Re: How/where in the code are segmentations saved?

Posted by dscho on Jun 05, 2011; 2:24pm
URL: http://imagej.273.s1.nabble.com/How-where-in-the-code-are-segmentations-saved-tp3684345p3684347.html

Hi Kynn,

On Sun, 5 Jun 2011, Kynn Jones wrote:

> On Sun, Jun 5, 2011 at 4:14 AM, Johannes Schindelin
> <[hidden email]> wrote:
>
> > On Sat, 4 Jun 2011, Kynn Jones wrote:
> >
> >> I understand that ImageJ offers the possibility of saving to disk the
> >> result of an image segmentation.
> >
> > Are you referring to ROIs?
>
> Not sure.  What I mean is this: suppose you run some image segmentation.  

Well, if you give me a concrete example what plugin you run, then I can
tell you the nature of the output. Frequently it is just binary (or
indexed) images. In which case saving/loading is the same as with other
images.

> The result of this segmentation can be used in further analyses, so one
> can think of them as "intermediate results".  It would be useful to be
> able to save these intermediate segmentation results to disk, and reload
> them later, so that various analyses can be performed on the same
> intermediate segmentation results at different times.  If these
> intermediate segmentation results are expressed, somehow, as a
> collection of ROIs, then yes this is what I mean.  In this case, my
> question reduces to "how are ROIs serialized?"
>  I'll look at the links you posted.  Thanks!

There is a quite thorough concept of ROIs (possibly overlapping, multiple
classes, iterators, etc) in ImageJ2. Maybe you want to have a look:

http://fiji.sc/cgi-bin/gitweb.cgi?p=imagej2/.git;a=tree;f=core/data/src/main/java/imagej/data/roi;h=620598150f9ea14ee4f6cf274c730680ea204a03;hb=3d8fe33cd541d021b677fe4ccabde8977e25ca57

Note, however, that this ROI framework is not yet in the form where you
can expect things to Just Work. But it gives you an idea of the future
direction.

Ciao,
Johannes