#Imagej threshold selection gui software#

“background”) 15, and where there are high levels of non-specific signal in cells 8.

#Imagej threshold selection gui software#

A second factor is that the software is often not suited to experiments that push the limits of detection, where the intensity of the intracellular signal is similar to the extracellular signal ( i.e. One factor is that customization of the software is often required for the equipment, reporters and samples 13, 14, and for automated analyses. Several factors limit the use of current software for visualizing the localization of reporters in biological samples and measuring colocalization 9, 10, 11, 12. colocalization, anticolocalization and noncolocalization respectively) in cells, tissues or organisms 8. In particular, it is often challenging to determine whether the different molecules of interest occur in the same locations, different locations or independent locations ( i.e. However, researchers often find it difficult to rigorously evaluate and interpret the images. Similar content being viewed by othersĪdvances in microscopy equipment and labeling techniques make it possible for researchers to image a variety of biological molecules in almost any cell, tissue, or organism 1, 2, 3, 4, 5, 6, 7. These features make EzColocalization well-suited for experiments with low reporter signal, complex patterns of localization, and heterogeneous populations of cells and organisms.

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. EzColocalization is designed to be easy to use and customize for researchers with minimal experience in quantitative microscopy and computer programming. Here we describe an open source plugin for ImageJ called EzColocalization to visualize and measure colocalization in microscopy images. 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.