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Showing papers on "Image processing published in 2017"


Journal ArticleDOI
TL;DR: Zhang et al. as mentioned in this paper proposed a feed-forward denoising convolutional neural networks (DnCNNs) to handle Gaussian denobling with unknown noise level.
Abstract: The discriminative model learning for image denoising has been recently attracting considerable attentions due to its favorable denoising performance. In this paper, we take one step forward by investigating the construction of feed-forward denoising convolutional neural networks (DnCNNs) to embrace the progress in very deep architecture, learning algorithm, and regularization method into image denoising. Specifically, residual learning and batch normalization are utilized to speed up the training process as well as boost the denoising performance. Different from the existing discriminative denoising models which usually train a specific model for additive white Gaussian noise at a certain noise level, our DnCNN model is able to handle Gaussian denoising with unknown noise level (i.e., blind Gaussian denoising). With the residual learning strategy, DnCNN implicitly removes the latent clean image in the hidden layers. This property motivates us to train a single DnCNN model to tackle with several general image denoising tasks, such as Gaussian denoising, single image super-resolution, and JPEG image deblocking. Our extensive experiments demonstrate that our DnCNN model can not only exhibit high effectiveness in several general image denoising tasks, but also be efficiently implemented by benefiting from GPU computing.

5,902 citations


Journal ArticleDOI
TL;DR: QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images, making it suitable for a wide range of additional image analysis applications across biomedical research.
Abstract: QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath’s flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

2,838 citations


Journal ArticleDOI
TL;DR: This article proposes a vision‐based method using a deep architecture of convolutional neural networks (CNNs) for detecting concrete cracks without calculating the defect features, and shows quite better performances and can indeed find concrete cracks in realistic situations.
Abstract: A number of image processing techniques IPTs have been implemented for detecting civil infrastructure defects to partially replace human-conducted onsite inspections. These IPTs are primarily used to manipulate images to extract defect features, such as cracks in concrete and steel surfaces. However, the extensively varying real-world situations e.g., lighting and shadow changes can lead to challenges to the wide adoption of IPTs. To overcome these challenges, this article proposes a vision-based method using a deep architecture of convolutional neural networks CNNs for detecting concrete cracks without calculating the defect features. As CNNs are capable of learning image features automatically, the proposed method works without the conjugation of IPTs for extracting features. The designed CNN is trained on 40 K images of 256 × 256 pixel resolutions and, consequently, records with about 98% accuracy. The trained CNN is combined with a sliding window technique to scan any image size larger than 256 × 256 pixel resolutions. The robustness and adaptability of the proposed approach are tested on 55 images of 5,888 × 3,584 pixel resolutions taken from a different structure which is not used for training and validation processes under various conditions e.g., strong light spot, shadows, and very thin cracks. Comparative studies are conducted to examine the performance of the proposed CNN using traditional Canny and Sobel edge detection methods. The results show that the proposed method shows quite better performances and can indeed find concrete cracks in realistic situations.

1,898 citations


Journal ArticleDOI
TL;DR: It is shown that the quality of the results improves significantly with better loss functions, even when the network architecture is left unchanged, and a novel, differentiable error function is proposed.
Abstract: Neural networks are becoming central in several areas of computer vision and image processing and different architectures have been proposed to solve specific problems. The impact of the loss layer of neural networks, however, has not received much attention in the context of image processing: the default and virtually only choice is $\ell _2$ . In this paper, we bring attention to alternative choices for image restoration. In particular, we show the importance of perceptually-motivated losses when the resulting image is to be evaluated by a human observer. We compare the performance of several losses, and propose a novel, differentiable error function. We show that the quality of the results improves significantly with better loss functions, even when the network architecture is left unchanged.

