Posted by
Michael Schmid on
Apr 08, 2011; 1:35pm
URL: http://imagej.273.s1.nabble.com/Segmentation-and-analysis-of-silver-grains-in-TEM-image-tp3685041p3685043.html
Hi,
just to give you one more pointer: You can get a top-hat filter by
Process>Math>Min and then Max, both with the same radius (or other
way around, first Max, then Min, if your foreground objects have
lower pixel values than the background as in the sample images).
Also, in the 'Fast Filters' plugin, the 'eliminate Maxima' and
'Eliminate Minima' filters are Top-Hat filters, and the "background
from..." filters there are top-hat filters with additional smoothing
of the background.
The ImageJ built-in 'Subtract background' is a more generalized type
of a top-hat filter, better than a simple top-hat filter in areas
with a gradient in the background.
Nevertheless, I could not get a decent removal of the fiber
background with any of these.
The best solution I found so far is the Versatile Wand with a value
tolerance including the full image range (255 for 8-bit) and a
gradient tolerance of about 10.
Just click on the background and then "Make Inverse" of the
selection. You will need some postprocessing to eliminate a few
remaining fibers (using either their shape or their gray value).
Also looping through the maxima from "Find Maxima" in a macro and
selecting each of them with the Versatile Wand would eliminate these
fibers, but you have to check that the selection really stops at the
particle center: Forget the result or decrease the threshold if the
Wand selects too large an area. You would need a simple macro for this.
Fast Filters & Versatile Wand are available at
http://imagejdocu.tudor.lu/doku.php?id=plugin:startMichael
________________________________________________________________
On 8 Apr 2011, at 14:44, Gabriel Landini wrote:
> On Friday 08 Apr 2011 01:02:10 you wrote:
>> The original bmp image sent to me by the researcher is attached
>> (Fig1.bmp). They want to analyse the dense black spots, which are
>> silver
>> grains and find out the following;
>
> This problem can be solved relatively easy via the so called Top
> Hat filters.
> There are (in addition to the dilation/erosion based top hat
> filters) some
> based on greyscale reconstruction. Have a look at the Morphological
> Image
> Analysis book of P Soille.
>
> Cheers
>
> Gabriel