Cross-system biological image quality enhancement based on the generative adversarial network as a foundation for establishing a multi-institute microscopy cooperative network

High-quality fluorescence imaging of biological systems is limited by processes like photobleaching and phototoxicity, and also in many cases, by limited access to the latest generations of microscopes. Moreover, low temporal resolution can lead to a motion blur effect in living systems. Our work presents a deep learning (DL) generative-adversarial approach to the problem of obtaining high-quality (HQ) images based on their low-quality (LQ) equivalents. We propose a generative-adversarial network (GAN) for contrast transfer between two different separate microscopy systems: a confocal microscope (producing HQ images) and a wide-field fluorescence microscope (producing LQ images). Our model proves that such transfer is possible, allowing us to receive HQ-generated images characterized by low mean squared error (MSE) values, high structural similarity index (SSIM), and high peak signal-to-noise ratio (PSNR) values. For our best model in the case of comparing HQ-generated images and HQ-ground truth images, the median values of the metrics are 6x10-4, 0.9413, and 31.87, for MSE, SSIM, and PSNR, respectively. In contrast, in the case of comparison between LQ and HQ ground truth median values of the metrics are equal to 0.0071, 0.8304, and 21.48 for MSE, SSIM, and PSNR respectively. Therefore, we observe a significant increase ranging from 14% to 49% for SSIM and PSNR respectively. These results, together with other single-system cross-modality studies, provide proof of concept for further implementation of a cross-system biological image quality enhancement.

SLOVA: Uncertainty Estimation Using Single Label One-Vs-All Classifier

Deep neural networks present impressive performance, yet they cannot reliably estimate their predictive confidence, limiting their applicability in high-risk domains. We show that applying a multi-label one-vs-all loss reveals classification ambiguity and reduces model overconfidence. The introduced SLOVA (Single Label One-Vs-All) model redefines typical one-vs-all predictive probabilities to a single label situation, where only one class is the correct answer. The proposed classifier is confident only if a single class has a high probability and other probabilities are negligible. Unlike the typical softmax function, SLOVA naturally detects out-of-distribution samples if the probabilities of all other classes are small. The model is additionally fine-tuned with exponential calibration, which allows us to precisely align the confidence score with model accuracy. We verify our approach on three tasks. First, we demonstrate that SLOVA is competitive with the state-of-the-art on in-distribution calibration. Second, the performance of SLOVA is robust under dataset shifts. Finally, our approach performs extremely well in the detection of out-of-distribution samples. Consequently, SLOVA is a tool that can be used in various applications where uncertainty modeling is required.

Introduction to Cross-Entropy Clustering The R Package CEC

The R Package CEC performs clustering based on the cross-entropy clustering (CEC) method, which was recently developed with the use of information theory. The main advantage of CEC is that it combines the speed and simplicity of $k$-means with the ability to use various Gaussian mixture models and reduce unnecessary clusters. In this work we present a practical tutorial to CEC based on the R Package CEC. Functions are provided to encompass the whole process of clustering.

Detection of elliptical shapes via cross-entropy clustering

The problem of finding elliptical shapes in an image will be considered. We discuss the solution which uses cross-entropy clustering. The proposed method allows the search for ellipses with predefined sizes and position in the space. Moreover, it works well for search of ellipsoids in higher dimensions.