1,758 citations


Journal ArticleDOI
TL;DR: The Trainable Weka Segmentation (TWS), a machine learning tool that leverages a limited number of manual annotations in order to train a classifier and segment the remaining data automatically, is introduced.
Abstract: Summary State-of-the-art light and electron microscopes are capable of acquiring large image datasets, but quantitatively evaluating the data often involves manually annotating structures of interest. This process is time-consuming and often a major bottleneck in the evaluation pipeline. To overcome this problem, we have introduced the Trainable Weka Segmentation (TWS), a machine learning tool that leverages a limited number of manual annotations in order to train a classifier and segment the remaining data automatically. In addition, TWS can provide unsupervised segmentation learning schemes (clustering) and can be customized to employ user-designed image features or classifiers. Availability and implementation TWS is distributed as open-source software as part of the Fiji image processing distribution of ImageJ at http://imagej.net/Trainable_Weka_Segmentation . Contact ignacio.arganda@ehu.eus. Supplementary information Supplementary data are available at Bioinformatics online.

1,416 citations


Proceedings ArticleDOI
21 Jul 2017
TL;DR: This paper reviews the first challenge on single image super-resolution (restoration of rich details in an low resolution image) with focus on proposed solutions and results and gauges the state-of-the-art in single imagesuper-resolution.
Abstract: This paper reviews the first challenge on single image super-resolution (restoration of rich details in an low resolution image) with focus on proposed solutions and results. A new DIVerse 2K resolution image dataset (DIV2K) was employed. The challenge had 6 competitions divided into 2 tracks with 3 magnification factors each. Track 1 employed the standard bicubic downscaling setup, while Track 2 had unknown downscaling operators (blur kernel and decimation) but learnable through low and high res train images. Each competition had ∽100 registered participants and 20 teams competed in the final testing phase. They gauge the state-of-the-art in single image super-resolution.

1,243 citations


Journal ArticleDOI
TL;DR: This work proposes a dynamic nonlinear reaction diffusion model with time-dependent parameters, which preserves the structural simplicity of diffusion models and take only a small number of diffusion steps, which makes the inference procedure extremely fast.
Abstract: Image restoration is a long-standing problem in low-level computer vision with many interesting applications. We describe a flexible learning framework based on the concept of nonlinear reaction diffusion models for various image restoration problems. By embodying recent improvements in nonlinear diffusion models, we propose a dynamic nonlinear reaction diffusion model with time-dependent parameters ( i.e. , linear filters and influence functions). In contrast to previous nonlinear diffusion models, all the parameters, including the filters and the influence functions, are simultaneously learned from training data through a loss based approach. We call this approach TNRD— Trainable Nonlinear Reaction Diffusion . The TNRD approach is applicable for a variety of image restoration tasks by incorporating appropriate reaction force. We demonstrate its capabilities with three representative applications, Gaussian image denoising, single image super resolution and JPEG deblocking. Experiments show that our trained nonlinear diffusion models largely benefit from the training of the parameters and finally lead to the best reported performance on common test datasets for the tested applications. Our trained models preserve the structural simplicity of diffusion models and take only a small number of diffusion steps, thus are highly efficient. Moreover, they are also well-suited for parallel computation on GPUs, which makes the inference procedure extremely fast.

1,181 citations


Journal ArticleDOI
TL;DR: Noise reduction improved quantification of low-density calcified inserts in phantom CT images and allowed coronary calcium scoring in low-dose patient CT images with high noise levels.
Abstract: Noise is inherent to low-dose CT acquisition We propose to train a convolutional neural network (CNN) jointly with an adversarial CNN to estimate routine-dose CT images from low-dose CT images and hence reduce noise A generator CNN was trained to transform low-dose CT images into routine-dose CT images using voxelwise loss minimization An adversarial discriminator CNN was simultaneously trained to distinguish the output of the generator from routine-dose CT images The performance of this discriminator was used as an adversarial loss for the generator Experiments were performed using CT images of an anthropomorphic phantom containing calcium inserts, as well as patient non-contrast-enhanced cardiac CT images The phantom and patients were scanned at 20% and 100% routine clinical dose Three training strategies were compared: the first used only voxelwise loss, the second combined voxelwise loss and adversarial loss, and the third used only adversarial loss The results showed that training with only voxelwise loss resulted in the highest peak signal-to-noise ratio with respect to reference routine-dose images However, CNNs trained with adversarial loss captured image statistics of routine-dose images better Noise reduction improved quantification of low-density calcified inserts in phantom CT images and allowed coronary calcium scoring in low-dose patient CT images with high noise levels Testing took less than 10 s per CT volume CNN-based low-dose CT noise reduction in the image domain is feasible Training with an adversarial network improves the CNNs ability to generate images with an appearance similar to that of reference routine-dose CT images

