http://imagej.273.s1.nabble.com/segmentation-with-some-user-input-tp5001828p5001837.html
thank you for your detailed information. I'll definitely follow this
> 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:Segmentation>
> Regards,
> 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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