http://permalink.gmane.org/gmane.comp.lib.itk.user hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://permalink.gmane.org/gmane.comp.lib.itk.user/40991 <pre>Richard, in our images dx=dy=dz, so in principle the closing should work fine in 3D. In fact I think the size of our images is going to make it impractical. I ran a test last night on a partial image, which is 1300x1100x200, about 1/5 of a full image (still being generated by the microscopy rig). It was still running after 9 hours this morning, when I stopped it, at 100% of the 8 cores on my PC. This is not really practical. I did implement the grayscale closing, but not exactly as in your code. I've been using ITK for a while, but in a very naive way, and writing a lot of my own code. I am not a C++ expert by any means, and in particular I do not know anything about templates. It is not important (since I have something that works) but if you felt motivated to send me a simple example of a main program that calls doClosing() I'm sure I would find it very instructional. It is not clear to me yet what radius to use for the structuring element. I've tried 30, 40 and 50. To generate the mas</pre> Gib Bogle 2013-05-23T21:58:32 http://permalink.gmane.org/gmane.comp.lib.itk.user/40990 <pre>Thanks Dan. The active contour method sounds very interesting, I'll give it a try. Gib On 23/05/2013 7:36 p.m., Dan Mueller wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Gib Bogle 2013-05-23T21:29:34 http://permalink.gmane.org/gmane.comp.lib.itk.user/40989 <pre>I got it working. My local repository doesn't have the new variable SCIFIO_SEP, and it still uses ":" for separator. I change it to ";" and it works. The program also works without SCIFIO_PATH being set. So the separator fix should resolve this issue. Thanks for you help! Joe On Thu, May 23, 2013 at 9:52 AM, Joe Ping-Lin Hsiao &lt;phsiao-+5Oa3zvhR2o3uPMLIKxrzw&lt; at &gt;public.gmane.org&gt;wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Joe Ping-Lin Hsiao 2013-05-23T14:29:55 http://permalink.gmane.org/gmane.comp.lib.itk.user/40988 <pre>Mark, Adding the SCIFIO_PATH environment variable doesn't work for me. I experimented with 'build/lib/jars' and 'build/lib/jars/', but I still have the same error. I can wait for the bug fix in ITK to get approved and try again. Thanks, Joe On Wed, May 22, 2013 at 3:00 PM, Mark Hiner &lt;hiner-63mtpxcE9Cs&lt; at &gt;public.gmane.org&gt; wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Joe Ping-Lin Hsiao 2013-05-23T13:52:39 http://permalink.gmane.org/gmane.comp.lib.itk.user/40987 <pre>On Wed, May 22, 2013 at 7:28 PM, Cary lorey &lt;developement.unity-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org&gt; wrote: It sounds like this is really a VTK question (if your comment that the right values are not produced by the GetComputedWorldValue function is correct). Have you seen these examples? http://www.vtk.org/Wiki/VTK/Examples/Cxx/Images/PickingAPixel http://www.vtk.org/Wiki/VTK/Examples/Cxx/Images/PickingAPixel2 David _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> David Doria 2013-05-23T11:59:29 http://permalink.gmane.org/gmane.comp.lib.itk.user/40986 <pre>The steps I've given should also work in 3D if the slice thickness is low enough to provide the connectivity between slices. Personally, I haven't had much luck with the vesselness family. My rule of thumb is that if they happen to work, then a simple morphological approach will probably work too, more reliably and with fewer parameters to fiddle :-). On Thu, May 23, 2013 at 5:36 PM, Dan Mueller &lt;dan.muel-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org&gt; wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Richard Beare 2013-05-23T10:04:39 http://permalink.gmane.org/gmane.comp.lib.itk.user/40985 <pre>Hi Gib, Some more food for thought: (1) If you have a 3D image (as opposed to 2D slices) you may consider using Hessian-based vesselness enhancement: http://www.itk.org/Doxygen/html/classitk_1_1Hessian3DToVesselnessMeasureImageFilter.html http://www.itk.org/Doxygen/html/classitk_1_1MultiScaleHessianBasedMeasureImageFilter.html http://www.insight-journal.org/browse/publication/314 http://www.insight-journal.org/browse/publication/175 http://www.insight-journal.org/browse/publication/163 This class of filters can enhance tube-like structures (e.g. vessels), while suppressing sheet like structures i.e. the outer border of your object. (2) You could consider using an active contour method to segment the outer structure (replacing step 1 in Richard's proposal above). You could achieve this by initializing the contour as the edge of your image, then shrink the contour until it attaches to the boundary of the tissue. Then continue to follow Richard's second step and remove the outer structure by erosion + maski</pre> Dan Mueller 2013-05-23T07:36:19 http://permalink.gmane.org/gmane.comp.lib.itk.user/40984 <pre>Hi Richard, I don't have other staining. Thanks for your suggestion of a procedure. I will have to study it and understand it, before I can comment on it. Gib On 23/05/2013 12:25 p.m., Richard Beare wrote: </pre> Gib Bogle 2013-05-23T01:46:49 http://permalink.gmane.org/gmane.comp.lib.itk.user/40983 <pre>Hi, I'm not sure I understand completely, but here's my suggestion of an approach. It may turn out to be easier if you have other staining too. 1) Segment the entire tissue - i.e generate one large object that contains all your small vessels and a boundary on your layer that you need to peel. More on how this might be achieved later. 