781 citations


Journal ArticleDOI
TL;DR: Zhang et al. as mentioned in this paper introduced a deep network architecture called DerainNet for removing rain streaks from an image, which directly learned the mapping relationship between rainy and clean image detail layers from data.
Abstract: We introduce a deep network architecture called DerainNet for removing rain streaks from an image. Based on the deep convolutional neural network (CNN), we directly learn the mapping relationship between rainy and clean image detail layers from data. Because we do not possess the ground truth corresponding to real-world rainy images, we synthesize images with rain for training. In contrast to other common strategies that increase depth or breadth of the network, we use image processing domain knowledge to modify the objective function and improve deraining with a modestly sized CNN. Specifically, we train our DerainNet on the detail (high-pass) layer rather than in the image domain. Though DerainNet is trained on synthetic data, we find that the learned network translates very effectively to real-world images for testing. Moreover, we augment the CNN framework with image enhancement to improve the visual results. Compared with the state-of-the-art single image de-raining methods, our method has improved rain removal and much faster computation time after network training.

701 citations


Journal ArticleDOI
TL;DR: This paper provides an alternative, more powerful, and more flexible framework for achieving Regularization by Denoising (RED): using the denoising engine in defining the regulariza...
Abstract: Removal of noise from an image is an extensively studied problem in image processing. Indeed, the recent advent of sophisticated and highly effective denoising algorithms has led some to believe that existing methods are touching the ceiling in terms of noise removal performance. Can we leverage this impressive achievement to treat other tasks in image processing? Recent work has answered this question positively, in the form of the Plug-and-Play Prior ($P^3$) method, showing that any inverse problem can be handled by sequentially applying image denoising steps. This relies heavily on the ADMM optimization technique in order to obtain this chained denoising interpretation. Is this the only way in which tasks in image processing can exploit the image denoising engine? In this paper we provide an alternative, more powerful, and more flexible framework for achieving the same goal. As opposed to the $P^3$ method, we offer Regularization by Denoising (RED): using the denoising engine in defining the regulariza...

697 citations


Journal ArticleDOI
TL;DR: A large publicly accessible data set of hematoxylin and eosin (H&E)-stained tissue images with more than 21000 painstakingly annotated nuclear boundaries is introduced, whose quality was validated by a medical doctor.
Abstract: Nuclear segmentation in digital microscopic tissue images can enable extraction of high-quality features for nuclear morphometrics and other analysis in computational pathology. Conventional image processing techniques, such as Otsu thresholding and watershed segmentation, do not work effectively on challenging cases, such as chromatin-sparse and crowded nuclei. In contrast, machine learning-based segmentation can generalize across various nuclear appearances. However, training machine learning algorithms requires data sets of images, in which a vast number of nuclei have been annotated. Publicly accessible and annotated data sets, along with widely agreed upon metrics to compare techniques, have catalyzed tremendous innovation and progress on other image classification problems, particularly in object recognition. Inspired by their success, we introduce a large publicly accessible data set of hematoxylin and eosin (H&E)-stained tissue images with more than 21000 painstakingly annotated nuclear boundaries, whose quality was validated by a medical doctor. Because our data set is taken from multiple hospitals and includes a diversity of nuclear appearances from several patients, disease states, and organs, techniques trained on it are likely to generalize well and work right out-of-the-box on other H&E-stained images. We also propose a new metric to evaluate nuclear segmentation results that penalizes object- and pixel-level errors in a unified manner, unlike previous metrics that penalize only one type of error. We also propose a segmentation technique based on deep learning that lays a special emphasis on identifying the nuclear boundaries, including those between the touching or overlapping nuclei, and works well on a diverse set of test images.

