Browse
Submit Data
Databases
API
Help

Dataset Information

33 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Machine learning denoising of high-resolution X-ray nanotomography data.

ABSTRACT: High-resolution X-ray nanotomography is a quantitative tool for investigating specimens from a wide range of research areas. However, the quality of the reconstructed tomogram is often obscured by noise and therefore not suitable for automatic segmentation. Filtering methods are often required for a detailed quantitative analysis. However, most filters induce blurring in the reconstructed tomograms. Here, machine learning (ML) techniques offer a powerful alternative to conventional filtering methods. In this article, we verify that a self-supervised denoising ML technique can be used in a very efficient way for eliminating noise from nanotomography data. The technique presented is applied to high-resolution nanotomography data and compared to conventional filters, such as a median filter and a nonlocal means filter, optimized for tomographic data sets. The ML approach proves to be a very powerful tool that outperforms conventional filters by eliminating noise without blurring relevant structural features, thus enabling efficient quantitative analysis in different scientific fields.

SUBMITTER: Flenner S

PROVIDER: S-EPMC8733986 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data.

Project description:MotivationNext-generation amplicon sequencing is a powerful tool for investigating microbial communities. A main challenge is to distinguish true biological variants from errors caused by amplification and sequencing. In traditional analyses, such errors are eliminated by clustering reads within a sequence similarity threshold, usually 97%, and constructing operational taxonomic units, but the arbitrary threshold leads to low resolution and high false positive rates. Recently developed "denoising" methods have proven able to resolve single-nucleotide amplicon variants, but they still miss low frequency sequences, especially those near more frequent sequences, because they ignore the sequencing quality information.ResultsWe introduce AmpliCI, a reference-free, model-based method for rapidly resolving the number, abundance and identity of error-free sequences in massive Illumina amplicon datasets. AmpliCI takes into account quality information and allows the data, not an arbitrary threshold or an external database, to drive conclusions. AmpliCI estimates a finite mixture model, using a greedy strategy to gradually select error-free sequences and approximately maximize the likelihood. AmpliCI has better performance than three popular denoising methods, with acceptable computation time and memory usage.AvailabilitySource code is available at https://github.com/DormanLab/AmpliCI.Supplementary informationSupplementary material are available at Bioinformatics online.

| S-EPMC7850112 | biostudies-literature

Deep denoising for multi-dimensional synchrotron X-ray tomography without high-quality reference data.

Project description:Synchrotron X-ray tomography enables the examination of the internal structure of materials at submicron spatial resolution and subsecond temporal resolution. Unavoidable experimental constraints can impose dose and time limits on the measurements, introducing noise in the reconstructed images. Convolutional neural networks (CNNs) have emerged as a powerful tool to remove noise from reconstructed images. However, their training typically requires collecting a dataset of paired noisy and high-quality measurements, which is a major obstacle to their use in practice. To circumvent this problem, methods for CNN-based denoising have recently been proposed that require no separate training data beyond the already available noisy reconstructions. Among these, the Noise2Inverse method is specifically designed for tomography and related inverse problems. To date, applications of Noise2Inverse have only taken into account 2D spatial information. In this paper, we expand the application of Noise2Inverse in space, time, and spectrum-like domains. This development enhances applications to static and dynamic micro-tomography as well as X-ray diffraction tomography. Results on real-world datasets establish that Noise2Inverse is capable of accurate denoising and enables a substantial reduction in acquisition time while maintaining image quality.

| S-EPMC8178391 | biostudies-literature

Machine learning driven by environmental covariates to estimate high-resolution PM2.5 in data-poor regions.