2) Erode this object and use the eroded version to mask out the accidental staining - i.e. do the peeling. Then apply your normal segmentation to what is left. If you have another channel where all the tissue has contrast then segmenting the tissue will be relatively easy. Otherwise it will be a bit more of a challenge. My first guess if the latter is the case is to use 2 markers in a watershed. One marker will be the image border (definitely outside the tissue). Create the marker image as follows. a) Apply a large closing, say about 15% of the tissue size. This will connect your interior objects together. Threshold the result, choose the largest connected component, then</pre> Richard Beare 2013-05-23T00:25:44 http://permalink.gmane.org/gmane.comp.lib.itk.user/40982 <pre>Hello, I am trying to retrieve the values of a pixel from a mouse clicks and I pass the x and y parameters to the crop function , but when I click on the image , the application crashes. here is my code: class MouseInteractorStyle3 : public vtkInteractorStyleTrackballCamera { public: static MouseInteractorStyle3* New(); virtual void OnLeftButtonDown() { typedef itk::Image&lt;unsigned short,2&gt; ImageType; std::cout &lt;&lt; "Pressed left mouse button." &lt;&lt; std::endl; int x = this-&gt;Interactor-&gt;GetEventPosition()[0]; int y = this-&gt;Interactor-&gt;GetEventPosition()[1]; vtkSmartPointer&lt;vtkCoordinate&gt; coordinate = vtkSmartPointer&lt;vtkCoordinate&gt;::New(); coordinate-&gt;SetCoordinateSystemToDisplay(); coordinate-&gt;SetValue(x,y,0); // This doesn't produce the right value if the sphere is zoomed in??? double* world = coordinate-&gt;GetComputedWorldValue(this-&gt;Interactor-&gt;GetRenderWindow()-&gt;GetRenderers()-&gt;GetFirstRenderer()); std::cout &lt;&lt; "World coordinate</pre> Cary lorey 2013-05-22T23:28:37 http://permalink.gmane.org/gmane.comp.lib.itk.user/40981 <pre>I didn't think there would be a stock filter, but maybe somebody else has addressed this. I have attached a typical frame. I can't show the wanted result, but I think it's obvious when you know that the interior of this piece of tissue has the blood vessels stained, while the faint rim is clearly not blood vessel. The problem is that there will in general be many vessels stained to a similar intensity as this rim. Gib On 23/05/2013 8:53 a.m., Dženan Zukić wrote: </pre> Gib Bogle 2013-05-22T21:47:41 http://permalink.gmane.org/gmane.comp.lib.itk.user/40980 <pre>The reason why I don't think erode will work is that the part of the image that contains the information of interest is made up of many disconnected pieces, not very different from the boundary layer that I want to remove. The only thing that I can use to distinguish the pixels that need to be removed is that they are near the outside of the region. If I apply erosion I will remove many small but important features (this is labelled vasculature, and I do not want to lose fine capillaries). Gib On 22/05/2013 11:12 p.m., Dženan Zukić wrote: </pre> Gib Bogle 2013-05-22T20:50:41 http://permalink.gmane.org/gmane.comp.lib.itk.user/40979 <pre>I don't think there is any stock filter which does what you want. And I still don't understand your situation. Can you show us an example slice and wanted result? On Wed, May 22, 2013 at 10:50 PM, Gib Bogle &lt;g.bogle-1/NbpDiVQt6SYBAHRPvY1A&lt; at &gt;public.gmane.org&gt; wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Dženan Zukić 2013-05-22T20:53:09 http://permalink.gmane.org/gmane.comp.lib.itk.user/40978 <pre>Hi Joe, Just wanted to send you an update... I eventually realized it wasn't a Debug/Release issue, but rather a classpath separator issue. The Linux/OSX separator was hard-coded in the SCIFIO ImageIO. So the scifio-imageio &lt;https://github.com/scifio/scifio-imageio&gt;repository has been updated to choose the correct separator for OSX or Windows. I also filed this bug fix &lt;http://review.source.kitware.com/#/c/11375/&gt;updating ITK to download the updated scifio-imageio commit. Also, while looking through the code, I had forgotten that the JVM classpath (where those jars need to be) isn't pulled from the PATH... it's taken from a special environment variable: SCIFIO_PATH. If you set SCIFIO_PATH to the directory containing the itk-bridge jar and loci_tools.jar (build/lib/jars) it should work without the update. (*should*work..) Note that the SCIFIO_PATH is prepended onto each jar dependency. Anyway, I hope this resolves everything for you. If you run into more trouble, let me know. Thanks, Mark On Fri, </pre> Mark Hiner 2013-05-22T19:00:28 http://permalink.gmane.org/gmane.comp.lib.itk.user/40977 <pre>Hello, I am a beginner in ITK, please can you help me with an example that uses startPickEvent , I read the documentation but is not clear. thank you in advance. _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Cary lorey 2013-05-22T16:33:14 http://permalink.gmane.org/gmane.comp.lib.itk.user/40976 <pre>http://www.itk.org/Doxygen/html/group__MathematicalMorphologyImageFilters.html What you probably want to do is BinaryErode and BinaryDilate. On Wed, May 22, 2013 at 7:04 AM, gib &lt;g.bogle-1/NbpDiVQt6SYBAHRPvY1A&lt; at &gt;public.gmane.org&gt; wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Dženan Zukić 2013-05-22T11:12:16 http://permalink.gmane.org/gmane.comp.lib.itk.user/40975 <pre>It's hard to know what to call the processing I want to apply. I have a set of biological images (actually a 3D image, but for now I'm happy to process the frames one-by-one) in which the region of interest has an irregular and incomplete labelled layer around the boundary. The staining of the layer was unintended, and its presence interferes with the segmentation that I am doing. The part of the image that I want to extract is made up of many disconnected objects, and there is not much difference in the intensity ranges of the objects of interest and the unwanted edge. I am willing to trim a few pixels off the boundary all the way around - this will not cause much loss of information. What I need is way to determine a sequence of pixels that in some sense defines the extent of the labelled region in the image, rather like a 2D shrink wrapping. I could then use this to shave or peel off the outer layer of pixels. Does this process have a name? Are there any existing filters or code to do this? Any c</pre> gib 2013-05-22T05:04:14 http://permalink.gmane.org/gmane.comp.lib.itk.user/40974 <pre>Hi David, The purpose of the "CreateDeformedImage" method is to warp the moving image according an inverse deformation field (direction: from the deformed mesh to the undeformed mesh). The FEMScatteredDataPointSetToImageFilter generates a direct field (direction: from the undeformed to the deformed mesh). In case that you want to warp the moving image by using the WarpImageFilter, you should generate an inverse deformation field and set this field as an input to the WarpImageFilter. Regards, Fotis On Tue, May 21, 2013 at 4:26 PM, David Fuentes &lt;fuentesdt-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org&gt; wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscrib</pre> Fotis Drakopoulos 2013-05-21T20:50:00 http://permalink.gmane.org/gmane.comp.lib.itk.user/40973 <pre>Hi, What was the purpose of the CreateDeformedImage Method for the PBNRR class ? http://review.source.kitware.com/#/c/7136/3 Is this code functionally different than using the WarpImageFilter to apply the output deformation field to the moving image ? Thanks, David _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> David Fuentes 2013-05-21T20:26:39 http://permalink.gmane.org/gmane.comp.lib.itk.user/40972 <pre>Hello Thomas, In SimpleITK the order of the image inputs is the same as that used in ITK. We hope to add name arguments to SimpleITK shortly which should help for this type of case. In many cases to under stand what it going on in a filter sometimes you need to look at the ITK Code for example for the MorphologicalWatershedFromMarkers[1] you can look at the header[2]. Sometime you need to look at the SimpleITK JSON which describes the filter too[3]. So for this particular filter this first image is the feature image and the second is the markers. And this will improve in SimpleITK in the future. [1] http://www.itk.org/Doxygen/html/classitk_1_1MorphologicalWatershedFromMarkersImageFilter.html [2] http://www.itk.org/Doxygen/html/itkMorphologicalWatershedFromMarkersImageFilter_8h_source.html [3]https://github.com/SimpleITK/SimpleITK/blob/master/Code/BasicFilters/json/MorphologicalWatershedFromMarkersImageFilter.json#L8 Brad On May 21, 2013, at 12:11 PM, Thomas Deschamps &lt;tdeschamps-/3juihCSby0&lt; at &gt;public.gman</pre> Bradley Lowekamp 2013-05-21T17:50:41 http://permalink.gmane.org/gmane.comp.lib.itk.user/40971 <pre>Thank you for your answer. Could you tell me if the convention for morphological reconstructions is always FunctionName( SeedImage, MaskImage, optional parameters) ? And is it the same for other routines like MorphologicalWatershedFromMarkersImageFilter? I could not find the answer in the documentation. Thanks! On Tue, May 21, 2013 at 3:01 AM, Richard Beare &lt;richard.beare-Re5JQEeQqe8AvxtiuMwx3w&lt; at &gt;public.gmane.org&gt;wrote: _____________________________________ Powered by www.kitware.com Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html Kitware offers ITK Training Courses, for more information visit: http://www.kitware.com/products/protraining.php Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ Follow this link to subscribe/unsubscribe: http://www.itk.org/mailman/listinfo/insight-users </pre> Thomas Deschamps 2013-05-21T16:11:16 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.lib.itk.user