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Deep learning methods, in particular, trained Convolutional Neural Networks (CNN) have recently been shown to produce compelling results for single image Super-Resolution (SR). Invariably, a CNN is learned to map the Low Resolution (LR) image to its corresponding High Resolution (HR) version in the spatial domain. We propose a novel network structure for learning the SR mapping function in an image transform domain, specifically the Discrete Cosine Transform (DCT). As the first contribution, we show that DCT can be integrated into the network structure as a Convolutional DCT (CDCT) layer. With the CDCT layer, we construct the DCT Deep SR (DCT-DSR) network. We further extend the DCT-DSR to allow the CDCT layer to become trainable (i.e., optimizable). Because this layer represents an image transform, we enforce pairwise orthogonality constraints and newly formulated complexity order constraints on the individual basis functions/filters. This Orthogonally Regularized Deep SR network (ORDSR) simplifies the SR task by taking advantage of image transform domain while adapting the design of transform basis to the training image set. Experimental results show ORDSR achieves state-of-the-art SR image quality with fewer parameters than most of the deep CNN methods. A particular success of ORDSR is in overcoming the artifacts introduced by bicubic interpolation. A key burden of deep SR has been identified as the requirement of generous training LR and HR image pairs; ORSDR exhibits a much more graceful degradation as training size is reduced with significant benefits in the regime of limited training. Analysis of memory and computation requirements confirms that ORDSR can allow for a more efficient network with faster inference.

H syndrome is a rare monogenic autosomal recessive disease with characteristic cutaneous findings and multisystem involvement. The aim of this study is to present an Iranian patient with H syndrome and to describe a novel frameshift mutation in SLC29A3 gene. The patient was diagnosed with a few small areas of hyperpigmentation and accompanying hypertrichosis in the lumbar area of her back. Her clinical phenotypes included short stature, hepatosplenomegaly, facial widespread bilateral telangiectatic lesions, bilateral hypertrophy of the parotid gland, upper extremity flexion contracture, elevated inflammatory markers (ESR, CRP) and diabetes mellitus. The identification of a novel homozygous frameshift mutation (c.307_308delTT, p.F103Ter) in SLC29A3 gene, together with the characteristic clinical manifestations of H syndrome, provided accurate diagnosis for this patient., (Copyright © 2019 Elsevier Masson SAS. All rights reserved.)

Sparsity constrained single image super-resolution (SR) has been of much recent interest. A typical approach involves sparsely representing patches in a low-resolution (LR) input image via a dictionary of example LR patches, and then using the coefficients of this representation to generate the high-resolution (HR) output via an analogous HR dictionary. However, most existing sparse representation methods for SR focus on the luminance channel information and do not capture interactions between color channels. In this paper, we extend sparsity-based SR to multiple color channels by taking the color information into account. Edge similarities amongst RGB color bands are exploited as cross channel correlation constraints. These additional constraints lead to a new optimization problem, which is not easily solvable; however, a tractable solution is proposed to solve it efficiently. Moreover, to fully exploit the complementary information among color channels, a dictionary learning method is also proposed specifically to learn color dictionaries that encourage edge similarities. Merits of the proposed method over state of the art are demonstrated both visually and quantitatively using image quality metrics.

In histopathological image analysis, feature extraction for classification is a challenging task due to the diversity of histology features suitable for each problem as well as presence of rich geometrical structures. In this paper, we propose an automatic feature discovery framework via learning class-specific dictionaries and present a low-complexity method for classification and disease grading in histopathology. Essentially, our Discriminative Feature-oriented Dictionary Learning (DFDL) method learns class-specific dictionaries such that under a sparsity constraint, the learned dictionaries allow representing a new image sample parsimoniously via the dictionary corresponding to the class identity of the sample. At the same time, the dictionary is designed to be poorly capable of representing samples from other classes. Experiments on three challenging real-world image databases: 1) histopathological images of intraductal breast lesions, 2) mammalian kidney, lung and spleen images provided by the Animal Diagnostics Lab (ADL) at Pennsylvania State University, and 3) brain tumor images from The Cancer Genome Atlas (TCGA) database, reveal the merits of our proposal over state-of-the-art alternatives. Moreover, we demonstrate that DFDL exhibits a more graceful decay in classification accuracy against the number of training images which is highly desirable in practice where generous training is often not available.