Project description:PM2.5, which refers to fine particles with an equivalent aerodynamic diameter of less than or equal to 2.5 µm, can not only affect air quality but also endanger public health. Nevertheless, the spatial distribution of PM2.5 is not well understood in data-poor regions where monitoring stations are scarce. Therefore, we constructed a random forest (RF) model and a bagging algorithm model based on ground-monitored PM2.5 data, aerosol optical depth (AOD) and meteorological data, and auxiliary geographical variables to accurately estimate the spatial distribution of PM2.5 concentrations in Xinjiang during 2015-2020 at a resolution of 1 km. Through 10-fold cross-validation (CV), the RF model and bagging algorithm model were verified and compared. The results showed the following: (1) The RF model achieved better model performance and thus can be used to estimate the PM2.5 concentration at a relatively high resolution. (2) The PM2.5 concentrations were high in southern Xinjiang and low in northern Xinjiang. The high values were concentrated mainly in the Tarim Basin, while most areas of northern Xinjiang maintained low PM2.5 levels year-round. (3) The PM2.5 values in Xinjiang showed significant seasonality, with the seasonally averaged concentrations decreasing as follows: winter (71.95 µg m-3) > spring (64.76 µg m-3) > autumn (46.01 µg m-3) > summer (43.40 µg m-3). Our model provides a way to monitor air quality in data-scarce places, thereby advancing efforts to achieve sustainable development in the future.

| S-EPMC8976473 | biostudies-literature

Ab initio nonrigid X-ray nanotomography.

Project description:Reaching the full potential of X-ray nanotomography, in particular for biological samples, is limited by many factors, of which one of the most serious is radiation damage. Although sample deformation caused by radiation damage can be partly mitigated by cryogenic protection, it is still present in these conditions and, as we exemplify here using a specimen extracted from scales of the Cyphochilus beetle, it will pose a limit to the achievable imaging resolution. We demonstrate a generalized tomographic model, which optimally follows the sample morphological changes and attempts to recover the original sample structure close to the ideal, damage-free reconstruction. Whereas our demonstration was performed using ptychographic X-ray tomography, the method can be adopted for any tomographic imaging modality. Our application demonstrates improved reconstruction quality of radiation-sensitive samples, which will be of increasing relevance with the higher brightness of 4th generation synchrotron sources.

| S-EPMC6565693 | biostudies-literature

Improving peak detection in high-resolution LC/MS metabolomics data using preexisting knowledge and machine learning approach.

Project description:Peak detection is a key step in the preprocessing of untargeted metabolomics data generated from high-resolution liquid chromatography-mass spectrometry (LC/MS). The common practice is to use filters with predetermined parameters to select peaks in the LC/MS profile. This rigid approach can cause suboptimal performance when the choice of peak model and parameters do not suit the data characteristics.Here we present a method that learns directly from various data features of the extracted ion chromatograms (EICs) to differentiate between true peak regions from noise regions in the LC/MS profile. It utilizes the knowledge of known metabolites, as well as robust machine learning approaches. Unlike currently available methods, this new approach does not assume a parametric peak shape model and allows maximum flexibility. We demonstrate the superiority of the new approach using real data. Because matching to known metabolites entails uncertainties and cannot be considered a gold standard, we also developed a probabilistic receiver-operating characteristic (pROC) approach that can incorporate uncertainties.The new peak detection approach is implemented as part of the apLCMS package available at http://web1.sph.emory.edu/apLCMS/ CONTACT: tyu8@emory.eduSupplementary data are available at Bioinformatics online.

| S-EPMC4184266 | biostudies-literature

High-Resolution Urban Air Quality Mapping for Multiple Pollutants Based on Dense Monitoring Data and Machine Learning.

Project description:Spatially explicit urban air quality information is important for urban fine-management and public life. However, existing air quality measurement methods still have some limitations on spatial coverage and system stability. A micro station is an emerging monitoring system with multiple sensors, which can be deployed to provide dense air quality monitoring data. Here, we proposed a method for urban air quality mapping at high-resolution for multiple pollutants. By using the dense air quality monitoring data from 448 micro stations in Lanzhou city, we developed a decision tree model to infer the distribution of citywide air quality at a 500 m × 500 m × 1 h resolution, with a coefficient of determination (R2) value of 0.740 for PM2.5, 0.754 for CO and 0.716 for SO2. Meanwhile, we also show that the deployment density of the monitoring stations can have a significant impact on the air quality inference results. Our method is able to show both short-term and long-term distribution of multiple important pollutants in the city, which demonstrates the potential and feasibility of dense monitoring data combined with advanced data science methods to support urban atmospheric environment fine-management, policy making, and public health studies.

| S-EPMC9265361 | biostudies-literature

A comparison of denoising pipelines in high temporal resolution task-based functional magnetic resonance imaging data.

