Systems Biology (Methods in Molecular Biology)

After finishing the segmentation and background subtraction

work, all the cells can be brought back to a single image, represent-

ing our virtual slide.

Before proceeding to the quantitative measurement of shape

parameters, it is usually necessary to perform other preprocessing

operations on the images. Figure2 shows binarization, smoothing,

and vectorization (find edges) as an example. At this point you can

start measuring shape parameters for each cell.

Each parameter is linked to a biological meaning, so that col-

laboration between bioinformatics and the biologist is really strate-

gic. Measurement and interpretation work should be understood as

a continuous work cycle. During this cycle, the bioinformatician

and the biologist further refine the measurement protocol and

decide which tasks can be left to automated calculations and

which others do not. It is important to observe that the quantitative

measurement of shape parameters can also provide useful indica-

tions for the evaluation of cell functions. The results of this measure

will be supplemented with those from confocal microscopy to

quantitatively characterize the cell phenotype. With the Systems

Biology approach, applying fusion between information from vari-

ous imaging techniques, we can realize the construction of an

electronic phenotype that virtually represents our cell culture.

In this part, we are briefly outlining how to extract the infor-

mation about the cell structures of Cytoskeleton from confocal

microscopy images with ImageJ and CellProfiler open source

Imaging collection

Computational imaging analysis

1. Subtract background *


2. Compose


3. Make binary *


4. Smoothing *


5. Cell count


6. Find edges *

Area

Roundness

Solidity

Coherency

Fractal dimension * affect the calculation

Entropy

Evaluate values and their distribution:

Manual snake *

Fig. 2Computational protocol to quantitative evaluation of cell shape parameters

Imaging and Systems Biology 347