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README.md
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Confocal fluorescence microscopy is one of the most accessible and widely used
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imaging techniques for the study of biological processes at the cellular and
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subcellular levels. Scanning confocal microscopy allows the capture of
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high-quality images from thick three-dimensional (3D) samples, yet suffers from
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well-known limitations such as photobleaching and phototoxicity of specimens
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caused by intense light exposure, which limits its use in some applications,
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especially for living cells. Cellular damage can be alleviated by changing
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imaging parameters to reduce light exposure, often at the expense of image
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quality. Machine/deep learning methods for single-image super-resolution
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can be applied to restore image quality by upscaling lower-resolution
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images to produce high-resolution images (HR). These SISR methods have
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successfully applied to photo-realistic images due partly to the abundance
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publicly available
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partly limits their application and success in scanning confocal
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In this paper, we introduce a large scanning confocal microscopy
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SR-CACO-2 that is comprised of low- and high-resolution image pairs
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three different fluorescent markers. It allows
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SISR methods on three different upscaling levels
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contains the human epithelial cell line Caco-2
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patches for experiments with SISR methods. Given the new SR-CACO-2 dataset,
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we also provide benchmarking results for
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representative of the main SISR families. Results show that these methods have
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limited success in producing high-resolution textures, indicating that SR-CACO-2
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represents a challenging problem.
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**Code: Pytorch 2.0.0**
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Confocal fluorescence microscopy is one of the most accessible and widely used
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imaging techniques for the study of biological processes at the cellular and
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subcellular levels. Scanning confocal microscopy allows the capture of
|
36 |
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high-quality images from thick three-dimensional (3D) samples, yet suffers from
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well-known limitations such as photobleaching and phototoxicity of specimens
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caused by intense light exposure, which limits its use in some applications,
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especially for living cells. Cellular damage can be alleviated by changing
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imaging parameters to reduce light exposure, often at the expense of image
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quality. Machine/deep learning methods for single-image super-resolution
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(SISR) can be applied to restore image quality by upscaling lower-resolution
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(LR) images to produce high-resolution images (HR). These SISR methods have
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been successfully applied to photo-realistic images due partly to the abundance
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of publicly available datasets. In contrast, the lack of publicly available
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data partly limits their application and success in scanning confocal
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microscopy. In this paper, we introduce a large scanning confocal microscopy
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dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs
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marked for three different fluorescent markers. It allows to evaluate the
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performance of SISR methods on three different upscaling levels
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(X2, x34, x8). SR-CACO-2 contains the human epithelial cell line Caco-2
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(ATCC HTB-37), and it is composed of 2,200 unique images, captured with four
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resolutions and three markers, that have been translated in the form of 9,937
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patches for experiments with SISR methods. Given the new SR-CACO-2 dataset,
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we also provide benchmarking results for 16 state-of-the-art methods that are
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representative of the main SISR families. Results show that these methods have
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limited success in producing high-resolution textures, indicating that SR-CACO-2
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represents a challenging problem. The dataset is released under a Creative
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Commons license (CC BY-NC-SA 4.0), and it can be accessed freely. Our dataset,
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code and pretrained weights for SISR methods are publicly available: https://github.com/sbelharbi/sr-caco-2.
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**Code: Pytorch 2.0.0**
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