Posted by
Jędrzejas, Magdalena on
URL: http://imagej.273.s1.nabble.com/segmentation-tp5004436p5004481.html
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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