Re: Isolating an object in image

Posted by ctrueden on
URL: http://imagej.273.s1.nabble.com/Isolating-an-object-in-image-tp5006745p5006750.html

Hi Sophie,

> I am trying to isolate unicellular algae from an image. I have tried
> to use filters, thresholds, math, gamma ...

Did you try the Trainable Weka Segmentation plugin?
http://fiji.sc/Trainable_Weka_Segmentation

It is bundled with the Fiji distribution of ImageJ: http://fiji.sc/

Regards,
Curtis

P.S. The ImageJ mailing list strips attachments so yours did not come
through.

P.P.S. See also: http://fiji.sc/Segmentation


On Mon, Mar 3, 2014 at 8:10 AM, Sophie Lorent <[hidden email]>wrote:

> Hi,
>
> I am trying to isolate unicellular algae from an image. I have tried to
> use filters, thresholds, math, gamma ...
>
> But the sometimes the inside of my cells are as nearly the same light
>  colour as the background. When this happens on the border of the cell,
> this part will be cut off the cell without being able to save it by
> "filling the holes" like I do it when these light parts occur in the middle
> on the cell. (See attachment figure 1 and 2)
>
> Is there something that can make can make kind on join two edges? (See
> figures 1 and 2). Or if someone has a good idea on how I could solve this
> problem.
>
> Cheers,
>
> Sophie
>
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