential. In this paper, a publicly available light field image dataset is introduced and described in details. The proposed dataset contains 118 light field images captured by using a Lytro Illum light field camera. Based on their content, acquired light field images were classified into ten different categories with various features covering wide range of potential usage, such as image compression and quality evaluation.

Scalable High-Performance Image Registration Framework by Unsupervised Deep Feature Representations Learning

Abstract: Feature selection is a critical step in deformable image registration. In particular, selecting the most discriminative features that accurately and concisely describe complex morphological patterns in image patches improves correspondence detection, which in turn improves image registration accuracy. Furthermore, since more and more imaging modalities are being invented to better identify morphological changes in medical imaging data, the development of deformable image registration method that scales well to new image modalities or new image applications with little to no human intervention would have a significant impact on the medical image analysis community. To address these concerns, a learning-based image registration framework is proposed that uses deep learning to discover compact and highly discriminative features upon observed imaging data. Specifically, the proposed feature selection method uses a convolutional stacked autoencoder to identify intrinsic deep feature representations in image patches. Since deep learning is an unsupervised learning method, no ground truth label knowledge is required. This makes the proposed feature selection method more flexible to new imaging modalities since feature representations can be directly learned from the observed imaging data in a very short amount of time. Using the LONI and ADNI imaging datasets, image registration performance was compared to two existing state-of-the-art deformable image registration methods that use handcrafted features. To demonstrate the scalability of the proposed image registration framework, image registration experiments were conducted on 7.0-T brain MR images. In all experiments, the results showed that the new image registration framework consistently demonstrated more accurate registration results when compared to state of the art.

ITK-SNAP: An interactive tool for semi-automatic segmentation of multi-modality biomedical images

Abstract: Obtaining quantitative measures from biomedical images often requires segmentation, i.e., finding and outlining the structures of interest. Multi-modality imaging datasets, in which multiple imaging measures are available at each spatial location, are increasingly common, particularly in MRI. In applications where fully automatic segmentation algorithms are unavailable or fail to perform at desired levels of accuracy, semi-automatic segmentation can be a time-saving alternative to manual segmentation, allowing the human expert to guide segmentation, while minimizing the effort expended by the expert on repetitive tasks that can be automated. However, few existing 3D image analysis tools support semi-automatic segmentation of multi-modality imaging data. This paper describes new extensions to the ITK-SNAP interactive image visualization and segmentation tool that support semi-automatic segmentation of multi-modality imaging datasets in a way that utilizes information from all available modalities simultaneously. The approach combines Random Forest classifiers, trained by the user by placing several brushstrokes in the image, with the active contour segmentation algorithm. The new multi-modality semi-automatic segmentation approach is evaluated in the context of high-grade glioblastoma segmentation.

Two Dimensional Signal And Image Processing

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Technologies for imaging neural activity in large volumes

Abstract: Neural circuitry has evolved to form distributed networks that act dynamically across large volumes. Conventional microscopy collects data from individual planes and cannot sample circuitry across large volumes at the temporal resolution relevant to neural circuit function and behaviors. Here we review emerging technologies for rapid volume imaging of neural circuitry. We focus on two critical challenges: the inertia of optical systems, which limits image speed, and aberrations, which restrict the image volume. Optical sampling time must be long enough to ensure high-fidelity measurements, but optimized sampling strategies and point-spread function engineering can facilitate rapid volume imaging of neural activity within this constraint. We also discuss new computational strategies for processing and analyzing volume imaging data of increasing size and complexity. Together, optical and computational advances are providing a broader view of neural circuit dynamics and helping elucidate how brain regions work in concert to support behavior.

How Transferable are Neural Networks in NLP Applications

Abstract: Transfer learning is aimed to make use of valuable knowledge in a source domain to help model performance in a target domain. It is particularly important to neural networks, which are very likely to be overfitting. In some fields like image processing, many studies have shown the effectiveness of neural network-based transfer learning. For neural NLP, however, existing studies have only casually applied transfer learning, and conclusions are inconsistent. In this paper, we conduct systematic case studies and provide an illuminating picture on the transferability of neural networks in NLP.

