Posted by
Philippe Grosjean on
Dec 10, 2005; 9:25am
URL: http://imagej.273.s1.nabble.com/Analyze-particle-Flood-fill-tp3704248p3704250.html
Gabriel Landini wrote:
> On Friday 09 December 2005 22:26, Philippe Grosjean wrote:
>
>>Now, the flood fill algorithm introduced recently (version 1.32 or 1.33
>>if my memory is correct) fills the *inside* of the blobs before
>>analyzing them, but excluding holes. So, once you use the flood fill,
>>ImageJ becomes aware of holes inside your blobs.
>
>
>>From the IJ News page:
> "v1.34l, 15 April 2005
> The "Flood Fill" particle analyzer option enables measurement of nested
> particles and causes interior holes to be ignored."
>
>
>>I tend to agree with you: the algorithm used is not important here. The
>>option should better be spelled '[] Fill holes' and it should use the
>>flood fill algorithm if you select that option.
>
>
> I guess that the above means "ignore the holes area as part of the particle"
> rather than filling them (and then count particles within particles). So the
> flood fill is to extract the connected thresholded area but not holes. (the
> particle is flood filled, not the holes).
Yes, wasn't it what I said: flood fill eliminates holes in the blobs.
> But even if this option is "off" (so the holes areas *are* counted as part of
> the particle area), the "Limit to threshold" seems to override it when "on"
> and counts only the thresholded area (without holes).
> Can you see the possibility of confusion? (If I am understanding this wrong, I
> would be happy to be corrected).
Hummm, I just double-check this (I use to check myself, and not to trust
the documentation too much, and I remember I did not care about "Limit
to threshold" in particle analysis, but don't remember why). Here is the
result on a particle with a hole in it:
Area Mean Skew Kurt
FF - LTT 6569 209 -0.579 -0.122
FF - no LTT 6569 209 -0.579 -0.122
no FF - LTT 6815 210 -0.471 -0.155
no FF - no LTT 6815 210 -0.471 -0.155
This is when I redirect to a 8bit grayscale picture, but the result is
the same without redirection (just Skew & Kurt is not usable in that case).
So, this confirm to me that LTT (Limit to threshold) has no effect in
particle analyzer. So, there is no clash between "Flood fill" and "Limit
to threshold": they are used in different contexts.
Best,
Philippe Grosjean
> As I see it, Limit to Threshold is useful for the Measure command, but
> confusing for the particle analysis.
> On Friday 09 December 2005 23:16, Corentin Cras-Méneur wrote:
>
>>In our case, we hardly ever want to measure the "holes'.
>
>
> That's great, but the idea is to make it flexible enough so it can be used in
> both ways.
>
> Cheers,
>
> Gabriel
>
>