ImageJ api - show multi-class segmentation

[Jirka]

Dear developers,
I am actually reimplementing SLIC superpixel segmentation in ImageJ (nearly
complete). I would like to ask if there is an simple (systematic) way how
to show final segmentation given by an array int[][] where each class has
own index (integer number {0..N}). I d like to visualise the region
boundaries and also all segments where neighbouring segments have different
colour (probably in other frame). Do you have any advice?

Thanks, JB
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Best regards and wishes of a nice day, Jiří Borovec
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Jiří Borovec <[e-mail]>
PhD student at CMP CTU, ISC member
http://cmp.felk.cvut.cz/~borovji3

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[dscho]

Hi Jiří,

On Mon, 3 Jun 2013, Jiří Borovec wrote:

> I am actually reimplementing SLIC superpixel segmentation in ImageJ
> (nearly complete). I would like to ask if there is an simple
> (systematic) way how to show final segmentation given by an array
> int[][] where each class has own index (integer number {0..N}). I d like
> to visualise the region boundaries and also all segments where
> neighbouring segments have different colour (probably in other frame).
> Do you have any advice?

There is a Segmentation Editor in Fiji, loosely based on the Materials
Editor in Amira. It can display multiple (non-overlapping) segmentations
both as overlay and as a separate stack (the segmentations are stored in
that stack anyway, whether it is shown or not).

Its central source code can be found here:

        https://github.com/fiji/fiji/blob/master/src-plugins/VIB_/src/main/java/Segmentation_Editor.java

with support classes also in

        https://github.com/fiji/fiji/tree/master/src-plugins/VIB-lib/src/main/java/vib/segment

I have a couple of long-standing TODOs such as converting it to a tool,
separate out the "materials" list from the image, clean up the code, make
it extensible...

Please let me know if you're interested in using it, I'll reprioritize
those TODOs.

Ciao,
Johannes

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