Dataset Information

EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organisms.

ABSTRACT: Insight into the function and regulation of biological molecules can often be obtained by determining which cell structures and other molecules they localize with (i.e. colocalization). Here we describe an open source plugin for ImageJ called EzColocalization to visualize and measure colocalization in microscopy images. EzColocalization is designed to be easy to use and customize for researchers with minimal experience in quantitative microscopy and computer programming. Features of EzColocalization include: (i) tools to select individual cells and organisms from images; (ii) filters to select specific types of cells and organisms based on physical parameters and signal intensity; (iii) heat maps and scatterplots to visualize the localization patterns of reporters; (iv) multiple metrics to measure colocalization for two or three reporters; (v) metric matrices to systematically measure colocalization at multiple combinations of signal intensity thresholds; and (vi) data tables that provide detailed information on each cell in a sample. These features make EzColocalization well-suited for experiments with low reporter signal, complex patterns of localization, and heterogeneous populations of cells and organisms.

SUBMITTER: Stauffer W

PROVIDER: S-EPMC6202351 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Publications

EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organisms.

Stauffer Weston W Sheng Huanjie H Lim Han N HN

Scientific reports 20181025 1

Insight into the function and regulation of biological molecules can often be obtained by determining which cell structures and other molecules they localize with (i.e. colocalization). Here we describe an open source plugin for ImageJ called EzColocalization to visualize and measure colocalization in microscopy images. EzColocalization is designed to be easy to use and customize for researchers with minimal experience in quantitative microscopy and computer programming. Features of EzColocaliza ...[more]

PMID: 30361629

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Project description:BACKGROUND:Quantification of axon regeneration in spinal cord tissue sections is a fundamental step to adequately determine if an applied treatment leads to an anatomical benefit following spinal cord injury. Recent advances have led to the development of therapies that can promote regeneration of thousands of injured axons in vivo. Axon labeling methods and in the application of regeneration-enabling stem cell grafts have increased the number of detectable regenerating axons by orders of magnitudes. Manual axon tracing in such cases is challenging and laborious, and as such there is a great need for automated algorithms that can perform accurate tracing and quantification in axon-dense tissue sections. RESULTS:We developed "AxonTracer", a fully automated software algorithm that traces and quantifies regenerating axons in spinal cord tissue sections. AxonTracer is an open source plugin for the freely available image-processing program ImageJ. The plugin identifies transplanted cells grafts or other regions of interest (ROIs) based on immunohistological staining and quantifies regenerating axons within the ROIs. Individual images or groups of images (batch mode) can be analyzed sequentially. In batch mode, a unique algorithm identifies a reference image for normalization, as well as a suitable image for defining detection parameters. An interactive user interface allows for adjustment of parameters defining ROI size, axon detection sensitivity and debris cleanup. Automated quantification of regenerating axons by AxonTracer correlates strongly with semi-manual quantification by the widely-used ImageJ plugin NeuronJ. However, quantification with AxonTracer is automated and reduces the need for user input compared to alternative methods. CONCLUSIONS:AxonTracer is a freely available open-source tool for automated analysis of regenerating axons in the injured nervous system. An interactive user interface provides detection-parameter adjustment, and usage does not require prior image analysis experience. Raw data as well as normalized results are stored in spreadsheet format and axon tracings are superimposed on raw images allowing for subjective visual verification. This software allows for automated, unbiased analysis of hundreds of axon-dense images, thus providing a useful tool in enabling in vivo screens of axon regeneration following spinal cord injury.

Dataset Information

EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organisms.

Publications

EzColocalization: An ImageJ plugin for visualizing and measuring colocalization in cells and organisms.

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