Radon-Gabor Barcodes for Medical Image Retrieval

In recent years, with the explosion of digital images on the Web, content-based retrieval has emerged as a significant research area. Shapes, textures, edges and segments may play a key role in describing the content of an image. Radon and Gabor transforms are both powerful techniques that have been widely studied to extract shape-texture-based information. The combined Radon-Gabor features may be more robust against scale/rotation variations, presence of noise, and illumination changes. The objective of this paper is to harness the potentials of both Gabor and Radon transforms in order to introduce expressive binary features, called barcodes, for image annotation/tagging tasks. We propose two different techniques: Gabor-of-Radon-Image Barcodes (GRIBCs), and Guided-Radon-of-Gabor Barcodes (GRGBCs). For validation, we employ the IRMA x-ray dataset with 193 classes, containing 12,677 training images and 1,733 test images. A total error score as low as 322 and 330 were achieved for GRGBCs and GRIBCs, respectively. This corresponds to $\approx 81\%$ retrieval accuracy for the first hit.Comment: To appear in proceedings of the 23rd International Conference on Pattern Recognition (ICPR 2016), Cancun, Mexico, December 201

Gabor Barcodes for Medical Image Retrieval

In recent years, advances in medical imaging have led to the emergence of massive databases, containing images from a diverse range of modalities. This has significantly heightened the need for automated annotation of the images on one side, and fast and memory-efficient content-based image retrieval systems on the other side. Binary descriptors have recently gained more attention as a potential vehicle to achieve these goals. One of the recently introduced binary descriptors for tagging of medical images are Radon barcodes (RBCs) that are driven from Radon transform via local thresholding. Gabor transform is also a powerful transform to extract texture-based information. Gabor features have exhibited robustness against rotation, scale, and also photometric disturbances, such as illumination changes and image noise in many applications. This paper introduces Gabor Barcodes (GBCs), as a novel framework for the image annotation. To find the most discriminative GBC for a given query image, the effects of employing Gabor filters with different parameters, i.e., different sets of scales and orientations, are investigated, resulting in different barcode lengths and retrieval performances. The proposed method has been evaluated on the IRMA dataset with 193 classes comprising of 12,677 x-ray images for indexing, and 1,733 x-rays images for testing. A total error score as low as $351$ ($\approx 80\%$ accuracy for the first hit) was achieved.Comment: To appear in proceedings of The 2016 IEEE International Conference on Image Processing (ICIP 2016), Sep 25-28, 2016, Phoenix, Arizona, US

Radon Projections as Image Descriptors for Content-Based Retrieval of Medical Images

Clinical analysis and medical diagnosis of diverse diseases adopt medical imaging techniques to empower specialists to perform their tasks by visualizing internal body organs and tissues for classifying and treating diseases at an early stage. Content-Based Image Retrieval (CBIR) systems are a set of computer vision techniques to retrieve similar images from a large database based on proper image representations. Particularly in radiology and histopathology, CBIR is a promising approach to effectively screen, understand, and retrieve images with similar level of semantic descriptions from a database of previously diagnosed cases to provide physicians with reliable assistance for diagnosis, treatment planning and research. Over the past decade, the development of CBIR systems in medical imaging has expedited due to the increase in digitized modalities, an increase in computational efficiency (e.g., availability of GPUs), and progress in algorithm development in computer vision and artificial intelligence. Hence, medical specialists may use CBIR prototypes to query similar cases from a large image database based solely on the image content (and no text). Understanding the semantics of an image requires an expressive descriptor that has the ability to capture and to represent unique and invariant features of an image. Radon transform, one of the oldest techniques widely used in medical imaging, can capture the shape of organs in form of a one-dimensional histogram by projecting parallel rays through a two-dimensional object of concern at a specific angle. In this work, the Radon transform is re-designed to (i) extract features and (ii) generate a descriptor for content-based retrieval of medical images. Radon transform is applied to feed a deep neural network instead of raw images in order to improve the generalization of the network. Specifically, the framework is composed of providing Radon projections of an image to a deep autoencoder, from which the deepest layer is isolated and fed into a multi-layer perceptron for classification. This approach enables the network to (a) train much faster as the Radon projections are computationally inexpensive compared to raw input images, and (b) perform more accurately as Radon projections can make more pronounced and salient features to the network compared to raw images. This framework is validated on a publicly available radiography data set called "Image Retrieval in Medical Applications" (IRMA), consisting of 12,677 train and 1,733 test images, for which an classification accuracy of approximately 82% is achieved, outperforming all autoencoder strategies reported on the Image Retrieval in Medical Applications (IRMA) dataset. The classification accuracy is calculated by dividing the total IRMA error, a calculation outlined by the authors of the data set, with the total number of test images. Finally, a compact handcrafted image descriptor based on Radon transform was designed in this work that is called "Forming Local Intersections of Projections" (FLIP). The FLIP descriptor has been designed, through numerous experiments, for representing histopathology images. The FLIP descriptor is based on Radon transform wherein parallel projections are applied in a local 3x3 neighborhoods with 2 pixel overlap of gray-level images (staining of histopathology images is ignored). Using four equidistant projection directions in each window, the characteristics of the neighborhood is quantified by taking an element-wise minimum between each adjacent projection in each window. Thereafter, the FLIP histogram (descriptor) for each image is constructed. A multi-resolution FLIP (mFLIP) scheme is also proposed which is observed to outperform many state-of-the-art methods, among others deep features, when applied on the histopathology data set KIMIA Path24. Experiments show a total classification accuracy of approximately 72% using SVM classification, which surpasses the current benchmark of approximately 66% on the KIMIA Path24 data set

