A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze C. elegans Embryonic Development

10.3791/60362 ◽  
2019 ◽  
Author(s):  
Renat N. Khaliullin ◽  
Jeffrey M. Hendel ◽  
Adina Gerson-Gurwitz ◽  
Shaohe Wang ◽  
Stacy D. Ochoa ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Data Visualization ◽  
High Throughput ◽  
Imaging Method ◽  
C Elegans ◽  
Visualization Toolkit ◽  
High Throughput Imaging

scholarly journals High-throughput imaging method for direct assessment of GM1 ganglioside levels in mammalian cells

Data in Brief ◽  
2016 ◽  
Vol 6 ◽  
pp. 1016-1022 ◽  
Author(s):  
Walter Acosta ◽  
Reid Martin ◽  
David N. Radin ◽  
Carole L. Cramer
Keyword(s):  
High Throughput ◽  
Mammalian Cells ◽  
Imaging Method ◽  
Gm1 Ganglioside ◽  
Direct Assessment ◽  
High Throughput Imaging

scholarly journals easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0252000
Author(s):  
Joy Nyaanga ◽  
Timothy A. Crombie ◽  
Samuel J. Widmayer ◽  
Erik C. Andersen
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
R Package ◽  
Summary Statistics ◽  
Data Filtering ◽  
Analysis Pipeline ◽  
C Elegans ◽  
Visualization Of Data ◽  
Microscopy Data ◽  
High Throughput Imaging

High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.

scholarly journals Behavioral fingerprints predict insecticide and anthelmintic mode of action

2021 ◽  
Author(s):  
Adam McDermott-Rouse ◽  
Eleni Minga ◽  
Ida Barlow ◽  
Luigi Feriani ◽  
Philippa H Harlow ◽  
...  
Keyword(s):  
High Throughput ◽  
Mode Of Action ◽  
Behavioral Responses ◽  
Physiological Data ◽  
Discovery Process ◽  
Crucial Step ◽  
C Elegans ◽  
Modes Of Action ◽  
Automated Phenotyping ◽  
High Throughput Imaging

AbstractNovel invertebrate-killing compounds are required in agriculture and medicine to overcome resistance to existing treatments. Because insecticides and anthelmintics are discovered in phenotypic screens, a crucial step in the discovery process is determining the mode of action of hits. Visible whole-organism symptoms are combined with molecular and physiological data to determine mode of action. However, manual symptomology is laborious and requires symptoms that are strong enough to see by eye. Here we use high-throughput imaging and quantitative phenotyping to measure C. elegans behavioral responses to compounds and train a classifier that predicts mode of action with an accuracy of 88% for a set of ten common modes of action. We also classify compounds within each mode of action to discover pharmacological relationships that are not captured in broad mode of action labels. High-throughput imaging and automated phenotyping could therefore accelerate mode of action discovery in invertebrate-targeting compound development and help to refine mode of action categories.

scholarly journals easyXpress: An R package to analyze and visualize high-throughput C. elegans microscopy data generated using CellProfiler

2021 ◽  
Author(s):  
Joy Nyaanga ◽  
Timothy A. Crombie ◽  
Samuel J. Widmayer ◽  
Erik C Andersen
Keyword(s):  
High Throughput ◽  
Imaging Techniques ◽  
R Package ◽  
Summary Statistics ◽  
Data Filtering ◽  
Analysis Pipeline ◽  
C Elegans ◽  
Visualization Of Data ◽  
Microscopy Data ◽  
High Throughput Imaging

High-throughput imaging techniques have become widespread in many fields of biology. These powerful platforms generate large quantities of data that can be difficult to process and visualize efficiently using existing tools. We developed easyXpress to process and review C. elegans high-throughput microscopy data in the R environment. The package provides a logical workflow for the reading, analysis, and visualization of data generated using CellProfiler’s WormToolbox. We equipped easyXpress with powerful functions to customize the filtering of noise in data, specifically by identifying and removing objects that deviate from expected animal measurements. This flexibility in data filtering allows users to optimize their analysis pipeline to match their needs. In addition, easyXpress includes tools for generating detailed visualizations, allowing the user to interactively compare summary statistics across wells and plates with ease. Researchers studying C. elegans benefit from this streamlined and extensible package as it is complementary to CellProfiler and leverages the R environment to rapidly process and analyze large high-throughput imaging datasets.

