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Register a new userInstant Image Denoising Plugin for ImageJ using Convolutional Neural Networks
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Added by
Varun Mannam
Publication date
2020
fields
Electronic Engineering
and research's language is
English
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We present a new convolutional neural network (CNN) based ImageJ plugin for fluorescence microscopy image denoising with an average improvement of 7.5 dB in peak signal-to-noise ratio (PSNR) and denoising instantly within 80 msec.
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Convolutional Neural Networks (CNNs) have recently become a favored technique for image denoising due to its adaptive learning ability, especially with a deep configuration. However, their efficacy is inherently limited owing to their homogenous network formation with the unique use of linear convolution. In this study, we propose a heterogeneous network model which allows greater flexibility for embedding additional non-linearity at the core of the data transformation. To this end, we propose the idea of an operational neuron or Operational Neural Networks (ONN), which enables a flexible non-linear and heterogeneous configuration employing both inter and intra-layer neuronal diversity. Furthermore, we propose a robust operator search strategy inspired by the Hebbian theory, called the Synaptic Plasticity Monitoring (SPM) which can make data-driven choices for non-linearities in any architecture. An extensive set of comparative evaluations of ONNs and CNNs over two severe image denoising problems yield conclusive evidence that ONNs enriched by non-linear operators can achieve a superior denoising performance against CNNs with both equivalent and well-known deep configurations.
During the image acquisition process, noise is usually added to the data mainly due to physical limitations of the acquisition sensor, and also regarding imprecisions during the data transmission and manipulation. In that sense, the resultant image needs to be processed to attenuate its noise without losing details. Non-learning-based strategies such as filter-based and noise prior modeling have been adopted to solve the image denoising problem. Nowadays, learning-based denoising techniques showed to be much more effective and flexible approaches, such as Residual Convolutional Neural Networks. Here, we propose a new learning-based non-blind denoising technique named Attention Residual Convolutional Neural Network (ARCNN), and its extension to blind denoising named Flexible Attention Residual Convolutional Neural Network (FARCNN). The proposed methods try to learn the underlying noise expectation using an Attention-Residual mechanism. Experiments on public datasets corrupted by different levels of Gaussian and Poisson noise support the effectiveness of the proposed approaches against some state-of-the-art image denoising methods. ARCNN achieved an overall average PSNR results of around 0.44dB and 0.96dB for Gaussian and Poisson denoising, respectively FARCNN presented very consistent results, even with slightly worsen performance compared to ARCNN.
Deep convolutional networks often append additive constant (bias) terms to their convolution operations, enabling a richer repertoire of functional mappings. Biases are also used to facilitate training, by subtracting mean response over batches of training images (a component of batch normalization). Recent state-of-the-art blind denoising methods (e.g., DnCNN) seem to require these terms for their success. Here, however, we show that these networks systematically overfit the noise levels for which they are trained: when deployed at noise levels outside the training range, performance degrades dramatically. In contrast, a bias-free architecture -- obtained by removing the constant terms in every layer of the network, including those used for batch normalization-- generalizes robustly across noise levels, while preserving state-of-the-art performance within the training range. Locally, the bias-free network acts linearly on the noisy image, enabling direct analysis of network behavior via standard linear-algebraic tools. These analyses provide interpretations of network functionality in terms of nonlinear adaptive filtering, and projection onto a union of low-dimensional subspaces, connecting the learning-based method to more traditional denoising methodology.
Colorectal cancer is the third most common cancer-related death after lung cancer and breast cancer worldwide. The risk of developing colorectal cancer could be reduced by early diagnosis of polyps during a colonoscopy. Computer-aided diagnosis systems have the potential to be applied for polyp screening and reduce the number of missing polyps. In this paper, we compare the performance of different deep learning architectures as feature extractors, i.e. ResNet, DenseNet, InceptionV3, InceptionResNetV2 and SE-ResNeXt in the encoder part of a U-Net architecture. We validated the performance of presented ensemble models on the CVC-Clinic (GIANA 2018) dataset. The DenseNet169 feature extractor combined with U-Net architecture outperformed the other counterparts and achieved an accuracy of 99.15%, Dice similarity coefficient of 90.87%, and Jaccard index of 83.82%.
Accurate medical image segmentation is essential for diagnosis and treatment planning of diseases. Convolutional Neural Networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they are still challenged by complicated conditions where the segmentation target has large variations of position, shape and scale, and existing CNNs have a poor explainability that limits their application to clinical decisions. In this work, we make extensive use of multiple attentions in a CNN architecture and propose a comprehensive attention-based CNN (CA-Net) for more accurate and explainable medical image segmentation that is aware of the most important spatial positions, channels and scales at the same time. In particular, we first propose a joint spatial attention module to make the network focus more on the foreground region. Then, a novel channel attention module is proposed to adaptively recalibrate channel-wise feature responses and highlight the most relevant feature channels. Also, we propose a scale attention module implicitly emphasizing the most salient feature maps among multiple scales so that the CNN is adaptive to the size of an object. Extensive experiments on skin lesion segmentation from ISIC 2018 and multi-class segmentation of fetal MRI found that our proposed CA-Net significantly improved the average segmentation Dice score from 87.77% to 92.08% for skin lesion, 84.79% to 87.08% for the placenta and 93.20% to 95.88% for the fetal brain respectively compared with U-Net. It reduced the model size to around 15 times smaller with close or even better accuracy compared with state-of-the-art DeepLabv3+. In addition, it has a much higher explainability than existing networks by visualizing the attention weight maps. Our code is available at https://github.com/HiLab-git/CA-Net
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