Electrical Engineering And Systems Science

Malignant brain tumors are among the deadliest neoplasms with the lowest survival rates of any cancer type. In considering surgical tumor resection, suboptimal extent of resection is linked to poor clinical outcomes and lower overall survival rates. Currently available tools for intraoperative histopathological assessment require an average of 20 minutes processing and are of limited diagnostic quality for guiding surgeries. Consequently, there is an unaddressed need for a rapid imaging technique to guide maximal resection of brain tumors. Working towards this goal, presented here is an all optical non-contact label-free reflection mode photoacoustic remote sensing (PARS) microscope. By using a tunable excitation laser, PARS takes advantage of the endogenous optical absorption peaks of DNA and cytoplasm to achieve virtual contrast analogous to standard hematoxylin and eosin (H and E) staining. In conjunction, a fast 266 nm excitation is used to generate large grossing scans and rapidly assess small fields in real-time with hematoxylin-like contrast. Images obtained using this technique show comparable quality and contrast to the current standard for histopathological assessment of brain tissues. Using the proposed method, rapid, high-throughput, histological-like imaging was achieved in unstained brain tissues, indicating PARS utility for intraoperative guidance to improve extent of surgical resection.

Structured Illumination Microscopy is a widespread methodology to image live and fixed biological structures smaller than the diffraction limits of conventional optical microscopy. Using recent advances in image up-scaling through deep learning models, we demonstrate a method to reconstruct 3D SIM image stacks with twice the axial resolution attainable through conventional SIM reconstructions. We further evaluate our method for robustness to noise & generalisability to varying observed specimens, and discuss potential adaptions of the method to further improvements in resolution.

Despite their remarkable expressibility, convolution neural networks (CNNs) still fall short of delivering satisfactory results on single image dehazing, especially in terms of faithful recovery of fine texture details. In this paper, we argue that the inadequacy of conventional CNN-based dehazing methods can be attributed to the fact that the domain of hazy images is too far away from that of clear images, rendering it difficult to train a CNN for learning direct domain shift through an end-to-end manner and recovering texture details simultaneously. To address this issue, we propose to add explicit constraints inside a deep CNN model to guide the restoration process. In contrast to direct learning, the proposed mechanism shifts and narrows the candidate region for the estimation output via multiple confident neighborhoods. Therefore, it is capable of consolidating the expressibility of different architectures, resulting in a more accurate indirect domain shift (IDS) from the hazy images to that of clear images. We also propose two different training schemes, including hard IDS and soft IDS, which further reveal the effectiveness of the proposed method. Our extensive experimental results indicate that the dehazing method based on this mechanism outperforms the state-of-the-arts.

Signal-to-Noise Ratios (SNRs) and the Shannon-Hartley channel capacity are metrics that help define the loss of known information while transferring data through a noisy channel. These metrics cannot be used for quantifying the opposite process: the harvesting of new information. Correlation functions and correlation coefficients do play an important role in collecting new information from noisy sources. However, Bershad and Rockmore [1974] based their formulas on contradictory a priori assumptions in Real-space and in Fourier-space. Their formulations were subsequently copied literally to the practical science of electron microscopy, where those a priori assumptions now distort most quality metrics in Cryo-EM. Cryo-EM became a great success in recent years [Wiley Award 2017; Nobel prize for Chemistry 2017] and became the method of choice for revealing structures of biological complexes like ribosomes, viruses, or corona-virus spikes, vitally important during the current COVID-19 pandemic. Those early misconceptions now interfere with the objective comparison of independently obtained results. We found that the roots of these problems significantly pre-date those 1970s publications and were already inherent in the original SNR definitions. We here propose novel metrics to assess the amount of information harvested in an experiment, information which is measured in bits. These new metrics assess the total amount of information collected on an object, as well as the information density distribution within that object. The new metrics can be applied everywhere where data is collected, processed, compressed, or compared. As an example, we compare the structures of two recently published SARS-CoV-2 spike proteins. We also introduce new metrics for transducer-quality assessment in many sciences including: cryo-EM, biomedical imaging, microscopy, signal processing, photography, tomography, etc.

Background and Objective:Computer-aided diagnosis (CAD) systems promote diagnosis effectiveness and alleviate pressure of radiologists. A CAD system for lung cancer diagnosis includes nodule candidate detection and nodule malignancy evaluation. Recently, deep learning-based pulmonary nodule detection has reached satisfactory performance ready for clinical application. However, deep learning-based nodule malignancy evaluation depends on heuristic inference from low-dose computed tomography volume to malignant probability, which lacks clinical cognition. Methods:In this paper, we propose a joint radiology analysis and malignancy evaluation network (R2MNet) to evaluate the pulmonary nodule malignancy via radiology characteristics analysis. Radiological features are extracted as channel descriptor to highlight specific regions of the input volume that are critical for nodule malignancy evaluation. In addition, for model explanations, we propose channel-dependent activation mapping to visualize the features and shed light on the decision process of deep neural network. Results:Experimental results on the LIDC-IDRI dataset demonstrate that the proposed method achieved area under curve of 96.27% on nodule radiology analysis and AUC of 97.52% on nodule malignancy evaluation. In addition, explanations of CDAM features proved that the shape and density of nodule regions were two critical factors that influence a nodule to be inferred as malignant, which conforms with the diagnosis cognition of experienced radiologists. Conclusion:Incorporating radiology analysis with nodule malignant evaluation, the network inference process conforms to the diagnostic procedure of radiologists and increases the confidence of evaluation results. Besides, model interpretation with CDAM features shed light on the regions which DNNs focus on when they estimate nodule malignancy probabilities.

