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Register a new userFocusLiteNN: High Efficiency Focus Quality Assessment for Digital Pathology
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Out-of-focus microscopy lens in digital pathology is a critical bottleneck in high-throughput Whole Slide Image (WSI) scanning platforms, for which pixel-level automated Focus Quality Assessment (FQA) methods are highly desirable to help significantly accelerate the clinical workflows. Existing FQA methods include both knowledge-driven and data-driven approaches. While data-driven approaches such as Convolutional Neural Network (CNN) based methods have shown great promises, they are difficult to use in practice due to their high computational complexity and lack of transferability. Here, we propose a highly efficient CNN-based model that maintains fast computations similar to the knowledge-driven methods without excessive hardware requirements such as GPUs. We create a training dataset using FocusPath which encompasses diverse tissue slides across nine different stain colors, where the stain diversity greatly helps the model to learn diverse color spectrum and tissue structures. In our attempt to reduce the CNN complexity, we find with surprise that even trimming down the CNN to the minimal level, it still achieves a highly competitive performance. We introduce a novel comprehensive evaluation dataset, the largest of its kind, annotated and compiled from TCGA repository for model assessment and comparison, for which the proposed method exhibits superior precision-speed trade-off when compared with existing knowledge-driven and data-driven FQA approaches.
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One of the challenges facing the adoption of digital pathology workflows for clinical use is the need for automated quality control. As the scanners sometimes determine focus inaccurately, the resultant image blur deteriorates the scanned slide to the point of being unusable. Also, the scanned slide images tend to be extremely large when scanned at greater or equal 20X image resolution. Hence, for digital pathology to be clinically useful, it is necessary to use computational tools to quickly and accurately quantify the image focus quality and determine whether an image needs to be re-scanned. We propose a no-reference focus quality assessment metric specifically for digital pathology images, that operates by using a sum of even-derivative filter bases to synthesize a human visual system-like kernel, which is modeled as the inverse of the lens point spread function. This kernel is then applied to a digital pathology image to modify high-frequency image information deteriorated by the scanners optics and quantify the focus quality at the patch level. We show in several experiments that our method correlates better with ground-truth $z$-level data than other methods, and is more computationally efficient. We also extend our method to generate a local slide-level focus quality heatmap, which can be used for automated slide quality control, and demonstrate the utility of our method for clinical scan quality control by comparison with subjective slide quality scores.
Automatic cell segmentation is an essential step in the pipeline of computer-aided diagnosis (CAD), such as the detection and grading of breast cancer. Accurate segmentation of cells can not only assist the pathologists to make a more precise diagnosis, but also save much time and labor. However, this task suffers from stain variation, cell inhomogeneous intensities, background clutters and cells from different tissues. To address these issues, we propose an Attention Enforced Network (AENet), which is built on spatial attention module and channel attention module, to integrate local features with global dependencies and weight effective channels adaptively. Besides, we introduce a feature fusion branch to bridge high-level and low-level features. Finally, the marker controlled watershed algorithm is applied to post-process the predicted segmentation maps for reducing the fragmented regions. In the test stage, we present an individual color normalization method to deal with the stain variation problem. We evaluate this model on the MoNuSeg dataset. The quantitative comparisons against several prior methods demonstrate the superiority of our approach.
To guarantee a satisfying Quality of Experience (QoE) for consumers, it is required to measure image quality efficiently and reliably. The neglect of the high-level semantic information may result in predicting a clear blue sky as bad quality, which is inconsistent with human perception. Therefore, in this paper, we tackle this problem by exploiting the high-level semantics and propose a novel no-reference image quality assessment method for realistic blur images. Firstly, the whole image is divided into multiple overlapping patches. Secondly, each patch is represented by the high-level feature extracted from the pre-trained deep convolutional neural network model. Thirdly, three different kinds of statistical structures are adopted to aggregate the information from different patches, which mainly contain some common statistics (i.e., the mean&standard deviation, quantiles and moments). Finally, the aggregated features are fed into a linear regression model to predict the image quality. Experiments show that, compared with low-level features, high-level features indeed play a more critical role in resolving the aforementioned challenging problem for quality estimation. Besides, the proposed method significantly outperforms the state-of-the-art methods on two realistic blur image databases and achieves comparable performance on two synthetic blur image databases.
Magnetic Resonance Imaging (MRI) suffers from several artifacts, the most common of which are motion artifacts. These artifacts often yield images that are of non-diagnostic quality. To detect such artifacts, images are prospectively evaluated by experts for their diagnostic quality, which necessitates patient-revisits and rescans whenever non-diagnostic quality scans are encountered. This motivates the need to develop an automated framework capable of accessing medical image quality and detecting diagnostic and non-diagnostic images. In this paper, we explore several convolutional neural network-based frameworks for medical image quality assessment and investigate several challenges therein.
The examination of histopathology images is considered to be the gold standard for the diagnosis and stratification of cancer patients. A key challenge in the analysis of such images is their size, which can run into the gigapixels and can require tedious screening by clinicians. With the recent advances in computational medicine, automatic tools have been proposed to assist clinicians in their everyday practice. Such tools typically process these large images by slicing them into tiles that can then be encoded and utilized for different clinical models. In this study, we propose a novel generative framework that can learn powerful representations for such tiles by learning to plausibly expand their visual field. In particular, we developed a progressively grown generative model with the objective of visual field expansion. Thus trained, our model learns to generate different tissue types with fine details, while simultaneously learning powerful representations that can be used for different clinical endpoints, all in a self-supervised way. To evaluate the performance of our model, we conducted classification experiments on CAMELYON17 and CRC benchmark datasets, comparing favorably to other self-supervised and pre-trained strategies that are commonly used in digital pathology. Our code is available at https://github.com/jcboyd/cdpath21-gan.
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