Segmentation Editor: Save/Load/Import?

[Daniel Hornung]

Hello,

I have a question regarding the segmentation editor plugin [1]:

Is it possible to save and load the current segmentation state? Or maybe even to
import a previous segmentation result (possibly by another tool) as an 8bit
image stack?

Thanks a lot,
Daniel


[1] http://132.187.25.13/home/?category=Download&page=SegmentationEditor

--
Max-Planck-Institute for Dynamics and Self-Organization
Laboratory for Fluid Dynamics, Pattern Formation and Nanobiocomplexity
Biomedical Physics Group

Am Fassberg 17
D-37077 Goettingen

([phone]

[Benjamin Schmid-2]

Hi Daniel,
>
> I have a question regarding the segmentation editor plugin [1]:
>
> Is it possible to save and load the current segmentation state? Or maybe even to
> import a previous segmentation result (possibly by another tool) as an 8bit
> image stack?

This is possible. Save the label image in Amira format (a plugin is
available on the same site). When you want to reload and continue
segmentation, open the label file, using again the Amira plugin, open
the image which you're about to segment, and start the Segmentation
Editor. The segmentations should be recognized automatically.

Best,
Bene

>
>
> [1] http://132.187.25.13/home/?category=Download&page=SegmentationEditor
>
> --
> Max-Planck-Institute for Dynamics and Self-Organization
> Laboratory for Fluid Dynamics, Pattern Formation and Nanobiocomplexity
> Biomedical Physics Group
>
> Am Fassberg 17
> D-37077 Goettingen
>
> ([phone]

[Daniel Hornung]

On 2011-03-17 14:00, Benjamin Schmid wrote:

> Hi Daniel,
>>
>> I have a question regarding the segmentation editor plugin [1]:
>>
>> Is it possible to save and load the current segmentation state? Or maybe even to
>> import a previous segmentation result (possibly by another tool) as an 8bit
>> image stack?
>
> This is possible. Save the label image in Amira format (a plugin is
> available on the same site). When you want to reload and continue
> segmentation, open the label file, using again the Amira plugin, open
> the image which you're about to segment, and start the Segmentation
> Editor. The segmentations should be recognized automatically.

Hi Benjamin,

thanks a lot, I will try this out asap. Could you also put this on the
segmentation editor's page somewhere?

Cheers,
Daniel

--
Max-Planck-Institute for Dynamics and Self-Organization
Laboratory for Fluid Dynamics, Pattern Formation and Nanobiocomplexity
Biomedical Physics Group

Am Fassberg 17
D-37077 Goettingen

([phone]

[kscaplen16]

Hi Daniel and Bene,

I realize this is an old post, but I was wondering if either of you ever got
Amira to work with segmentation editor. I am interested in doing exactly
what Daniel has proposed: to save and load a current segmentation or even
save a finalized segmentation so that I can analyze or reanalyze it at a
later time (in 3D ROI manager). Thus far, I am able to save the labels (as a
tiff file), which is basically the black screen with my labeled segments,
but I am not able to merge it with the actual file that was segmented (the
file that has my brain image).

I have downloaded the Amira reader and writer plugins to save my
segmentation progress, but Segmentation Editor doesn't seem to recognize the
loaded file. Do either of you have any idea as to what I am doing wrong.

Thanks so much in advance for your insight!
Kristin



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