Journal ArticleDOI
TL;DR: It is found that supervised object- based classification is currently experiencing rapid advances, while development of the fuzzy technique is limited in the object-based framework, and spatial resolution correlates with the optimal segmentation scale and study area, and Random Forest shows the best performance inobject-based classification.
Abstract: Object-based image classification for land-cover mapping purposes using remote-sensing imagery has attracted significant attention in recent years. Numerous studies conducted over the past decade have investigated a broad array of sensors, feature selection, classifiers, and other factors of interest. However, these research results have not yet been synthesized to provide coherent guidance on the effect of different supervised object-based land-cover classification processes. In this study, we first construct a database with 28 fields using qualitative and quantitative information extracted from 254 experimental cases described in 173 scientific papers. Second, the results of the meta-analysis are reported, including general characteristics of the studies (e.g., the geographic range of relevant institutes, preferred journals) and the relationships between factors of interest (e.g., spatial resolution and study area or optimal segmentation scale, accuracy and number of targeted classes), especially with respect to the classification accuracy of different sensors, segmentation scale, training set size, supervised classifiers, and land-cover types. Third, useful data on supervised object-based image classification are determined from the meta-analysis. For example, we find that supervised object-based classification is currently experiencing rapid advances, while development of the fuzzy technique is limited in the object-based framework. Furthermore, spatial resolution correlates with the optimal segmentation scale and study area, and Random Forest (RF) shows the best performance in object-based classification. The area-based accuracy assessment method can obtain stable classification performance, and indicates a strong correlation between accuracy and training set size, while the accuracy of the point-based method is likely to be unstable due to mixed objects. In addition, the overall accuracy benefits from higher spatial resolution images (e.g., unmanned aerial vehicle) or agricultural sites where it also correlates with the number of targeted classes. More than 95.6% of studies involve an area less than 300 ha, and the spatial resolution of images is predominantly between 0 and 2 m. Furthermore, we identify some methods that may advance supervised object-based image classification. For example, deep learning and type-2 fuzzy techniques may further improve classification accuracy. Lastly, scientists are strongly encouraged to report results of uncertainty studies to further explore the effects of varied factors on supervised object-based image classification.

Journal ArticleDOI
TL;DR: A deep convolutional neural network is here used to map low-dose CT images towards its corresponding normal-dose counterparts in a patch-by-patch fashion, demonstrating a great potential of the proposed method on artifact reduction and structure preservation.
Abstract: In order to reduce the potential radiation risk, low-dose CT has attracted an increasing attention. However, simply lowering the radiation dose will significantly degrade the image quality. In this paper, we propose a new noise reduction method for low-dose CT via deep learning without accessing original projection data. A deep convolutional neural network is here used to map low-dose CT images towards its corresponding normal-dose counterparts in a patch-by-patch fashion. Qualitative results demonstrate a great potential of the proposed method on artifact reduction and structure preservation. In terms of the quantitative metrics, the proposed method has showed a substantial improvement on PSNR, RMSE and SSIM than the competing state-of-art methods. Furthermore, the speed of our method is one order of magnitude faster than the iterative reconstruction and patch-based image denoising methods.

Journal ArticleDOI
20 Sep 2017
TL;DR: In this paper, the authors demonstrate that deep neural networks (DNNs) can be trained to solve end-to-end inverse problems in computational imaging, where a DNN was trained to recover phase objects given their propagated intensity diffraction patterns.
Abstract: Deep learning has been proven to yield reliably generalizable solutions to numerous classification and decision tasks. Here, we demonstrate for the first time to our knowledge that deep neural networks (DNNs) can be trained to solve end-to-end inverse problems in computational imaging. We experimentally built and tested a lensless imaging system where a DNN was trained to recover phase objects given their propagated intensity diffraction patterns.

