Measure circumfence of cells (cannot use particle analyzer)

[Ulrik Stervbo]

Hi all,

I been (quite unsuccessfully) looking for a way to identify the
circumference of a cell. Does anyone know if there is a plugin for ImageJ?

The point is to end up with the area of the cell, but is it only the
membrane of the cells which is stained, so the particle analyzer is no good.
Also, because of background and such, the line, indicating the edge of the
cell, may be broken (there is no guarantee that it is not broken).

Thank in advance for any suggestions.
Ulrik

[Gary Chinga]

You can try to measure the convex area and perimeter. This may be a  
good estimator of the "unbroken" membrane/cell area. The following  
method measures the convex area:

        float[][] findConvexArea(ResultsTable rt, ImageProcessor ipTemp){
                int nParticles = rt.getCounter();
                ResultsTable systemRT= ResultsTable.getResultsTable();
                float[][] cValues = new float[2][nParticles]; //Array for the area
and perimeter convex dimension for each particle
                ImagePlus impTemp = new ImagePlus("Test", ipTemp);
                WindowManager.setTempCurrentImage(impTemp);

                for (int i=0; i<nParticles;i++){
                    IJ.doWand((int)rt.getValue("XStart", i),(int)rt.getValue
("YStart", i));
                        IJ.run("Convex Hull");
                        IJ.run("Measure");
                        cValues[0][i] = (float)systemRT.getValue("Area", i);
                        cValues[1][i] = (float)systemRT.getValue("Perim.", i);
                }
                systemRT.reset();
                IJ.run("Select None");
                return cValues;
        }

or try the shape descriptor plugin: http://www.gcsca.net/IJ/Shapes.html


Gary.



On Sep 4, 2006, at 2:28 PM, Ulrik Stervbo wrote:

> Hi all,
>
> I been (quite unsuccessfully) looking for a way to identify the
> circumference of a cell. Does anyone know if there is a plugin for  
> ImageJ?
>
> The point is to end up with the area of the cell, but is it only the
> membrane of the cells which is stained, so the particle analyzer is  
> no good.
> Also, because of background and such, the line, indicating the edge  
> of the
> cell, may be broken (there is no guarantee that it is not broken).
>
> Thank in advance for any suggestions.
> Ulrik
>
>