Re: average above threshold

Posted by Gabriel Landini on
URL: http://imagej.273.s1.nabble.com/average-above-threshold-tp3689549p3689554.html

On Friday 29 Jan 2010  11:43:46 you wrote:
> This worked:
> Duplicate stack
> threshold, dark bg
> make binary
> divide by 255
> multiply result with original to set pixels <t to 0
> Z-axis projection to sum slices - automatically creates 32-bit result.
 
> The structure of interest in each stack is at an angle, and Plot Profile
>  doesn't work with rectangular ROIs created with the Polygon tool.  Which
>  means the final step is to draw a line along the structure's axis to set
>  image rotation so we can use a rectangular ROI to get an averaged profile
>  plot of the summed intensities.

However the "sum intensities" should be divided by the "sum of binary slices
with values 0 and 1" because the first sum is not guaranteed to be due to the
same number of contributing slices. (not sure I am being clear).

Let's say for a pixel, your sum of 200 can be contributed by 4 slices with a
value of 50 in each slice, or by 2 slices with 100 in each slice.
In the first case your average should be 50 in the second 100.

Cheers

Gabriel