How/where in the code are segmentations saved?
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How/where in the code are segmentations saved?
 
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I understand that ImageJ offers the possibility of saving to disk the
result of an image segmentation. What format is used to save a segmentation? IOW, how is the segmentation encoded/serialized? Also, where in the source code should I look to get the algorithmic details of how this is done? Thanks! kynnjo |
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Hi Kynn,
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? > What format is used to save a segmentation? IOW, how is the > segmentation encoded/serialized? Also, where in the source code should > I look to get the algorithmic details of how this is done? If you are referring to ROIs, the saving is implemented here: http://fiji.sc/cgi-bin/gitweb.cgi?p=ImageJA.git;a=blob;f=ij/io/RoiEncoder.java;hb=refs/heads/master and the loading here: http://fiji.sc/cgi-bin/gitweb.cgi?p=ImageJA.git;a=blob;f=ij/io/RoiDecoder.java;hb=refs/heads/master Ciao, Johannes |
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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 |
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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/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. 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=464f3be5f7bddfc33069dc574f1afe4a8316a63c Ciao, Johannes |
Re: How/where in the code are segmentations saved?
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On Sun, Jun 5, 2011 at 10:29 AM, Johannes Schindelin
<[hidden email]> wrote: >> 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. > > 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=464f3be5f7bddfc33069dc574f1afe4a8316a63c Hi Johannes, this info is all I need for now. Thanks! kj |
Re: How/where in the code are segmentations saved?
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In reply to this post by dscho
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?
---------------------------------------------------- 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=464f3be5f7bddfc33069dc574f1afe4a8316a63c Ciao, Johannes |
Re: How/where in the code are segmentations saved?
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Yes and no. If you are not a programmer, then no.
If you are a programmer, you should download the source code and use these 2 class files: ij.gui.Roi.java ij.io.RoiDecoder.java Source code: http://rsbweb.nih.gov/ij/download/src/ Also, it depends on how much control you have with the other software. If you don't know exactly what type of input the other software uses, then you won't be able to use the Roi's even if you are a programmer.
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