3D reconstruction (I need help)
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3D reconstruction (I need help)
 
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Hello!
I'm new in the list and this is my first message. I need help to reconstruct in 3D a burrow system that is inside of a rock. Yes, its a fossil. It is a complex network of interconected burrows. Burrows are not empty, they are filled with rock, but slightly different to the enclosing rock. So a difference of density is between rock and burrow sufficient for to be detected in a tomograph. I've scanned the sample in a conventional medical scanner and then, I have a lot of images of sections, spaced every 1 mm, of the sample. I need help for 1) In every image to select atomatically the zones corresponding to burrows and then to eliminate the rest of the image; and 2) with the resulting series of images of "burrows sections" to make a three dimensional reconstruction of the burrow system. My computer skills have been exceeded when I tried to do it alone using ImageJ, in fact I never use any other images software than Photoshop or similar. If someone can help me or at least tell me if it is, or not, possible of make using ImageJ I will be very grateful. Also if someone know about other software that can help me, please let me know. Thanks to all of you Sincerely Emilio Bedatou CONICET-UNLPam Av. Uruguay 151 Santa Rosa-La Pampa Argentina --------------------------------- Preguntá. Respondé. Descubrí. Todo lo que querías saber, y lo que ni imaginabas, está en Yahoo! Respuestas (Beta). ¡Probalo ya! |
Re: 3D reconstruction (I need help)
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Hi Emilio
If both burrow and rock are different and consistent densities, and the boundary is reasonably sharp, you could try thresholding the volume in Volume Viewer. 1. Install Volume Viewer: http://rsb.info.nih.gov/ij/plugins/volume-viewer.html 2. Import your set of slices into a stack - File->Import->Image Sequence 3. Select Volume Viewer from the Plugins Menu of ImageJ 4. Play with the threshold value until you find the cutoff at the boundary between rock and burrow (you may have to invert [Edit->Invert] the images first so that the burrows are higher grey values than the rock) 5. If you want to make some animations then try my macro: http://doube.org/macros.html#volslice There is a nice Open Source 3D renderer called Drishti that I have been using, but it requires a recent 3D graphics card to run - it's worth a try for your sort of work: http://sf.anu.edu.au/Vizlab/drishti/ Let us know how you get on! Mike Emilio Bedatou wrote: > Hello! > > I'm new in the list and this is my first message. > > I need help to reconstruct in 3D a burrow system that is inside of a rock. Yes, its a fossil. It is a complex network of interconected burrows. Burrows are not empty, they are filled with rock, but slightly different to the enclosing rock. So a difference of density is between rock and burrow sufficient for to be detected in a tomograph. > I've scanned the sample in a conventional medical scanner and then, I have a lot of images of sections, spaced every 1 mm, of the sample. > > I need help for > 1) In every image to select atomatically the zones corresponding to burrows and then to eliminate the rest of the image; and > 2) with the resulting series of images of "burrows sections" to make a three dimensional reconstruction of the burrow system. > > My computer skills have been exceeded when I tried to do it alone using ImageJ, in fact I never use any other images software than Photoshop or similar. > > If someone can help me or at least tell me if it is, or not, possible of make using ImageJ I will be very grateful. > > Also if someone know about other software that can help me, please let me know. > > Thanks to all of you > > Sincerely > > Emilio Bedatou > CONICET-UNLPam > Av. Uruguay 151 > Santa Rosa-La Pampa > Argentina > > > --------------------------------- > Preguntá. Respondé. Descubrí. > Todo lo que querías saber, y lo que ni imaginabas, > está en Yahoo! Respuestas (Beta). > ¡Probalo ya! > -- Michael Doube BPhil BVSc MRCVS PhD Student Dental Institute Queen Mary, University of London New Rd London E1 1BB United Kingdom Phone +44 (0)20 7377 7000 ext 2681 |
Re: 3D reconstruction (I need help)
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In reply to this post by Emilio Bedatou
