Posted by
Jędrzejas, Magdalena on
Aug 19, 2013; 11:28am
URL: http://imagej.273.s1.nabble.com/segmentation-tp5004436p5004485.html
Unfortunately the functions you mentioned only work with the black and white image. I have an image with black, white and two different shades of grey, is there an option to fill the holes in such image?
Magda
-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:
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Gesendet: Montag, 19. August 2013 11:59
An:
[hidden email]
Betreff: Re: segmentation
In ImageJ, there are standard binary operations such as Closing (which would help you with small holes), or even a "Fill Holes" under
Process>Binary. Be aware though, that the foreground will be affected,
i.e. take care whether you define your objects to be white or rather black (defined in the binary options menu).
Johannes
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Am 19.08.2013 11:51, schrieb Jędrzejas, Magdalena:
> Hello,
> Thank you, this plugin works really good. I only have one question: is there some kind of 'tool' which works like 'fill holes' or sth like that? After segmentation I obtained a segmented image, but I cannot get rid of really small areas of another label in the middle of large area of the basic one. I worked before with BZ II Analyzer, and there I used a 'fill holes' effect, where you could define the maximal size of the holes inside the larger area of other label, which should be covered. How can I do it in Fiji?
> Thanks in advance
> Regards
> Magda
>
> -----Ursprüngliche Nachricht-----
> Von: ImageJ Interest Group [mailto:
[hidden email]] Im Auftrag von
> Rob van 't Hof
> Gesendet: Donnerstag, 15. August 2013 16:56
> An:
[hidden email]
> Betreff: Re: segmentation
>
> Hi,
> Normally, go to image>adjust>color threshold. However, doing this successfully depends rather a lot on staining /image quality. Do you have an example?
> Also is your section from demineralised bone, or undemineralised? In
> the latter case there are a number of stains (such as von Kossa or
> Aniline
> blue) that nicely stain only the mineralised tissue.
> For more difficult segmentation have a look at the trainable WEKA segmentation plugin. This is included in the Fiji distribution of ImageJ.
>
> bye,
> Rob
>
> On 15/08/2013 15:04, Jędrzejas, Magdalena wrote:
>> Hello,
>>
>> I would like to do a segmentation of a microscopy image using ImageJ. I want to divide the picture into three labels: bone (originally more or less yellow), cartilage (originally green) and connective tissue which has other colors. Then Id like to measure these three areas. What tool/plugin should I use? The contrast between the tissues is not so good.....
>>
>> I would really appreciate any help
>>
>> Magda
>>
>>
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