Journal ArticleDOI
TL;DR: In this paper, a detailed survey is conducted to identify the research challenges and the achievements till in this field, and those research papers are reviewed based on the image processing techniques, objectives, accuracy level, error level, and the image data sets.
Abstract: Cracks on the concrete surface are one of the earliest indications of degradation of the structure which is critical for the maintenance as well the continuous exposure will lead to the severe damage to the environment. Manual inspection is the acclaimed method for the crack inspection. In the manual inspection, the sketch of the crack is prepared manually, and the conditions of the irregularities are noted. Since the manual approach completely depends on the specialist’s knowledge and experience, it lacks objectivity in the quantitative analysis. So, automatic image-based crack detection is proposed as a replacement. Literature presents different techniques to automatically identify the crack and its depth using image processing techniques. In this research, a detailed survey is conducted to identify the research challenges and the achievements till in this field. Accordingly, 50 research papers are taken related to crack detection, and those research papers are reviewed. Based on the review, analysis is provided based on the image processing techniques, objectives, accuracy level, error level, and the image data sets. Finally, we present the various research issues which can be useful for the researchers to accomplish further research on the crack detection.

Journal ArticleDOI
TL;DR: In this paper, a convolutional neural network is used to predict the coefficients of a locally affine model in bilateral space, which is then applied to the full-resolution image.
Abstract: Performance is a critical challenge in mobile image processing. Given a reference imaging pipeline, or even human-adjusted pairs of images, we seek to reproduce the enhancements and enable real-time evaluation. For this, we introduce a new neural network architecture inspired by bilateral grid processing and local affine color transforms. Using pairs of input/output images, we train a convolutional neural network to predict the coefficients of a locally-affine model in bilateral space. Our architecture learns to make local, global, and content-dependent decisions to approximate the desired image transformation. At runtime, the neural network consumes a low-resolution version of the input image, produces a set of affine transformations in bilateral space, upsamples those transformations in an edge-preserving fashion using a new slicing node, and then applies those upsampled transformations to the full-resolution image. Our algorithm processes high-resolution images on a smartphone in milliseconds, provides a real-time viewfinder at 1080p resolution, and matches the quality of state-of-the-art approximation techniques on a large class of image operators. Unlike previous work, our model is trained off-line from data and therefore does not require access to the original operator at runtime. This allows our model to learn complex, scene-dependent transformations for which no reference implementation is available, such as the photographic edits of a human retoucher.

Journal ArticleDOI
TL;DR: The steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images are introduced and techniques that have proven useful in each stage of the data analysis process are recommended on the basis of the experience of 20 laboratories worldwide that are refining their image- based cell-profiling methodologies.
Abstract: Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences.

Posted Content
TL;DR: Graph Signal Processing (GSP) as discussed by the authors aims to develop tools for processing data defined on irregular graph domains, including sampling, filtering, and graph learning, which can be used for processing sensor network data, biological data, and image processing and machine learning.
Abstract: Research in Graph Signal Processing (GSP) aims to develop tools for processing data defined on irregular graph domains. In this paper we first provide an overview of core ideas in GSP and their connection to conventional digital signal processing. We then summarize recent developments in developing basic GSP tools, including methods for sampling, filtering or graph learning. Next, we review progress in several application areas using GSP, including processing and analysis of sensor network data, biological data, and applications to image processing and machine learning. We finish by providing a brief historical perspective to highlight how concepts recently developed in GSP build on top of prior research in other areas.