Hi Emilio,
You can do 3D reconstruction with TrakEM2. 1 - Install these jars in the plugins folder: http://www.ini.uzh.ch/~acardona/edge/TrakEM2_.jar http://www.ini.uzh.ch/~acardona/edge/ImageJ_3D_Viewer.jar You need java 3d installed as well (present by default in MacOSX 10.4) 2 - Restart ImageJ 3 - Plugins -> TrakEM2 -> New Project (blank) 4 - Drag and drop a stack from your folders directly into the opened display. 5 - Go to the TrakEM2 window with the trees, and add nodes to the template tree (right-click to see "new"). The "area_list" is a free paint-bush operated segmentation type which is what you want. 6 - Drag and drop nodes from the template tree to the project tree, to create new ones, as many as desired (so you have one template, but many instances). 7 - Having an area list selected, just paint in the screen the area to segment. See the manual for all key bindings controling the brush (brush diameter, flood-fill, erase, flood-erase ...) http://www.ini.uzh.ch/~acardona/trakem2_manual.html#arealists 8 - In the TrakEM2 window, right-click on a node and select "Show in 3D". General tips: - Don't forget to "save" or "save as" your project. - right-click is your friend. Explore the menus for all options (such as "Autoresize canvas/layer set" to fit the window to your stack.) The 3D window enables you to take snaphsots, or export to other CAD applications for finer rendering of the 3D meshes. Albert |
Re: 3D reconstruction (I need help)
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In reply to this post by Emilio Bedatou
Hi Emilio,
I would just like to point you to our homepage. We have worked on plugins regarding segmentation and 3D reconstruction. Our segmentation tool is mainly made for manual segmentation, so it may not be what you are looking for, but we can help you with the 3D reconstruction of the segmented images. Our segmentation editor can be found at http://132.187.25.13/bene/my/?category=Download&page=SegmentationEditor the 3D reconstruction and visualisation plugin at http://132.187.25.13/bene/my/?category=Download&page=Viewer3D We are working with flies, so all the screenshots you find there are made from fly brains, but nevertheless the software is not restricted to that. Best wishes, Benjamin On Jun 7, 2007, at 2:26 PM, Emilio Bedatou wrote: > Hello! > > I'm new in the list and this is my first message. > > I need help to reconstruct in 3D a burrow system that is inside > of a rock. Yes, its a fossil. It is a complex network of > interconected burrows. Burrows are not empty, they are filled with > rock, but slightly different to the enclosing rock. So a difference > of density is between rock and burrow sufficient for to be detected > in a tomograph. > I've scanned the sample in a conventional medical scanner and > then, I have a lot of images of sections, spaced every 1 mm, of the > sample. > > I need help for > 1) In every image to select atomatically > the zones corresponding to burrows and then to eliminate the rest > of the image; and > 2) with the resulting series of images of > "burrows sections" to make a three dimensional reconstruction of > the burrow system. > > My computer skills have been exceeded when I tried to do it alone > using ImageJ, in fact I never use any other images software than > Photoshop or similar. > > If someone can help me or at least tell me if it is, or not, > possible of make using ImageJ I will be very grateful. > > Also if someone know about other software that can help me, > please let me know. > > Thanks to all of you > > Sincerely > > Emilio Bedatou > CONICET-UNLPam > Av. Uruguay 151 > Santa Rosa-La Pampa > Argentina > > > --------------------------------- > Preguntá. Respondé. Descubrí. > Todo lo que querías saber, y lo que ni imaginabas, > está en Yahoo! Respuestas (Beta). > ¡Probalo ya! |
Re: 3D reconstruction (I need help)
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Hi All,
