Fill small holes only

[Anna M.]

Hi,
I am new to imageJ and could not find anything on that topic. I am segmenting 2D images of blood vessels. the images aren't of very good quality and lighter spots in the tubules lead to small holes in the binary image. If I now skeletonize this, ring form structures appear which are counted as 2 or more branches (around the hole) by the AnalyzeSkeleton Plugin. I have tried optimizing the images as much as possible, but there obviously is a limit.
Isn't there a way to use the fill holes function conditionally? Sometimes, vessels will form an enclosure by themselves which would be also filled by "fill holes" or the particle analyzer and I would like to avoid that.
It would be great if anyone could help here.
Cheers,
Anna

[Gabriel Landini]

On Friday 20 February 2009, Anna M. wrote:
> Isn't there a way to use the fill holes function conditionally?

Yes there is.
The principle is to invert the image (so the holes are the particles) and
delete (fill) those which are too large or too small or round, etc (depending
what you want) and invert back the image.

G.

[Anna M.]

Oh, Thanks!
That is exactly what I needed. Too obvious for me to see. ;-)
Cheers,
Anna