Journal ArticleDOI
TL;DR: A novel framework combining convolutional neural networks (CNN) and graph search methods (termed as CNN-GS) for the automatic segmentation of nine layer boundaries on retinal optical coherence tomography (OCT) images is presented.
Abstract: We present a novel framework combining convolutional neural networks (CNN) and graph search methods (termed as CNN-GS) for the automatic segmentation of nine layer boundaries on retinal optical coherence tomography (OCT) images. CNN-GS first utilizes a CNN to extract features of specific retinal layer boundaries and train a corresponding classifier to delineate a pilot estimate of the eight layers. Next, a graph search method uses the probability maps created from the CNN to find the final boundaries. We validated our proposed method on 60 volumes (2915 B-scans) from 20 human eyes with non-exudative age-related macular degeneration (AMD), which attested to effectiveness of our proposed technique.

Journal ArticleDOI
TL;DR: This work maps the spatial and temporal properties of the global signal, individually, in 1000+ fMRI scans from 8 sites to demonstrate the need for methods capable of isolating and removing global artifactual variance while preserving putative “neural” variance.

Journal ArticleDOI
TL;DR: A comprehensive overview and discussion of research in light field image processing, including basic light field representation and theory, acquisition, super-resolution, depth estimation, compression, editing, processing algorithms for light field display, and computer vision applications of light field data are presented.
Abstract: Light field imaging has emerged as a technology allowing to capture richer visual information from our world. As opposed to traditional photography, which captures a 2D projection of the light in the scene integrating the angular domain, light fields collect radiance from rays in all directions, demultiplexing the angular information lost in conventional photography. On the one hand, this higher dimensional representation of visual data offers powerful capabilities for scene understanding, and substantially improves the performance of traditional computer vision problems such as depth sensing, post-capture refocusing, segmentation, video stabilization, material classification, etc. On the other hand, the high-dimensionality of light fields also brings up new challenges in terms of data capture, data compression, content editing, and display. Taking these two elements together, research in light field image processing has become increasingly popular in the computer vision, computer graphics, and signal processing communities. In this paper, we present a comprehensive overview and discussion of research in this field over the past 20 years. We focus on all aspects of light field image processing, including basic light field representation and theory, acquisition, super-resolution, depth estimation, compression, editing, processing algorithms for light field display, and computer vision applications of light field data.

Journal ArticleDOI
TL;DR: A new method for classifying medical images that uses an ensemble of different convolutional neural network (CNN) architectures that achieves a higher accuracy than established CNNs and is only overtaken by those methods that source additional training data.
Abstract: The availability of medical imaging data from clinical archives, research literature, and clinical manuals, coupled with recent advances in computer vision offer the opportunity for image-based diagnosis, teaching, and biomedical research. However, the content and semantics of an image can vary depending on its modality and as such the identification of image modality is an important preliminary step. The key challenge for automatically classifying the modality of a medical image is due to the visual characteristics of different modalities: some are visually distinct while others may have only subtle differences. This challenge is compounded by variations in the appearance of images based on the diseases depicted and a lack of sufficient training data for some modalities. In this paper, we introduce a new method for classifying medical images that uses an ensemble of different convolutional neural network (CNN) architectures. CNNs are a state-of-the-art image classification technique that learns the optimal image features for a given classification task. We hypothesise that different CNN architectures learn different levels of semantic image representation and thus an ensemble of CNNs will enable higher quality features to be extracted. Our method develops a new feature extractor by fine-tuning CNNs that have been initialized on a large dataset of natural images. The fine-tuning process leverages the generic image features from natural images that are fundamental for all images and optimizes them for the variety of medical imaging modalities. These features are used to train numerous multiclass classifiers whose posterior probabilities are fused to predict the modalities of unseen images. Our experiments on the ImageCLEF 2016 medical image public dataset (30 modalities; 6776 training images, and 4166 test images) show that our ensemble of fine-tuned CNNs achieves a higher accuracy than established CNNs. Our ensemble also achieves a higher accuracy than methods in the literature evaluated on the same benchmark dataset and is only overtaken by those methods that source additional training data.