Project description:It has been known for decades that head motion/other artifacts affect the blood oxygen level-dependent signal. Recent recommendations predominantly focus on denoising resting state data, which may not apply to task data due to the different statistical relationships that exist between signal and noise sources. Several blind-source denoising strategies (FIX and AROMA) and more standard motion parameter (MP) regression (0, 12, or 24 parameters) analyses were therefore compared across four sets of event-related functional magnetic resonance imaging (erfMRI) and block-design (bdfMRI) datasets collected with multiband 32- (repetition time [TR] = 460 ms) or older 12-channel (TR = 2,000 ms) head coils. The amount of motion varied across coil designs and task types. Quality control plots indicated small to moderate relationships between head motion estimates and percent signal change in both signal and noise regions. Blind-source denoising strategies eliminated signal as well as noise relative to MP24 regression; however, the undesired effects on signal depended both on algorithm (FIX > AROMA) and design (bdfMRI > erfMRI). Moreover, in contrast to previous results, there were minimal differences between MP12/24 and MP0 pipelines in both erfMRI and bdfMRI designs. MP12/24 pipelines were detrimental for a task with both longer block length (30 ± 5 s) and higher correlations between head MPs and design matrix. In summary, current results suggest that there does not appear to be a single denoising approach that is appropriate for all fMRI designs. However, even nonaggressive blind-source denoising approaches appear to remove signal as well as noise from task-related data at individual subject and group levels.

| S-EPMC6865567 | biostudies-literature

Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions.

Project description:Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vectors and how a simple k-nearest neighbor approach is able to retrieve information on overall particle shape and maximal diameter (Dmax) as well as molecular mass directly from experimental scattering data. Based on this transformation, we develop a rapid multiclass shape-classification ranging from compact, extended, and flat categories to hollow and random-chain-like objects. This classification may be employed, e.g., as a decision block in automated data analysis pipelines. Further, we map protein structures from the Protein Data Bank into the classification space and, in a second step, use this mapping as a data source to obtain accurate estimates for the structural parameters (Dmax, molecular mass) of the macromolecule under study based on the experimental scattering pattern alone, without inverse Fourier transform for Dmax. All methods presented are implemented in a Fortran binary DATCLASS, part of the ATSAS data analysis suite, available on Linux, Mac, and Windows and free for academic use.

| S-EPMC6129182 | biostudies-literature

Data denoising with transfer learning in single-cell transcriptomics.

Project description:Single-cell RNA sequencing (scRNA-seq) data are noisy and sparse. Here, we show that transfer learning across datasets remarkably improves data quality. By coupling a deep autoencoder with a Bayesian model, SAVER-X extracts transferable gene-gene relationships across data from different labs, varying conditions and divergent species, to denoise new target datasets.

| S-EPMC7781045 | biostudies-literature

A cone-beam X-ray computed tomography data collection designed for machine learning.

Project description:Unlike previous works, this open data collection consists of X-ray cone-beam (CB) computed tomography (CT) datasets specifically designed for machine learning applications and high cone-angle artefact reduction. Forty-two walnuts were scanned with a laboratory X-ray set-up to provide not only data from a single object but from a class of objects with natural variability. For each walnut, CB projections on three different source orbits were acquired to provide CB data with different cone angles as well as being able to compute artefact-free, high-quality ground truth images from the combined data that can be used for supervised learning. We provide the complete image reconstruction pipeline: raw projection data, a description of the scanning geometry, pre-processing and reconstruction scripts using open software, and the reconstructed volumes. Due to this, the dataset can not only be used for high cone-angle artefact reduction but also for algorithm development and evaluation for other tasks, such as image reconstruction from limited or sparse-angle (low-dose) scanning, super resolution, or segmentation.

| S-EPMC6805882 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data