Thanks Benjamin for your reply to Emilio, I tried your plugin after installing Java 3D (I can see a rotating cube) The plugin opens I used your sample stack in your web page, after selecting volume mode nad parameters, ImageJ crashes and is shut. Any suggestions? The memory of ImageJ is 1000MB in my settings... Orkun ERSOY -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Benjamin Schmid Sent: Friday, June 08, 2007 5:05 PM To: [hidden email] Subject: Re: 3D reconstruction (I need help) Hi Emilio, I would just like to point you to our homepage. We have worked on plugins regarding segmentation and 3D reconstruction. Our segmentation tool is mainly made for manual segmentation, so it may not be what you are looking for, but we can help you with the 3D reconstruction of the segmented images. Our segmentation editor can be found at http://132.187.25.13/bene/my/?category=Download&page=SegmentationEditor the 3D reconstruction and visualisation plugin at http://132.187.25.13/bene/my/?category=Download&page=Viewer3D We are working with flies, so all the screenshots you find there are made from fly brains, but nevertheless the software is not restricted to that. Best wishes, Benjamin On Jun 7, 2007, at 2:26 PM, Emilio Bedatou wrote: > Hello! > > I'm new in the list and this is my first message. > > I need help to reconstruct in 3D a burrow system that is inside > of a rock. Yes, its a fossil. It is a complex network of > interconected burrows. Burrows are not empty, they are filled with > rock, but slightly different to the enclosing rock. So a difference > of density is between rock and burrow sufficient for to be detected > in a tomograph. > I've scanned the sample in a conventional medical scanner and > then, I have a lot of images of sections, spaced every 1 mm, of the > sample. > > I need help for > 1) In every image to select atomatically > the zones corresponding to burrows and then to eliminate the rest > of the image; and > 2) with the resulting series of images of > "burrows sections" to make a three dimensional reconstruction of > the burrow system. > > My computer skills have been exceeded when I tried to do it alone > using ImageJ, in fact I never use any other images software than > Photoshop or similar. > > If someone can help me or at least tell me if it is, or not, > possible of make using ImageJ I will be very grateful. > > Also if someone know about other software that can help me, > please let me know. > > Thanks to all of you > > Sincerely > > Emilio Bedatou > CONICET-UNLPam > Av. Uruguay 151 > Santa Rosa-La Pampa > Argentina > > > --------------------------------- > Preguntá. Respondé. DescubrÃ. > Todo lo que querÃas saber, y lo que ni imaginabas, > está en Yahoo! Respuestas (Beta). > ¡Probalo ya! |
Re: 3D reconstruction (I need help)
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Hi Orkun,
can you tell me more about your system? Which computer are you using, which operating system, and which graphics card? It would be also helpful, if you could start it in a console, which would probably provide you with more details about the reason for the crash. If you are interested, I will tell you how to do that once you told me your operating system. Cheers, Benjamin On Jun 8, 2007, at 12:23 PM, Orkun Ersoy wrote: > Hi All, > Thanks Benjamin for your reply to Emilio, > I tried your plugin after installing Java 3D (I can see a rotating > cube) > The plugin opens I used your sample stack in your web page, after > selecting volume mode nad parameters, ImageJ crashes and is shut. > > Any suggestions? > The memory of ImageJ is 1000MB in my settings... > > Orkun ERSOY > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Benjamin Schmid > Sent: Friday, June 08, 2007 5:05 PM > To: [hidden email] > Subject: Re: 3D reconstruction (I need help) > > Hi Emilio, > > I would just like to point you to our homepage. We have worked on > plugins regarding segmentation and > 3D reconstruction. Our segmentation tool is mainly made for manual > segmentation, so it may not be what > you are looking for, but we can help you with the 3D reconstruction > of the segmented images. > > Our segmentation editor can be found at > http://132.187.25.13/bene/my/? > category=Download&page=SegmentationEditor > > the 3D reconstruction and visualisation plugin at > http://132.187.25.13/bene/my/?category=Download&page=Viewer3D > > We are working with flies, so all the screenshots you find there are > made from fly brains, but nevertheless > the software is not restricted to that. > > Best wishes, > > Benjamin > > On Jun 7, 2007, at 2:26 PM, Emilio Bedatou wrote: > >> Hello! >> >> I'm new in the list and this is my first message. >> >> I need help to reconstruct in 3D a burrow system that is inside >> of a rock. Yes, its a fossil. It is a complex network of >> interconected burrows. Burrows are not