Stain Specific Standardization of Whole-Slide Histopathological Images

Abstract: Variations in the color and intensity of hematoxylin and eosin (H&E) stained histological slides can potentially hamper the effectiveness of quantitative image analysis. This paper presents a fully automated algorithm for standardization of whole-slide histopathological images to reduce the effect of these variations. The proposed algorithm, called whole-slide image color standardizer (WSICS), utilizes color and spatial information to classify the image pixels into different stain components. The chromatic and density distributions for each of the stain components in the hue-saturation-density color model are aligned to match the corresponding distributions from a template whole-slide image (WSI). The performance of the WSICS algorithm was evaluated on two datasets. The first originated from 125 H&E stained WSIs of lymph nodes, sampled from 3 patients, and stained in 5 different laboratories on different days of the week. The second comprised 30 H&E stained WSIs of rat liver sections. The result of qualitative and quantitative evaluations using the first dataset demonstrate that the WSICS algorithm outperforms competing methods in terms of achieving color constancy. The WSICS algorithm consistently yields the smallest standard deviation and coefficient of variation of the normalized median intensity measure. Using the second dataset, we evaluated the impact of our algorithm on the performance of an already published necrosis quantification system. The performance of this system was significantly improved by utilizing the WSICS algorithm. The results of the empirical evaluations collectively demonstrate the potential contribution of the proposed standardization algorithm to improved diagnostic accuracy and consistency in computer-aided diagnosis for histopathology data.

No-Reference Image Blur Assessment Based on Discrete Orthogonal Moments

Abstract: Blur is a key determinant in the perception of image quality. Generally, blur causes spread of edges, which leads to shape changes in images. Discrete orthogonal moments have been widely studied as effective shape descriptors. Intuitively, blur can be represented using discrete moments since noticeable blur affects the magnitudes of moments of an image. With this consideration, this paper presents a blind image blur evaluation algorithm based on discrete Tchebichef moments. The gradient of a blurred image is first computed to account for the shape, which is more effective for blur representation. Then the gradient image is divided into equal-size blocks and the Tchebichef moments are calculated to characterize image shape. The energy of a block is computed as the sum of squared non-DC moment values. Finally, the proposed image blur score is defined as the variance-normalized moment energy, which is computed with the guidance of a visual saliency model to adapt to the characteristic of human visual system. The performance of the proposed method is evaluated on four public image quality databases. The experimental results demonstrate that our method can produce blur scores highly consistent with subjective evaluations. It also outperforms the state-of-the-art image blur metrics and several general-purpose no-reference quality metrics.

Estimating CT Image From MRI Data Using Structured Random Forest and Auto-Context Model

Abstract: Computed tomography (CT) imaging is an essential tool in various clinical diagnoses and radiotherapy treatment planning. Since CT image intensities are directly related to positron emission tomography (PET) attenuation coefficients, they are indispensable for attenuation correction (AC) of the PET images. However, due to the relatively high dose of radiation exposure in CT scan, it is advised to limit the acquisition of CT images. In addition, in the new PET and magnetic resonance (MR) imaging scanner, only MR images are available, which are unfortunately not directly applicable to AC. These issues greatly motivate the development of methods for reliable estimate of CT image from its corresponding MR image of the same subject. In this paper, we propose a learning-based method to tackle this challenging problem. Specifically, we first partition a given MR image into a set of patches. Then, for each patch, we use the structured random forest to directly predict a CT patch as a structured output, where a new ensemble model is also used to ensure the robust prediction. Image features are innovatively crafted to achieve multi-level sensitivity, with spatial information integrated through only rigid-body alignment to help avoiding the error-prone inter-subject deformable registration. Moreover, we use an auto-context model to iteratively refine the prediction. Finally, we combine all of the predicted CT patches to obtain the final prediction for the given MR image. We demonstrate the efficacy of our method on two datasets: human brain and prostate images. Experimental results show that our method can accurately predict CT images in various scenarios, even for the images undergoing large shape variation, and also outperforms two state-of-the-art methods.

An Efficient SVD-Based Method for Image Denoising

Abstract: Nonlocal self-similarity of images has attracted considerable interest in the field of image processing and has led to several state-of-the-art image denoising algorithms, such as block matching and 3-D, principal component analysis with local pixel grouping, patch-based locally optimal wiener, and spatially adaptive iterative singular-value thresholding. In this paper, we propose a computationally simple denoising algorithm using the nonlocal self-similarity and the low-rank approximation (LRA). The proposed method consists of three basic steps. First, our method classifies similar image patches by the block-matching technique to form the similar patch groups, which results in the similar patch groups to be low rank. Next, each group of similar patches is factorized by singular value decomposition (SVD) and estimated by taking only a few largest singular values and corresponding singular vectors. Finally, an initial denoised image is generated by aggregating all processed patches. For low-rank matrices, SVD can provide the optimal energy compaction in the least square sense. The proposed method exploits the optimal energy compaction property of SVD to lead an LRA of similar patch groups. Unlike other SVD-based methods, the LRA in SVD domain avoids learning the local basis for representing image patches, which usually is computationally expensive. The experimental results demonstrate that the proposed method can effectively reduce noise and be competitive with the current state-of-the-art denoising algorithms in terms of both quantitative metrics and subjective visual quality.