DNA MicroArray Image Processing Case Study

Description

In this case study, MATLAB, the Image Processing and Signal Processing toolboxes were used to determine the green intensities from a small portion of a microarray image containing 4,800 spots. A 10x10 pattern of spots was detected by averaging rows and columns to produce horizontal and vertical profiles. Periodicity was determined automatically by autocorrelation and used to form an optimal length filter for morphological background removal. A rectangular grid of bounding boxes was defined. Each spot was individually addressed and segmented by thresholding to form a mask. The mask was used to isolate each spot from surrounding background. Individual spot intensity was determined by integrating pixel intensities. Finally, integrated intensities were tabulated and saved to a data file for subsequent statistical analysis to determine which genes matter most.

3D intensity profile

Description

This Javascript works in ImageJ to measure 3D intensity profile along cylindrical space with variable radius.

ICY batch pixel density measurement

Description

For each ROI, provides the ratio of pixels over a given threshold over the total number of pixels in the ROI.

Track cell intensity

Description

Tracks a cell in a 2D video using active contours, and produces a list of ROI where intensity is measured and reported into a workbook. The cell must be first delineated with a ROI in the first image of the video.

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Human cytoplasm-nucleus translocation assay using CellProfiler

Description

In this human cytoplasm-nucleus translocation assay, learn how to load a previously calculated illumination correction function for two separate channels, measure protein content in the nucleus and cytoplasm, and calculate the ratio as a measure of translocation. This is a clumpy cell type, so studying the settings in primary object identification may be helpful for users interested in the more advanced options that module offers. More about these images can be found at the BBBC.

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Protein Micro-array Analysis

Description

This macro performs measurements of average and standard deviation intensity inside wells of a protein microarray (the number of wells is limited to 250, the image should be cropped for larger arrays). The macro requires the "ImageJ plugins toolkit". To ensure compatibility with Fiji you should download the version 1.6.1The installation instructions can be found here, it only consists in un-compressing the .jar file from the previous archive to Fiji plugins folder.

 

sample image: link

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Analyzing gels and western blots with ImageJ

Description

It explains how to use ImageJ to compare the density (aka intensity) of bands on an agar gel or western blot.

Some notes can be found here: http://cellnetmcweb.bioquant.uni-heidelberg.de/image-analysis/ShortTutorials/Fiji_GelAnalyzer.pdf

Measure Image Intensity (deprecated)

Description

This module has been deprecated; in Cell Profiler 3.0, it is a function in module "Measurement"

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DensitoQuant

Description

DensitoQuant is a simple and fast, yet effective tool for IHC measurements. It measures the density of immunostain on the digital slides by distributing pixels to negative and 3 grades of positive classes by their RGB values. DensitoQuant is especially suitable for quick TMA evaluation. Analyzing a whole digital slide takes only a couple of minutes.

Cicardian Gene Expression

Description

"This ImageJ plugin (CGE) is a semi-automatic tool to detect and track moving cell, and to measure the fluorescent protein expression level. CGE extracts the trajectory of the cells by tracking their displacements, makes the delineation of cell nucleus or whole cell, and finally yields measurements of various features, like reporter protein expression level, cell displacement."

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