Posted by
CARL Philippe (LBP) on
URL: http://imagej.273.s1.nabble.com/Radial-profile-ext-to-work-with-Macros-tp5005598p5006503.html
Dear James
> When I run this I get a results list with Time = Slice# and The intensity
of the first radius.
> This looks good.
Ok good...
> How do i get this to plot, or add the other radius.
Getting the data in a result table or plot is not very different in terms of
use of the "Ext." methods ; nevertheless, the following macro will do the
job you are looking for:
for(rad = 200; rad <= 210; rad += 10)
raduisPlot(rad);
function raduisPlot(radius)
{
selectWindow("confocal-series.tif");
run("Radial Profile Angle", "x_center=200 y_center=200 radius=" +
radius + " starting_angle=0 integration_angle=180 use_spatial_calibration
calculate_radial_profile_on_stack");
color = newArray("black", "blue", "cyan", "darkGray", "gray",
"green", "lightGray", "magenta", "orange", "pink", "red", "yellow");
xValues = newArray(Ext.getStackSize);
yValues = newArray(Ext.getStackSize);
Plot.create("Radius = " + radius, "Time", "Fluorescence (A.U.)",
xValues, yValues);
Plot.setLimits(0, Ext.getStackSize, 0, 150);
for(j = 0; j != Ext.getBinSize; j++)
{
for(i = 0; i != Ext.getStackSize; i++)
{
xValues[i] = i;
yValues[i] = Ext.getYValue(i, j);
}
Plot.add("line", xValues, yValues);
Plot.setColor(color[j % 12]);
}
Plot.show();
}
> I was also wondering if you could clarify exactly what the starting angle
(*seems pretty self explanatory)* and integration angle - (*Does this
define the number of sections the measurements are broken down into?
> each half of the ROI is analysed and then averaged to give the final
result?)* are.
I have added an "Application" tab at the bottom of the plugin Website that
can be found under the following link:
http://punias.free.fr/radial-profile-ext.htmlis this new addition answering clearly your questions now or do you still
have some doubts or misunderstanding?
> Also, What defines the size and number of the radii Cheers, James
I'm afraid that I don't understand this question.
Do you want to know what the values of "Ext.getStackSize" and
"Ext.getBinSize" are or something else?
Best regards,
Philippe
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