Purpose. Early squamous cell neoplasia (ESCN) in the oesophagus is a highly treatable condition. Lesions confined to the mucosal layer can be curatively treated endoscopically. We build a computer-assisted detection (CADe) system that can classify still images or video frames as normal or abnormal with high diagnostic accuracy. Methods. We present a new benchmark dataset containing 68K binary labeled frames extracted from 114 patient videos whose imaged areas have been resected and correlated to histopathology. Our novel convolutional network (CNN) architecture solves the binary classification task and explains what features of the input domain drive the decision-making process of the network. Results. The proposed method achieved an average accuracy of 91.7 % compared to the 94.7 % achieved by a group of 12 senior clinicians. Our novel network architecture produces deeply supervised activation heatmaps that suggest the network is looking at intrapapillary capillary loop (IPCL) patterns when predicting abnormality. Conclusion. We believe that this dataset and baseline method may serve as a reference for future benchmarks on both video frame classification and explainability in the context of ESCN detection. A future work path of high clinical relevance is the extension of the classification to ESCN types.

There is uncertainty around the effect of aging of children on biometric characteristics impacting applications relying on biometric recognition, particularly as the time between enrollment and query increases. Though there have been studies of such effects for iris recognition in adults, there have been few studies evaluating impact in children. This paper presents longitudinal analysis from 209 subjects aged 4 to 11 years at enrollment and six additional sessions over a period of 3 years. The influence of time, dilation and enrollment age on iris recognition have been analyzed and their statistical importance has been evaluated. A minor aging effect is noted which is statistically significant, but practically insignificant and is comparatively less important than other variability factors. Practical biometric applications of iris recognition in children are feasible for a time frame of at least 3 years between samples, for ages 4 to 11 years, even in presence of aging, though we note practical difficulties in enrolling young children with cameras not designed for the purpose. To the best of our knowledge, the database used in this study is the only dataset of longitudinal iris images from children for this age group and time period that is available for research.

Facial image inpainting is a challenging problem as it requires generating new pixels that include semantic information for masked key components in a face, e.g., eyes and nose. Recently, remarkable methods have been proposed in this field. Most of these approaches use encoder-decoder architectures and have different limitations such as allowing unique results for a given image and a particular mask. Alternatively, some approaches generate promising results using different masks with generator networks. However, these approaches are optimization-based and usually require quite a number of iterations. In this paper, we propose an efficient solution to the facial image painting problem using the Cyclic Reverse Generator (CRG) architecture, which provides an encoder-generator model. We use the encoder to embed a given image to the generator space and incrementally inpaint the masked regions until a plausible image is generated; a discriminator network is utilized to assess the generated images during the iterations. We empirically observed that only a few iterations are sufficient to generate realistic images with the proposed model. After the generation process, for the post processing, we utilize a Unet model that we trained specifically for this task to remedy the artifacts close to the mask boundaries. Our method allows applying sketch-based inpaintings, using variety of mask types, and producing multiple and diverse results. We qualitatively compared our method with the state-of-the-art models and observed that our method can compete with the other models in all mask types; it is particularly better in images where larger masks are utilized.

Dose reduction in computed tomography (CT) is essential for decreasing radiation risk in clinical applications. Iterative reconstruction is one of the most promising ways to compensate for the increased noise due to reduction of photon flux. Rather than most existing prior-driven algorithms that benefit from manually designed prior functions or supervised learning schemes, in this work we integrate the data-consistency as a conditional term into the iterative generative model for low-dose CT. At the stage of prior learning, the gradient of data density is directly learned from normal-dose CT images as a prior. Then at the iterative reconstruction stage, the stochastic gradient descent is employed to update the trained prior with annealed and conditional schemes. The distance between the reconstructed image and the manifold is minimized along with data fidelity during reconstruction. Experimental comparisons demonstrated the noise reduction and detail preservation abilities of the proposed method.

Inpainting-based image compression is emerging as a promising competitor to transform-based compression techniques. Its key idea is to reconstruct image information from only few known regions through inpainting. Specific partial differential equations (PDEs) such as edge-enhancing diffusion (EED) give high quality reconstructions of image structures with low or medium texture. Even though the strengths of PDE- and transform-based compression are complementary, they have rarely been combined within a hybrid codec. We propose to sparsify blocks of a JPEG compressed image and reconstruct them with EED inpainting. Our codec consistently outperforms JPEG and gives useful indications for successfully developing hybrid codecs further. Furthermore, our method is the first to choose regions rather than pixels as known data for PDE-based compression. It also gives novel insights into the importance of corner regions for EED-based codecs.