scholarly journals Paper-Supported High-Throughput 3D Culturing, Trapping, and Monitoring of Caenorhabditis Elegans

Micromachines ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 99 ◽  
Author(s):  
Mehdi Tahernia ◽  
Maedeh Mohammadifar ◽  
Seokheun Choi
Keyword(s):  
High Throughput ◽  
Developmental Stages ◽  
3D Culture ◽  
Natural Habitats ◽  
Paper Substrate ◽  
C Elegans ◽  
Cultivation Technique ◽  
Plastic Frame ◽  
Pass Through ◽  
High Throughput Imaging

We developed an innovative paper-based platform for high-throughput culturing, trapping, and monitoring of C. elegans. A 96-well array was readily fabricated by placing a nutrient-replenished paper substrate on a micromachined 96-well plastic frame, providing high-throughput 3D culturing environments and in situ analysis of the worms. The paper allows C. elegans to pass through the porous and aquatic paper matrix until the worms grow and reach the next developmental stages with the increased body size comparable to the paper pores. When the diameter of C. elegans becomes larger than the pore size of the paper substrate, the worms are trapped and immobilized for further high-throughput imaging and analysis. This work will offer a simple yet powerful technique for high-throughput sorting and monitoring of C. elegans at a different larval stage by controlling and choosing different pore sizes of paper. Furthermore, we developed another type of 3D culturing system by using paper-like transparent polycarbonate substrates for higher resolution imaging. The device used the multi-laminate structure of the polycarbonate layers as a scaffold to mimic the worm’s 3D natural habitats. Since the substrate is thin, mechanically strong, and largely porous, the layered structure allowed C. elegans to move and behave freely in 3D and promoted the efficient growth of both C. elegans and their primary food, E. coli. The transparency of the structure facilitated visualization of the worms under a microscope. Development, fertility, and dynamic behavior of C. elegans in the 3D culture platform outperformed those of the standard 2D cultivation technique.

scholarly journals A microfluidic platform for lifelong high-resolution and high throughput imaging of subtle aging phenotypes in C. elegans

Lab on a Chip ◽  
2018 ◽  
Vol 18 (20) ◽  
pp. 3090-3100 ◽  
Author(s):  
Sahand Saberi-Bosari ◽  
Javier Huayta ◽  
Adriana San-Miguel
Keyword(s):  
High Resolution ◽  
High Throughput ◽  
Structure And Function ◽  
Neuronal Structure ◽  
Microfluidic Platform ◽  
C Elegans ◽  
And Function ◽  
High Throughput Imaging

Aging produces a number of changes in the neuronal structure and function throughout a variety of organisms.

scholarly journals HiHiMap: single-cell quantitation of histones and histone posttranslational modifications across the cell cycle by high-throughput imaging

2017 ◽  
Vol 28 (17) ◽  
pp. 2290-2302 ◽  
Author(s):  
Linda Zane ◽  
Fleur Chapus ◽  
Gianluca Pegoraro ◽  
Tom Misteli
Keyword(s):  
Cell Cycle ◽  
High Throughput ◽  
Posttranslational Modifications ◽  
Single Cells ◽  
Histone Variants ◽  
Imaging Method ◽  
Histone Ptms ◽  
Core Histones ◽  
High Throughput Imaging ◽  
High Throughput Study

We describe High-throughput Histone Mapping (HiHiMap), a high-throughput imaging method to measure histones and histone posttranslational modifications (PTMs) in single cells. HiHiMap uses imaging-based quantification of DNA and cyclin A to stage individual cells in the cell cycle to determine the levels of histones or histone PTMs in each stage of the cell cycle. As proof of principle, we apply HiHiMap to measure the level of 21 core histones, histone variants, and PTMs in primary, immortalized, and transformed cells. We identify several histone modifications associated with oncogenic transformation. HiHiMap allows the rapid, high-throughput study of histones and histone PTMs across the cell cycle and the study of subpopulations of cells.

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