Introduction: Histopathological images have rich structural information, are multi-channel in nature and contain meaningful pathological information at various scales. Sophisticated image analysis tools that can automatically extract discriminative information from the histopathology image slides for diagnosis remain an area of significant research activity. In this work, we focus on automated brain cancer grading, specifically glioma grading. Grading of a glioma is a highly important problem in pathology and is largely done manually by medical experts based on an examination of pathology slides (images). To complement the efforts of clinicians engaged in brain cancer diagnosis, we develop novel image processing algorithms and systems to automatically grade glioma tumor into two categories: Low-grade glioma (LGG) and high-grade glioma (HGG) which represent a more advanced stage of the disease., Results: We propose novel image processing algorithms based on spatial domain analysis for glioma tumor grading that will complement the clinical interpretation of the tissue. The image processing techniques are developed in close collaboration with medical experts to mimic the visual cues that a clinician looks for in judging of the grade of the disease. Specifically, two algorithmic techniques are developed: (1) A cell segmentation and cell-count profile creation for identification of Pseudopalisading Necrosis, and (2) a customized operation of spatial and morphological filters to accurately identify microvascular proliferation (MVP). In both techniques, a hierarchical decision is made via a decision tree mechanism. If either Pseudopalisading Necrosis or MVP is found present in any part of the histopathology slide, the whole slide is identified as HGG, which is consistent with World Health Organization guidelines. Experimental results on the Cancer Genome Atlas database are presented in the form of: (1) Successful detection rates of pseudopalisading necrosis and MVP regions, (2) overall classification accuracy into LGG and HGG categories, and (3) receiver operating characteristic curves which can facilitate a desirable trade-off between HGG detection and false-alarm rates., Conclusion: The proposed method demonstrates fairly high accuracy and compares favorably against best-known alternatives such as the state-of-the-art WND-CHARM feature set provided by NIH combined with powerful support vector machine classifier. Our results reveal that the proposed method can be beneficial to a clinician in effectively separating histopathology slides into LGG and HGG categories, particularly where the analysis of a large number of slides is needed. Our work also reveals that MVP regions are much harder to detect than Pseudopalisading Necrosis and increasing accuracy of automated image processing for MVP detection emerges as a significant future research direction.

The multi-channel nature of digital histopathological images presents an opportunity to exploit the correlated color channel information for better image modeling. Inspired by recent work in sparsity for single channel image classification, we propose a new simultaneous sparsity model for multi-channel histopathological image representation and classification (SHIRC). Essentially, we represent a histopathological image as a sparse linear combination of training examples under suitable channel-wise constraints. Classification is performed by solving a newly formulated simultaneous sparsity-based optimization problem. A practical challenge is the correspondence of image objects (cellular and nuclear structures) at different spatial locations in the image. We propose a robust locally adaptive variant of SHIRC (LA-SHIRC) to tackle this issue. Experiments on two challenging real-world image data sets: 1) mammalian tissue images acquired by pathologists of the animal diagnostics lab (ADL) at Pennsylvania State University, and 2) human intraductal breast lesions, reveal the merits of our proposal over state-of-the-art alternatives. Further, we demonstrate that LA-SHIRC exhibits a more graceful decay in classification accuracy against the number of training images which is highly desirable in practice where generous training per class is often not available.

The mathematical theory of compressed sensing (CS) asserts that one can acquire signals from measurements whose rate is much lower than the total bandwidth. Whereas the CS theory is now well developed, challenges concerning hardware implementations of CS-based acquisition devices--especially in optics--have only started being addressed. This paper presents an implementation of compressive sensing in fluorescence microscopy and its applications to biomedical imaging. Our CS microscope combines a dynamic structured wide-field illumination and a fast and sensitive single-point fluorescence detection to enable reconstructions of images of fluorescent beads, cells, and tissues with undersampling ratios (between the number of pixels and number of measurements) up to 32. We further demonstrate a hyperspectral mode and record images with 128 spectral channels and undersampling ratios up to 64, illustrating the potential benefits of CS acquisition for higher-dimensional signals, which typically exhibits extreme redundancy. Altogether, our results emphasize the interest of CS schemes for acquisition at a significantly reduced rate and point to some remaining challenges for CS fluorescence microscopy.