Dataset Information

Particle morphomics by high-throughput dynamic image analysis.

ABSTRACT: A novel omics-like method referred to as "particle morphomics" has been proposed in the present study. The dynamic images of >2,000,000 particles per sample in sediments, soils and dusts were collected by a Sympatec GmbH QICPIC particle size and shape analyzer, and the morphological descriptors of each particle including equivalent diameter, sphericity, aspect ratio and convexity were extracted as the "particle morphome". Various multivariate analyses were adopted to process the high-throughput data of particle morphome including analyses of alpha and beta diversities, similarity, correlation, network, redundancy, discretion and principal coordinate. The outcome of particle morphomics could estimate the morphological diversity and sketch the profile of morphological structure, which aided to develop a morphological fingerprint for specific particle samples. The distribution and properties of particle assemblages of specific morphology could also be evaluated by selecting particles with respect to filter criteria. More importantly, the particle morphomics may be extended to investigate and explain the biogeochemical and environmental processes involved with particle morphology if linked with external variables.

SUBMITTER: Sun Y

PROVIDER: S-EPMC6610128 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Publications

Particle morphomics by high-throughput dynamic image analysis.

Sun Youmin Y Cai Zhengqing Z Fu Jie J

Scientific reports 20190703 1

A novel omics-like method referred to as "particle morphomics" has been proposed in the present study. The dynamic images of >2,000,000 particles per sample in sediments, soils and dusts were collected by a Sympatec GmbH QICPIC particle size and shape analyzer, and the morphological descriptors of each particle including equivalent diameter, sphericity, aspect ratio and convexity were extracted as the "particle morphome". Various multivariate analyses were adopted to process the high-throughput ...[more]

PMID: 31270428

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Project description:BACKGROUND:Image-based high throughput (HT) screening provides a rich source of information on dynamic cellular response to external perturbations. The large quantity of data generated necessitates computer-aided quality control (QC) methodologies to flag imaging and staining artifacts. Existing image- or patch-level QC methods require separate thresholds to be simultaneously tuned for each image quality metric used, and also struggle to distinguish between artifacts and valid cellular phenotypes. As a result, extensive time and effort must be spent on per-assay QC feature thresholding, and valid images and phenotypes may be discarded while image- and cell-level artifacts go undetected. RESULTS:We present a novel cell-level QC workflow built on machine learning approaches for classifying artifacts from HT image data. First, a phenotype sampler based on unlabeled clustering collects a comprehensive subset of cellular phenotypes, requiring only the inspection of a handful of images per phenotype for validity. A set of one-class support vector machines are then trained on each biologically valid image phenotype, and used to classify individual objects in each image as valid cells or artifacts. We apply this workflow to two real-world large-scale HT image datasets and observe that the ratio of artifact to total object area (ARcell) provides a single robust assessment of image quality regardless of the underlying causes of quality issues. Gating on this single intuitive metric, partially contaminated images can be salvaged and highly contaminated images can be excluded before image-level phenotype summary, enabling a more reliable characterization of cellular response dynamics. CONCLUSIONS:Our cell-level QC workflow enables identification of artificial cells created not only by staining or imaging artifacts but also by the limitations of image segmentation algorithms. The single readout ARcell that summaries the ratio of artifacts contained in each image can be used to reliably rank images by quality and more accurately determine QC cutoff thresholds. Machine learning-based cellular phenotype clustering and sampling reduces the amount of manual work required for training example collection. Our QC workflow automatically handles assay-specific phenotypic variations and generalizes to different HT image assays.

Project description:BackgroundIn order to select for quantitative plant resistance to pathogens, high throughput approaches that can precisely quantify disease severity are needed. Automation and use of calibrated image analysis should provide more accurate, objective and faster analyses than visual assessments. In contrast to conventional visible imaging, chlorophyll fluorescence imaging is not sensitive to environmental light variations and provides single-channel images prone to a segmentation analysis by simple thresholding approaches. Among the various parameters used in chlorophyll fluorescence imaging, the maximum quantum yield of photosystem II photochemistry (Fv/Fm) is well adapted to phenotyping disease severity. Fv/Fm is an indicator of plant stress that displays a robust contrast between infected and healthy tissues. In the present paper, we aimed at the segmentation of Fv/Fm images to quantify disease severity.ResultsBased on the Fv/Fm values of each pixel of the image, a thresholding approach was developed to delimit diseased areas. A first step consisted in setting up thresholds to reproduce visual observations by trained raters of symptoms caused by Xanthomonas fuscans subsp. fuscans (Xff) CFBP4834-R on Phaseolus vulgaris cv. Flavert. In order to develop a thresholding approach valuable on any cultivars or species, a second step was based on modeling pixel-wise Fv/Fm-distributions as mixtures of Gaussian distributions. Such a modeling may discriminate various stages of the symptom development but over-weights artifacts that can occur on mock-inoculated samples. Therefore, we developed a thresholding approach based on the probability of misclassification of a healthy pixel. Then, a clustering step is performed on the diseased areas to discriminate between various stages of alteration of plant tissues. Notably, the use of chlorophyll fluorescence imaging could detect pre-symptomatic area. The interest of this image analysis procedure for assessing the levels of quantitative resistance is illustrated with the quantitation of disease severity on five commercial varieties of bean inoculated with Xff CFBP4834-R.ConclusionsIn this paper, we describe an image analysis procedure for quantifying the leaf area impacted by the pathogen. In a perspective of high throughput phenotyping, the procedure was automated with the software R downloadable at http://www.r-project.org/. The R script is available at http://lisa.univ-angers.fr/PHENOTIC/telechargements.html.

Dataset Information

Particle morphomics by high-throughput dynamic image analysis.

Publications

Particle morphomics by high-throughput dynamic image analysis.

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