Posted by
ctrueden on
Feb 21, 2013; 8:17pm
URL: http://imagej.273.s1.nabble.com/segmentation-with-some-user-input-tp5001828p5001830.html
Hi Rainer,
> There are several plugins for segmentation. Which one is best for my
> purposes?
It really depends on your data. The simplest segmentation technique is
thresholding (Image > Adjust > Threshold) with one of the built-in
auto-thresholding methods. Steps would be:
1) Generate your inner and outer masks.
2) AND the inner mask to your image (using the Image Calculator).
3) AND the outer mask to your image.
You should now have an image that is all zeroes except for the area between
the masks. (If not, invert one or both masks first before ANDing.)
4) Run the Auto Threshold plugin on the resultant image with the desired
method, checking the "Ignore black" or "Ignore white" and "White objects on
black background" boxes as appropriate. (You can also choose the "Try all"
method to get a nice big side-by-side comparison of results.)
5) Recombine the resultant mask (produced by Auto Threshold) with your
inner mask, outer mask and/or original data as desired for further
processing.
If you have very noisy data, you could alternately try the Advanced Weka
Segmentation Editor to use machine learning on the ambiguous area, rather
than simple thresholding. If you go that route, you can mark everything in
your inner mask as class 1, and everything in your outer mask as class 2,
which should give it plenty of fodder for further deduction.
The complete list of segmentation plugins available in Fiji can be browsed
here:
http://fiji.sc/Category:SegmentationRegards,
Curtis
On Thu, Feb 21, 2013 at 11:24 AM, Rainer M. Engel <
[hidden email]> wrote:
> Hey there.
>
> I'd like to find a way to get a segmentation mask automatically and it
> should be guided by two other inputs which I want to create in a
> preceding step.
>
> Please have a look at this picture:
>
https://dl.dropbox.com/u/414433/imagej/auto-segmentation.jpg>
> I managed to create a very robust outer mask of pixels which are not
> important (can be deleted/transparent). A second "inner mask"
> incorporates opaque pixels I want to keep. The wanted segmentation mask
> can be found between these two inside of the white area.
>
> There are several plugins for segmentation. Which one is best for my
> purposes? Any tips are appreciated.
>
> Best regards,
> Rainer
>
>
> --
> Rainer M. Engel, Dipl. Digital Artist
> scientific|Media GbR
> Pichelsdorfer Str. 143
> 13595 Berlin
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>
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