scholarly journals Protocol for applying Machine Learning models for the transformation of conventional fluorescence images to super-resolution

2021 ◽  
Author(s):  
Vadim Zinchuk ◽  
Olga Grossenbacher-Zinchuk
Keyword(s):  
Machine Learning ◽  
Fluorescence Microscopy ◽  
Super Resolution ◽  
Learning Models ◽  
Conventional Fluorescence Microscopy ◽  
Mobile Computers ◽  
Analytical Tools ◽  
Image Details ◽  
Microscopy Images ◽  
Machine Learning Models

Abstract Machine Learning offers the opportunity to visualize the invisible in conventional fluorescence microscopy images by improving their resolution while preserving and enhancing image details. This protocol describes the application of GAN-based Machine Learning models to transform the resolution of conventional fluorescence microscopy images to a resolution comparable with super-resolution. It provides a flexible environment using a modern app functioning on both desktop and mobile computers. This approach can be extended for use on other types of microscopy images empowering life science researchers with modern analytical tools.

scholarly journals Application of Convolutional Neural Networks Towards Nuclei Segmentation in Localization-based Super-Resolution Fluorescence Microscopy Images

2021 ◽  
Author(s):  
Christopher Mela ◽  
Yang Liu
Keyword(s):  
Neural Networks ◽  
Fluorescence Microscopy ◽  
Convolutional Neural Networks ◽  
Super Resolution ◽  
Biological Research ◽  
Nuclei Segmentation ◽  
Segmentation Accuracy ◽  
Conventional Fluorescence Microscopy ◽  
Microscopy Images ◽  
Resolution Data

Abstract Background Automated segmentation of nuclei in microscopic images has been conducted to enhance throughput in pathological diagnostics and biological research. Segmentation accuracy and speed has been significantly enhanced with the advent of convolutional neural networks. A barrier in the broad application of neural networks to nuclei segmentation is the necessity to train the network using a set of application specific images and image labels. Previous works have attempted to create broadly trained networks for universal nuclei segmentation; however, such networks do not work on all imaging modalities, and best results are still commonly found when the network is retrained on user specific data. Stochastic optical reconstruction microscopy (STORM) based super-resolution fluorescence microscopy has opened a new avenue to image nuclear architecture at nanoscale resolutions. Due to the large size and discontinuous features typical of super-resolution images, automatic nuclei segmentation can be difficult. In this study, we apply commonly used networks (Mask R-CNN and UNet architectures) towards the task of segmenting super-resolution images of nuclei. First, we assess whether networks broadly trained on conventional fluorescence microscopy datasets can accurately segment super-resolution images. Then, we compare the resultant segmentations with results obtained using networks trained directly on our super-resolution data. We next attempt to optimize and compare segmentation accuracy using three different neural network architectures. Results Results indicate that super-resolution images are not broadly compatible with neural networks trained on conventional bright-field or fluorescence microscopy images. When the networks were trained on super-resolution data, however, we attained nuclei segmentation accuracies (F1-Score) in excess of 0.8, comparable to past results found when conducting nuclei segmentation on conventional fluorescence microscopy images. Overall, we achieved the best results utilizing the Mask R-CNN architecture. Conclusions We found that convolutional neural networks are powerful tools capable of accurately and quickly segmenting localization-based super-resolution microscopy images of nuclei. While broadly trained and widely applicable segmentation algorithms are desirable for quick use with minimal input, optimal results are still found when the network is both trained and tested on visually similar images. We provide a set of Colab notebooks to disseminate the software into the broad scientific community (https://github.com/YangLiuLab/Super-Resolution-Nuclei-Segmentation).

scholarly journals Super-resolution reconstruction of turbulent flows with machine learning

2019 ◽  
Vol 870 ◽  
pp. 106-120 ◽  
Author(s):  
Kai Fukami ◽  
Koji Fukagata ◽  
Kunihiko Taira
Keyword(s):  
Machine Learning ◽  
Flow Field ◽  
Turbulent Flow ◽  
Turbulent Flows ◽  
Field Data ◽  
Super Resolution ◽  
Two Dimensional ◽  
Learning Models ◽  
Resolution Analysis ◽  
Machine Learning Models

We use machine learning to perform super-resolution analysis of grossly under-resolved turbulent flow field data to reconstruct the high-resolution flow field. Two machine learning models are developed, namely, the convolutional neural network (CNN) and the hybrid downsampled skip-connection/multi-scale (DSC/MS) models. These machine learning models are applied to a two-dimensional cylinder wake as a preliminary test and show remarkable ability to reconstruct laminar flow from low-resolution flow field data. We further assess the performance of these models for two-dimensional homogeneous turbulence. The CNN and DSC/MS models are found to reconstruct turbulent flows from extremely coarse flow field images with remarkable accuracy. For the turbulent flow problem, the machine-leaning-based super-resolution analysis can greatly enhance the spatial resolution with as little as 50 training snapshot data, holding great potential to reveal subgrid-scale physics of complex turbulent flows. With the growing availability of flow field data from high-fidelity simulations and experiments, the present approach motivates the development of effective super-resolution models for a variety of fluid flows.

scholarly journals Application of convolutional neural networks towards nuclei segmentation in localization-based super-resolution fluorescence microscopy images

