Fluorescence microscopy imaging speed is fundamentally limited by the measurement signal-to-noise ratio (SNR). To improve image SNR for a given image acquisition rate, computational denoising techniques can be used to suppress noise. However, common techniques to estimate a denoised image from a single frame either are computationally expensive or rely on simple noise statistical models. These models assume Poisson or Gaussian noise statistics, which are not appropriate for many fluorescence microscopy applications that contain quantum shot noise and electronic Johnson–Nyquist noise, therefore a mixture of Poisson and Gaussian noise. In this paper, we show convolutional neural networks (CNNs) trained on mixed Poisson and Gaussian noise images to overcome the limitations of existing image denoising methods. The trained CNN is presented as an open-source ImageJ plugin that performs real-time image denoising (within tens of milliseconds) with superior performance (SNR improvement) compared to conventional fluorescence microscopy denoising methods. The method is validated on external datasets with out-of-distribution noise, contrast, structure, and imaging modalities from the training data and consistently achieves high-performance (
This content will become publicly available on September 15, 2023
Denoising diffusion weighted imaging data using convolutional neural networks
Diffusion weighted imaging (DWI) with multiple, high b-values is critical for extracting tissue microstructure measurements; however, high b-value DWI images contain high noise levels that can overwhelm the signal of interest and bias microstructural measurements. Here, we propose a simple denoising method that can be applied to any dataset, provided a low-noise, single-subject dataset is acquired using the same DWI sequence. The denoising method uses a one-dimensional convolutional neural network (1D-CNN) and deep learning to learn from a low-noise dataset, voxel-by-voxel. The trained model can then be applied to high-noise datasets from other subjects. We validated the 1D-CNN denoising method by first demonstrating that 1D-CNN denoising resulted in DWI images that were more similar to the noise-free ground truth than comparable denoising methods, e.g., MP-PCA, using simulated DWI data. Using the same DWI acquisition but reconstructed with two common reconstruction methods, i.e. SENSE1 and sum-of-square, to generate a pair of low-noise and high-noise datasets, we then demonstrated that 1D-CNN denoising of high-noise DWI data collected from human subjects showed promising results in three domains: DWI images, diffusion metrics, and tractography. In particular, the denoised images were very similar to a low-noise reference image of that subject, more than the similarity more »
- Editors:
- Yap, Pew-Thian
- Award ID(s):
- 2004877
- Publication Date:
- NSF-PAR ID:
- 10377352
- Journal Name:
- PLOS ONE
- Volume:
- 17
- Issue:
- 9
- Page Range or eLocation-ID:
- e0274396
- ISSN:
- 1932-6203
- Sponsoring Org:
- National Science Foundation
More Like this
-
) denoising in less time than other fluorescence microscopy denoising methods. -
Flooding is one of the leading threats of natural disasters to human life and property, especially in densely populated urban areas. Rapid and precise extraction of the flooded areas is key to supporting emergency-response planning and providing damage assessment in both spatial and temporal measurements. Unmanned Aerial Vehicles (UAV) technology has recently been recognized as an efficient photogrammetry data acquisition platform to quickly deliver high-resolution imagery because of its cost-effectiveness, ability to fly at lower altitudes, and ability to enter a hazardous area. Different image classification methods including SVM (Support Vector Machine) have been used for flood extent mapping. In recent years, there has been a significant improvement in remote sensing image classification using Convolutional Neural Networks (CNNs). CNNs have demonstrated excellent performance on various tasks including image classification, feature extraction, and segmentation. CNNs can learn features automatically from large datasets through the organization of multi-layers of neurons and have the ability to implement nonlinear decision functions. This study investigates the potential of CNN approaches to extract flooded areas from UAV imagery. A VGG-based fully convolutional network (FCN-16s) was used in this research. The model was fine-tuned and a k-fold cross-validation was applied to estimate the performance of the modelmore »
-
Performing a direct match between images from different spectra (i.e., passive infrared and visible) is challenging because each spectrum contains different information pertaining to the subject’s face. In this work, we investigate the benefits and limitations of using synthesized visible face images from thermal ones and vice versa in cross-spectral face recognition systems. For this purpose, we propose utilizing canonical correlation analysis (CCA) and manifold learning dimensionality reduction (LLE). There are four primary contributions of this work. First, we formulate the cross-spectral heterogeneous face matching problem (visible to passive IR) using an image synthesis framework. Second, a new processed database composed of two datasets consistent of separate controlled frontal face subsets (VIS-MWIR and VIS-LWIR) is generated from the original, raw face datasets collected in three different bands (visible, MWIR and LWIR). This multi-band database is constructed using three different methods for preprocessing face images before feature extraction methods are applied. There are: (1) face detection, (2) CSU’s geometric normalization, and (3) our recommended geometric normalization method. Third, a post-synthesis image denoising methodology is applied, which helps alleviate different noise patterns present in synthesized images and improve baseline FR accuracy (i.e. before image synthesis and denoising is applied) in practical heterogeneousmore »
-
Deep convolutional neural networks (CNNs) for image denoising are usually trained on large datasets. These models achieve the current state of the art, but they have difficulties generalizing when applied to data that deviate from the training distribution. Recent work has shown that it is possible to train denoisers on a single noisy image. These models adapt to the features of the test image, but their performance is limited by the small amount of information used to train them. Here we propose "GainTuning", in which CNN models pre-trained on large datasets are adaptively and selectively adjusted for individual test images. To avoid overfitting, GainTuning optimizes a single multiplicative scaling parameter (the "Gain") of each channel in the convolutional layers of the CNN. We show that GainTuning improves state-of-the-art CNNs on standard image-denoising benchmarks, boosting their denoising performance on nearly every image in a held-out test set. These adaptive improvements are even more substantial for test images differing systematically from the training data, either in noise level or image type. We illustrate the potential of adaptive denoising in a scientific application, in which a CNN is trained on synthetic data, and tested on real transmission-electron-microscope images. In contrast to the existingmore »
-
Abstract Purpose The ability to identify the scholarship of individual authors is essential for performance evaluation. A number of factors hinder this endeavor. Common and similarly spelled surnames make it difficult to isolate the scholarship of individual authors indexed on large databases. Variations in name spelling of individual scholars further complicates matters. Common family names in scientific powerhouses like China make it problematic to distinguish between authors possessing ubiquitous and/or anglicized surnames (as well as the same or similar first names). The assignment of unique author identifiers provides a major step toward resolving these difficulties. We maintain, however, that in and of themselves, author identifiers are not sufficient to fully address the author uncertainty problem. In this study we build on the author identifier approach by considering commonalities in fielded data between authors containing the same surname and first initial of their first name. We illustrate our approach using three case studies. Design/methodology/approach The approach we advance in this study is based on commonalities among fielded data in search results. We cast a broad initial net—i.e., a Web of Science (WOS) search for a given author’s last name, followed by a comma, followed by the first initial of his ormore »