Colour Vignetting Correction for Microscopy Image Mosaics Used for Quantitative Analyses

Prior Visual-Guided Self-Supervised Learning Enables Color Vignetting Correction for High-Throughput Microscopic Imaging

Vignetting constitutes a prevalent optical degradation that significantly compromises the quality of biomedical microscopic imaging. However, a robust and efficient vignetting correction methodology in multi-channel microscopic images remains absent at present. In this paper, we take advantage of a prior knowledge about the homogeneity of microscopic images and radial attenuation property of vignetting to develop a self-supervised deep learning algorithm that achieves complex vignetting removal in color microscopic images. Our proposed method, vignetting correction lookup table (VCLUT), is trainable on both single and multiple images, which employs adversarial learning to effectively transfer good imaging conditions from the user visually defined central region of its own light field to the entire image. To illustrate its effectiveness, we performed individual correction experiments on data from five distinct biological specimens. The results demonstrate that VCLUT exhibits enhanced performance compared to classical methods. We further examined its performance as a multi-image-based approach on a pathological dataset, revealing its advantage over other state-of-the-art approaches in both qualitative and quantitative measurements. Moreover, it uniquely possesses the capacity for generalization across various levels of vignetting intensity and an ultra-fast model computation capability, rendering it well-suited for integration into high-throughput imaging pipelines of digital microscopy.

Image Vignetting Correction Using a Deformable Radial Polynomial Model

Image vignetting is one of the major radiometric errors that occur in lens-camera systems. In many applications, vignetting is an undesirable effect; therefore, when it is impossible to fully prevent its occurrence, it is necessary to use computational methods for its correction. In probably the most frequently used approach to the vignetting correction, that is, the flat-field correction, the use of appropriate vignetting models plays a pivotal role. The radial polynomial (RP) model is commonly used, but for its proper use, the actual vignetting of the analyzed lens-camera system has to be a radial function. However, this condition is not fulfilled by many systems. There exist more universal models of vignetting; however, these models are much more sophisticated than the RP model. In this article, we propose a new model of vignetting named the Deformable Radial Polynomial (DRP) model, which joins the simplicity of the RP model with the universality of more sophisticated models. The DRP model uses a simple distance transformation and minimization method to match the radial vignetting model to the non-radial vignetting of the analyzed lens-camera system. The real-data experiment confirms that the DRP model, in general, gives better (up 35% or 50%, depending on the measure used) results than the RP model.

A Novel Low Rank Smooth Flat-Field Correction Algorithm for Hyperspectral Microscopy Imaging

A flat-field correction method is proposed for multiple measured hyperspectral microscopy imaging in this paper. As the most crucial preprocessing process in quantitative microscopic analysis, flat-field correction solves the uneven illumination caused by vignetting in microscopic images, and guarantees the precision of spatial and spectral information in hyperspectral microscopic imaging. In order to carry out flat-field correction and extract uneven illumination among groups of hyperspectral microscopic data containing hundreds of bands simultaneously, two properties of vignetting have been exploited: i) low-rank property is reflected by little information contained in vignetting; ii) local smoothness can be observed as a gradual change in brightness of vignetting, which is typically equivalent to the sparseness in spatial frequency domain. Combining the two properties above, a novel Low Rank Smooth Flat-field Correction (LRSFC) model modified from common orthogonal basis extraction is proposed, while an optimization is solved based on alternating direction multiplier method (ADMM), obtaining a unique flat-field term with low-rank and smooth properties. Qualitative and quantitative experimental assessments indicate that LRSFC does not add extra cell texture to the extracted flat-field term, whose performance appears prior to other state-of-the-art flat-field correction methods.

A Smooth Non-Iterative Local Polynomial (SNILP) Model of Image Vignetting

Image vignetting is one of the major radiometric errors, which occurs in lens-camera systems. In many applications, vignetting is an undesirable phenomenon; therefore, when it is impossible to fully prevent its occurrence, it is necessary to use computational methods for its correction in the acquired image. In the most frequently used approach to the vignetting correction, i.e., the flat-field correction, the usage of appropriate vignetting models plays a crucial role. In the article, the new model of vignetting, i.e., Smooth Non-Iterative Local Polynomial (SNILP) model, is proposed. The SNILP model was compared with the models known from the literature, e.g., the polynomial 2D and radial polynomial models, in a series of numerical tests and in the real-data experiment. The obtained results prove that the SNILP model usually gives better vignetting correction results than the other aforementioned tested models. For images larger than UXGA format (1600×1200), the proposed model is also faster than other tested models. Moreover, among the tested models, the SNILP model requires the least hardware resources for its application. This means that the SNILP model is suitable for its usage in devices with limited computing power.

Correction of uneven illumination in color microscopic image based on fully convolutional network

The correction of uneven illumination in microscopic image is a basic task in medical imaging. Most of the existing methods are designed for monochrome images. An effective fully convolutional network (FCN) is proposed to directly process color microscopic image in this paper. The proposed method estimates the distribution of illumination information in input image, and then carry out the correction of the corresponding uneven illumination through a feature encoder module, a feature decoder module, and a detail supplement module. In this process, overlapping residual blocks are designed to better transfer the illumination information, and in particular a well-designed weighted loss function ensures that the network can not only correct the illumination but also preserve image details. The proposed method is compared with some related methods on real pathological cell images qualitatively and quantitatively. Experimental results show that our method achieves the excellent performance. The proposed method is also applied to the preprocessing of whole slide imaging (WSI) tiles, which greatly improves the effect of image mosaicking.

Cauliflower Mosaic Virus TAV, a Plant Virus Protein That Functions like Ribonuclease H1 and is Cytotoxic to Glioma Cells

Recent comparisons between plant and animal viruses reveal many common principles that underlie how all viruses express their genetic material, amplify their genomes, and link virion assembly with replication. Cauliflower mosaic virus (CaMV) is not infectious for human beings. Here, we show that CaMV transactivator/viroplasmin protein (TAV) shares sequence similarity with and behaves like the human ribonuclease H1 (RNase H1) in reducing DNA/RNA hybrids detected with S9.6 antibody in HEK293T cells. We showed that TAV is clearly expressed in the cytosol and in the nuclei of transiently transfected human cells, similar to its distribution in plants. TAV also showed remarkable cytotoxic effects in U251 human glioma cells in vitro. These characteristics pave the way for future analysis on the use of the plant virus protein TAV, as an alternative to human RNAse H1 during gene therapy in human cells.