Machine Learning-based Detection of Compensatory Balance Responses and Environmental Fall Risks Using Wearable Sensors

Falls are the leading cause of fatal and non-fatal injuries among seniors worldwide, with serious and costly consequences. Compensatory balance responses (CBRs) are reactions to recover stability following a loss of balance, potentially resulting in a fall if sufficient recovery mechanisms are not activated. While performance of CBRs are demonstrated risk factors for falls in seniors, the frequency, type, and underlying cause of these incidents occurring in everyday life have not been well investigated. This study was spawned from the lack of research on development of fall risk assessment methods that can be used for continuous and long-term mobility monitoring of the geri- atric population, during activities of daily living, and in their dwellings. Wearable sensor systems (WSS) offer a promising approach for continuous real-time detection of gait and balance behavior to assess the risk of falling during activities of daily living. To detect CBRs, we record movement signals (e.g. acceleration) and activity patterns of four muscles involving in maintaining balance using wearable inertial measurement units (IMUs) and surface electromyography (sEMG) sensors. To develop more robust detection methods, we investigate machine learning approaches (e.g., support vector machines, neural networks) and successfully detect lateral CBRs, during normal gait with accuracies of 92.4% and 98.1% using sEMG and IMU signals, respectively. Moreover, to detect environmental fall-related hazards that are associated with CBRs, and affect balance control behavior of seniors, we employ an egocentric mobile vision system mounted on participants chest. Two algorithms (e.g. Gabor Barcodes and Convolutional Neural Networks) are developed. Our vision-based method detects 17 different classes of environmental risk factors (e.g., stairs, ramps, curbs) with 88.5% accuracy. To the best of the authors knowledge, this study is the first to develop and evaluate an automated vision-based method for fall hazard detection

Autoencoding the Retrieval Relevance of Medical Images

Content-based image retrieval (CBIR) of medical images is a crucial task that can contribute to a more reliable diagnosis if applied to big data. Recent advances in feature extraction and classification have enormously improved CBIR results for digital images. However, considering the increasing accessibility of big data in medical imaging, we are still in need of reducing both memory requirements and computational expenses of image retrieval systems. This work proposes to exclude the features of image blocks that exhibit a low encoding error when learned by a $n/p/n$ autoencoder ($p\!<\!n$). We examine the histogram of autoendcoding errors of image blocks for each image class to facilitate the decision which image regions, or roughly what percentage of an image perhaps, shall be declared relevant for the retrieval task. This leads to reduction of feature dimensionality and speeds up the retrieval process. To validate the proposed scheme, we employ local binary patterns (LBP) and support vector machines (SVM) which are both well-established approaches in CBIR research community. As well, we use IRMA dataset with 14,410 x-ray images as test data. The results show that the dimensionality of annotated feature vectors can be reduced by up to 50% resulting in speedups greater than 27% at expense of less than 1% decrease in the accuracy of retrieval when validating the precision and recall of the top 20 hits.Comment: To appear in proceedings of The 5th International Conference on Image Processing Theory, Tools and Applications (IPTA'15), Nov 10-13, 2015, Orleans, Franc

Eyes-Free Vision-Based Scanning of Aligned Barcodes and Information Extraction from Aligned Nutrition Tables

Visually impaired (VI) individuals struggle with grocery shopping and have to rely on either friends, family or grocery store associates for shopping. ShopMobile 2 is a proof-of-concept system that allows VI shoppers to shop independently in a grocery store using only their smartphone. Unlike other assistive shopping systems that use dedicated hardware, this system is a software only solution that relies on fast computer vision algorithms. It consists of three modules - an eyes free barcode scanner, an optical character recognition (OCR) module, and a tele-assistance module. The eyes-free barcode scanner allows VI shoppers to locate and retrieve products by scanning barcodes on shelves and on products. The OCR module allows shoppers to read nutrition facts on products and the tele-assistance module allows them to obtain help from sighted individuals at remote locations. This dissertation discusses, provides implementations of, and presents laboratory and real-world experiments related to all three modules

TAMEE: data management and analysis for tissue microarrays

BACKGROUND: With the introduction of tissue microarrays (TMAs) researchers can investigate gene and protein expression in tissues on a high-throughput scale. TMAs generate a wealth of data calling for extended, high level data management. Enhanced data analysis and systematic data management are required for traceability and reproducibility of experiments and provision of results in a timely and reliable fashion. Robust and scalable applications have to be utilized, which allow secure data access, manipulation and evaluation for researchers from different laboratories. RESULTS: TAMEE (Tissue Array Management and Evaluation Environment) is a web-based database application for the management and analysis of data resulting from the production and application of TMAs. It facilitates storage of production and experimental parameters, of images generated throughout the TMA workflow, and of results from core evaluation. Database content consistency is achieved using structured classifications of parameters. This allows the extraction of high quality results for subsequent biologically-relevant data analyses. Tissue cores in the images of stained tissue sections are automatically located and extracted and can be evaluated using a set of predefined analysis algorithms. Additional evaluation algorithms can be easily integrated into the application via a plug-in interface. Downstream analysis of results is facilitated via a flexible query generator. CONCLUSION: We have developed an integrated system tailored to the specific needs of research projects using high density TMAs. It covers the complete workflow of TMA production, experimental use and subsequent analysis. The system is freely available for academic and non-profit institutions from