Journal ArticleDOI
20 Nov 2017
TL;DR: In this paper, a deep neural network was used to improve optical microscopy, enhancing its spatial resolution over a large field of view and depth of field. But, the only input to this network is an image acquired using a regular optical microscope, without any changes to its design.
Abstract: We demonstrate that a deep neural network can significantly improve optical microscopy, enhancing its spatial resolution over a large field of view and depth of field. After its training, the only input to this network is an image acquired using a regular optical microscope, without any changes to its design. We blindly tested this deep learning approach using various tissue samples that are imaged with low-resolution and wide-field systems, where the network rapidly outputs an image with better resolution, matching the performance of higher numerical aperture lenses and also significantly surpassing their limited field of view and depth of field. These results are significant for various fields that use microscopy tools, including, e.g., life sciences, where optical microscopy is considered as one of the most widely used and deployed techniques. Beyond such applications, the presented approach might be applicable to other imaging modalities, also spanning different parts of the electromagnetic spectrum, and can be used to design computational imagers that get better as they continue to image specimens and establish new transformations among different modes of imaging.

Journal ArticleDOI
TL;DR: In this article, a variety of methods for obtaining both 3D super-resolution images and 3D tracking infers structures or motions extending in the axial direction can easily be missed or confused.
Abstract: Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking inf...

Journal Article
TL;DR: This work introduces SalGAN, a deep convolutional neural network for visual saliency prediction trained with adversarial examples and shows how adversarial training allows reaching state-of-the-art performance across different metrics when combined with a widely-used loss function like BCE.
Abstract: We introduce SalGAN, a deep convolutional neural network for visual saliency prediction trained with adversarial examples. The first stage of the network consists of a generator model whose weights are learned by back-propagation computed from a binary cross entropy (BCE) loss over downsampled versions of the saliency maps. The resulting prediction is processed by a discriminator network trained to solve a binary classification task between the saliency maps generated by the generative stage and the ground truth ones. Our experiments show how adversarial training allows reaching state-of-the-art performance across different metrics when combined with a widely-used loss function like BCE. Our results can be reproduced with the source code and trained models available at https://imatge-upc.github. io/saliency-salgan-2017/.

Journal ArticleDOI
TL;DR: In this paper, a general-purpose image segmentation approach is used, including two feature learning algorithms; multiscale multilayered perceptrons (MLP) and convolutional neural networks (CNN).
Abstract: Ground vehicles equipped with monocular vision systems are a valuable source of high-resolution image data for precision agriculture applications in orchards This paper presents an image processing framework for fruit detection and counting using orchard image data A general-purpose image segmentation approach is used, including two feature learning algorithms; multiscale multilayered perceptrons (MLP) and convolutional neural networks (CNN) These networks were extended by including contextual information about how the image data was captured (metadata), which correlates with some of the appearance variations and/or class distributions observed in the data The pixel-wise fruit segmentation output is processed using the watershed segmentation (WS) and circular Hough transform (CHT) algorithms to detect and count individual fruits Experiments were conducted in a commercial apple orchard near Melbourne, Australia The results show an improvement in fruit segmentation performance with the inclusion of metadata on the previously benchmarked MLP network We extend this work with CNNs, bringing agrovision closer to the state-of-the-art in computer vision, where although metadata had negligible influence, the best pixel-wise F1-score of 0791 was achieved The WS algorithm produced the best apple detection and counting results, with a detection F1-score of 0861 As a final step, image fruit counts were accumulated over multiple rows at the orchard and compared against the post-harvest fruit counts that were obtained from a grading and counting machine The count estimates using CNN and WS resulted in the best performance for this data set, with a squared correlation coefficient of r2=0826

