Systems Biology (Methods in Molecular Biology)

software. ImageJ is one of the principal and most popular scientific

image analysis software. To facilitate more advanced and clear

results the program provides many plugins, made by a lively scien-

tific community, to add functionality and visualization tools. This

program is used in over 30,000 laboratories. ImageJ is a very

popular research tool helpful in imaging processing and run in

any web browser. Cell profiler enables gathering information

regarding number, thickness and length of actin, internal filaments,

and microtubules. Thus, it provides comprehensive structural

information about the cytoskeleton under investigation.

Details of how to acquire the information about the image

processing of the cellular data from ImageJ are descripted in

[19, 20]. In our experience, we applied the algorithms for the

identification of functional information, analyzing molecular imag-

ing data regarding experiments with cell line. In doing so, we have

used the built-in functions of ImageJ to filter and analyze our data.

An outline of the algorithmic steps is given in Tables3 and 4.

We investigate area, roundness, fractal dimensions, solidity,

entropy, coherence to evaluate the cytoskeleton morphotype and

phenotype properties and to compare the results retained from

treated and untreated cells data.SeeinNote 2for more details

about these steps.

Table 4
Pipeline for performing quantitative morphological analysis on confocal images with CellProfiler

Step 1 lCalculate the ratios (area nucleus)

lMeasuring the image area occupied

lCalculating the image intensity (cells)

lMeasure object intensity (nuclei)

lPredict correlation behavior of the cells

Step 2 lMeasuring object size shape (nuclei)

lPerforming the calculation and setting up the parameters for graphical representation

to display the data comparison

Table 3
Pipeline for performing quantitative morphological analysis on confocal images with ImageJ

Step 1 lIdentifying the cells in ImageJ Software

lCalculate the split channels to separate the microtubules and nuclei

Step 2 lRefining and adjusting the threshold

lAdjust the top slider

lAdjust the bottom slider

lCalculate the threshold of each confocal image

348 Garima Verma et al.