Along these lines is it possible to save the ROI or segmentation so that the positions and shapes of the segments can be reconstructed in another piece of software?
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Sean Burke
Technical Applications Specialist
De Novo Software
[hidden email]Phone: (213)814-1240 Ext. 806
-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Johannes Schindelin
Sent: Sunday, June 05, 2011 10:29 AM
To:
[hidden email]Subject: Re: How/where in the code are segmentations saved?
Hi Kynn,
On Sun, 5 Jun 2011, Johannes Schindelin wrote:
> 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/sr> c/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.
Of course I forgot to add the link to the actual data structures:
http://fiji.sc/cgi-bin/gitweb.cgi?p=imglib.git;a=tree;f=imglib2/core/src/main/java/net/imglib2/roi;h=517700ada29c3ed1b3337ade8bc2a8dc0a913f8f;hb=464f3be5f7bddfc33069dc574f1afe4a8316a63cCiao,
Johannes