Imagej Software
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11:01
Automated Quantification and Analysis of Cell Counting Procedures Using ImageJ Plugins
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Cited by 90 •
2016
This paper describes the quantification of hemocytometer and migration/invasion micrographs through two new open-source ImageJ plugins Cell Concentration Calculator and migration assay Counter. Furthermore, it describes image acquisition and calibration protocols as well as discusses in detail the input requirements of the plugins.
07:19
Clock Scan Protocol for Image Analysis: ImageJ Plugins
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Cited by 16 •
2017
This paper describes two novel ImageJ plugins for 'Clock Scan' image analysis. These plugins expand the functionality of the original visual basic 6 program and, most importantly, make the program available to a large research community by bundling it with the ImageJ free image analysis software package.
10:39
Automated Analysis of Intracellular Phenotypes of Salmonella Using ImageJ
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Cited by 3 •
2022
Salmonella invades and replicates inside intestinal epithelial cells both in Salmonella-specific vacuoles and free in the cytosol (hyper-replication). A high-throughput fluorescence microscopy-based protocol is described here to quantify the intracellular phenotypes of Salmonella by two complementary image analyses through ImageJ, reaching single-cell resolution and scoring.
10:41
VisualEyes: A Modular Software System for Oculomotor Experimentation
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Cited by 28 •
2011
Neural control and cognitive processes can be studied through eye movements. The VisualEyes software allows an operator to program stimuli on two computer screens independently using a simple, custom scripting language. The system can stimulate tandem eye movements (saccades and smooth pursuit) or opposing eye movements (vergence) or any combination.
09:39
TACI: An ImageJ Plugin for 3D Calcium Imaging Analysis
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Cited by 3 •
2022
TrackMate Analysis of Calcium Imaging (TACI) is an open-source ImageJ plugin for 3D calcium imaging analysis that examines motion on the z-axis and identifies the maximum value of each z-stack to represent a cell's intensity at the corresponding time point. It can separate neurons overlapping in the lateral (x/y) direction but on different z-planes.
FAQs
ImageJ Software treats a scientific image as pixel data, allowing each pixel’s recorded value to be processed and measured rather than viewed only visually. Filtering can modify or clarify image information, while thresholding separates selected pixel values and segmentation organizes image regions for analysis. These operations support quantitative measurements from microscopy data.
Thresholding and segmentation determine which image regions enter a measurement. Thresholding selects pixels according to their values, and segmentation converts that selection into analyzable regions. The resulting regions can then support measurements such as cell size, fluorescence, tissue structure, or spatial patterns. Their use links image-processing choices directly to the biological quantities being compared.
Plug-ins and macros add specialized capabilities beyond core image operations. They allow ImageJ Software to support workflows tailored to particular research needs, rather than limiting analysis to standard viewing, filtering, thresholding, segmentation, and intensity measurement. This extensibility helps researchers apply the platform across varied biological imaging questions while retaining a common analysis environment.
To analyze a microscopy image, a researcher can first view the image, apply relevant processing, and then use thresholding or segmentation before taking measurements. The selected workflow depends on the intended quantity, such as intensity, cell size, tissue structure, or spatial pattern. Keeping these stages explicit supports comparisons among samples.
In biology, ImageJ Software can turn microscopy observations into measurements of cell size, fluorescence, tissue structure, and spatial patterns. These outputs help researchers compare samples instead of relying only on visual impressions. The same capabilities also support teaching, where image-processing operations and quantitative interpretation can be examined through accessible analysis workflows.
Image analysis is especially useful when a biological question concerns differences among samples or studies. ImageJ Software provides measurements that make visual features comparable, provided the same relevant analysis approach is used across the images. This supports data-driven interpretation of microscopy results and helps connect observed structures or signals with quantitative evidence.