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Christopher A. Mela ◽  
Yang Liu
Keyword(s):  
Neural Networks ◽  
Fluorescence Microscopy ◽  
Convolutional Neural Networks ◽  
Super Resolution ◽  
Biological Research ◽  
Nuclei Segmentation ◽  
Segmentation Accuracy ◽  
Conventional Fluorescence Microscopy ◽  
Microscopy Images ◽  
Resolution Data

Abstract Background Automated segmentation of nuclei in microscopic images has been conducted to enhance throughput in pathological diagnostics and biological research. Segmentation accuracy and speed has been significantly enhanced with the advent of convolutional neural networks. A barrier in the broad application of neural networks to nuclei segmentation is the necessity to train the network using a set of application specific images and image labels. Previous works have attempted to create broadly trained networks for universal nuclei segmentation; however, such networks do not work on all imaging modalities, and best results are still commonly found when the network is retrained on user specific data. Stochastic optical reconstruction microscopy (STORM) based super-resolution fluorescence microscopy has opened a new avenue to image nuclear architecture at nanoscale resolutions. Due to the large size and discontinuous features typical of super-resolution images, automatic nuclei segmentation can be difficult. In this study, we apply commonly used networks (Mask R-CNN and UNet architectures) towards the task of segmenting super-resolution images of nuclei. First, we assess whether networks broadly trained on conventional fluorescence microscopy datasets can accurately segment super-resolution images. Then, we compare the resultant segmentations with results obtained using networks trained directly on our super-resolution data. We next attempt to optimize and compare segmentation accuracy using three different neural network architectures. Results Results indicate that super-resolution images are not broadly compatible with neural networks trained on conventional bright-field or fluorescence microscopy images. When the networks were trained on super-resolution data, however, we attained nuclei segmentation accuracies (F1-Score) in excess of 0.8, comparable to past results found when conducting nuclei segmentation on conventional fluorescence microscopy images. Overall, we achieved the best results utilizing the Mask R-CNN architecture. Conclusions We found that convolutional neural networks are powerful tools capable of accurately and quickly segmenting localization-based super-resolution microscopy images of nuclei. While broadly trained and widely applicable segmentation algorithms are desirable for quick use with minimal input, optimal results are still found when the network is both trained and tested on visually similar images. We provide a set of Colab notebooks to disseminate the software into the broad scientific community (https://github.com/YangLiuLab/Super-Resolution-Nuclei-Segmentation).

Improving XGBoost with Imagination Sampling

2020 ◽  
Vol 2 (1) ◽  
pp. 3-6
Author(s):  
Eric Holloway
Keyword(s):  
Machine Learning ◽  
General System ◽  
Learning Models ◽  
Starting Point ◽  
Machine Learning Models

Imagination Sampling is the usage of a person as an oracle for generating or improving machine learning models. Previous work demonstrated a general system for using Imagination Sampling for obtaining multibox models. Here, the possibility of importing such models as the starting point for further automatic enhancement is explored.

Epigenetic Target Prediction with Accurate Machine Learning Models

2021 ◽  
Author(s):  
Norberto Sánchez-Cruz ◽  
Jose L. Medina-Franco
Keyword(s):  
Machine Learning ◽  
Small Molecules ◽  
Predictive Models ◽  
Large Scale ◽  
Target Prediction ◽  
Quantitative Measure ◽  
Learning Models ◽  
Discovery Research ◽  
Drug Discovery Research ◽  
Machine Learning Models

<p>Epigenetic targets are a significant focus for drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents a large amount of structure-activity relationships that has not been exploited thus far for the development of predictive models to support medicinal chemistry efforts. Herein, we report the first large-scale study of 26318 compounds with a quantitative measure of biological activity for 55 protein targets with epigenetic activity. Through a systematic comparison of machine learning models trained on molecular fingerprints of different design, we built predictive models with high accuracy for the epigenetic target profiling of small molecules. The models were thoroughly validated showing mean precisions up to 0.952 for the epigenetic target prediction task. Our results indicate that the herein reported models have considerable potential to identify small molecules with epigenetic activity. Therefore, our results were implemented as freely accessible and easy-to-use web application.</p>

Utilizing Blockchain Technology in Social Media Bot Identification

2020 ◽  
Author(s):  
Shreya Reddy ◽  
Lisa Ewen ◽  
Pankti Patel ◽  
Prerak Patel ◽  
Ankit Kundal ◽  
...  
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Gold Standard ◽  
The Internet ◽  
Learning Models ◽  
Current Time ◽  
Machine Learning Methods ◽  
Blockchain Technology ◽  
Modern Age ◽  
Machine Learning Models

<p>As bots become more prevalent and smarter in the modern age of the internet, it becomes ever more important that they be identified and removed. Recent research has dictated that machine learning methods are accurate and the gold standard of bot identification on social media. Unfortunately, machine learning models do not come without their negative aspects such as lengthy training times, difficult feature selection, and overwhelming pre-processing tasks. To overcome these difficulties, we are proposing a blockchain framework for bot identification. At the current time, it is unknown how this method will perform, but it serves to prove the existence of an overwhelming gap of research under this area.<i></i></p>

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