Journal ArticleDOI
TL;DR: In this article, the analysis of imaging data derived from micro-Fourier transform infrared (μFTIR) microscopy is presented, which is a powerful tool allowing to analyze microplastics enriched on membrane filters.
Abstract: The analysis of imaging data derived from micro-Fourier transform infrared (μFTIR) microscopy is a powerful tool allowing the analysis of microplastics enriched on membrane filters. In this study we present an automated approach to reduce the time demand currently needed for data analyses. We developed a novel analysis pipeline, based on the OPUS© Software by Bruker, followed by image analysis with Python and Simple ITK image processing modules. By using this newly developed pipeline it was possible to analyse datasets from focal plane array (FPA) μFTIR mapping of samples containing up to 1.8 million single spectra. All spectra were compared against a database of different synthetic and natural polymers by various routines followed by benchmark tests with focus on accuracy and quality. The spectral correlation was optimized for high quality data generation, which allowed image analysis. Based on these results an image analysis approach was developed, providing information on particle numbers and sizes for each polymer detected. It was possible to collect all data with relative ease even for complex sample matrices. This approach significantly decreases the time demand for the interpretation of complex FTIR-imaging data and significantly increases the data quality.

Journal ArticleDOI
TL;DR: It is shown that the interference effects associated with surface plasmon excitations at a metal-dielectric interface can perform spatial differentiation and points to a simple yet powerful mechanism for optical analog computing at the nanoscale.
Abstract: Optical analog computing offers high-throughput low-power-consumption operation for specialized computational tasks Traditionally, optical analog computing in the spatial domain uses a bulky system of lenses and filters Recent developments in metamaterials enable the miniaturization of such computing elements down to a subwavelength scale However, the required metamaterial consists of a complex array of meta-atoms, and direct demonstration of image processing is challenging Here, we show that the interference effects associated with surface plasmon excitations at a single metal-dielectric interface can perform spatial differentiation And we experimentally demonstrate edge detection of an image without any Fourier lens This work points to a simple yet powerful mechanism for optical analog computing at the nanoscale

Journal ArticleDOI
TL;DR: AstroImageJ (AIJ) as discussed by the authors is a GUI-driven, public domain, Java-based, software package for general image processing traditionally used mainly in life sciences fields.
Abstract: ImageJ is a graphical user interface (GUI) driven, public domain, Java-based, software package for general image processing traditionally used mainly in life sciences fields. The image processing capabilities of ImageJ are useful and extendable to other scientific fields. Here we present AstroImageJ (AIJ), which provides an astronomy specific image display environment and tools for astronomy specific image calibration and data reduction. Although AIJ maintains the general purpose image processing capabilities of ImageJ, AIJ is streamlined for time-series differential photometry, light curve detrending and fitting, and light curve plotting, especially for applications requiring ultra-precise light curves (e.g., exoplanet transits). AIJ reads and writes standard Flexible Image Transport System (FITS) files, as well as other common image formats, provides FITS header viewing and editing, and is World Coordinate System aware, including an automated interface to the astrometry.net web portal for plate solving images. AIJ provides research grade image calibration and analysis tools with a GUI driven approach, and easily installed cross-platform compatibility. It enables new users, even at the level of undergraduate student, high school student, or amateur astronomer, to quickly start processing, modeling, and plotting astronomical image data with one tightly integrated software package.

Journal ArticleDOI
TL;DR: It is concluded that systems employing 2D views of 3D data typically surpass voxel-based (3D) deep models, which however, can perform better with more layers and severe data augmentation, therefore, larger-scale datasets and increased resolutions are required.
Abstract: Deep learning has recently gained popularity achieving state-of-the-art performance in tasks involving text, sound, or image processing. Due to its outstanding performance, there have been efforts to apply it in more challenging scenarios, for example, 3D data processing. This article surveys methods applying deep learning on 3D data and provides a classification based on how they exploit them. From the results of the examined works, we conclude that systems employing 2D views of 3D data typically surpass voxel-based (3D) deep models, which however, can perform better with more layers and severe data augmentation. Therefore, larger-scale datasets and increased resolutions are required.