empty, they are filled with >> rock, but slightly different to the enclosing rock. So a difference >> of density is between rock and burrow sufficient for to be detected >> in a tomograph. >> I've scanned the sample in a conventional medical scanner and >> then, I have a lot of images of sections, spaced every 1 mm, of the >> sample. >> >> I need help for >> 1) In every image to select atomatically >> the zones corresponding to burrows and then to eliminate the rest >> of the image; and >> 2) with the resulting series of images of >> "burrows sections" to make a three dimensional reconstruction of >> the burrow system. >> >> My computer skills have been exceeded when I tried to do it alone >> using ImageJ, in fact I never use any other images software than >> Photoshop or similar. >> >> If someone can help me or at least tell me if it is, or not, >> possible of make using ImageJ I will be very grateful. >> >> Also if someone know about other software that can help me, >> please let me know. >> >> Thanks to all of you >> >> Sincerely >> >> Emilio Bedatou >> CONICET-UNLPam >> Av. Uruguay 151 >> Santa Rosa-La Pampa >> Argentina >> >> >> --------------------------------- >> Preguntá. Respondé. Descubrà . >> Todo lo que querà as saber, y lo que ni imaginabas, >> está en Yahoo! Respuestas (Beta). >> ¡Probalo ya! |
Re: 3D reconstruction (I need help)
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In reply to this post by Benjamin Schmid-2
I tried the ImageJ 3D reconstruction plugin below, and receive the following
error: Plugin or class not found: "ImageJ_3D_Viewer" (java.lang.NoClassDefFoundError: com/sun/j3d/utils/behaviors/mouse/MouseBehaviorCallback). The volume viewer from Osirix works but is slow for even modest volume sizes. Shawn -- Shawn Mikula, Ph.D., Postdoctoral Scholar Center for Neuroscience University of California-Davis, 1544 Newton Court, Davis, CA 95618, Phone: 530-754-9209 Fax: 530-754-9136 mail: [hidden email] web: http://brainmaps.org ----- Original Message ----- From: "Benjamin Schmid" <[hidden email]> To: <[hidden email]> Sent: Friday, June 08, 2007 8:04 AM Subject: Re: 3D reconstruction (I need help) > Hi Emilio, > > I would just like to point you to our homepage. We have worked on plugins > regarding segmentation and > 3D reconstruction. Our segmentation tool is mainly made for manual > segmentation, so it may not be what > you are looking for, but we can help you with the 3D reconstruction of > the segmented images. > > Our segmentation editor can be found at > http://132.187.25.13/bene/my/?category=Download&page=SegmentationEditor > > the 3D reconstruction and visualisation plugin at > http://132.187.25.13/bene/my/?category=Download&page=Viewer3D > > We are working with flies, so all the screenshots you find there are made > from fly brains, but nevertheless > the software is not restricted to that. > > Best wishes, > > Benjamin > > On Jun 7, 2007, at 2:26 PM, Emilio Bedatou wrote: > >> Hello! >> >> I'm new in the list and this is my first message. >> >> I need help to reconstruct in 3D a burrow system that is inside of a >> rock. Yes, its a fossil. It is a complex network of interconected >> burrows. Burrows are not empty, they are filled with rock, but slightly >> different to the enclosing rock. So a difference of density is between >> rock and burrow sufficient for to be detected in a tomograph. >> I've scanned the sample in a conventional medical scanner and then, I >> have a lot of images of sections, spaced every 1 mm, of the sample. >> >> I need help for >> 1) In every image to select atomatically the >> zones corresponding to burrows and then to eliminate the rest of the >> image; and >> 2) with the resulting series of images of >> "burrows sections" to make a three dimensional reconstruction of the >> burrow system. >> >> My computer skills have been exceeded when I tried to do it alone >> using ImageJ, in fact I never use any other images software than >> Photoshop or similar. >> >> If someone can help me or at least tell me if it is, or not, possible >> of make using ImageJ I will be very grateful. >> >> Also if someone know about other software that can help me, please let >> me know. >> >> Thanks to all of you >> >> Sincerely >> >> Emilio Bedatou >> CONICET-UNLPam >> Av. Uruguay 151 >> Santa Rosa-La Pampa >> Argentina >> >> --------------------------------- >> Preguntá. Respondé. Descubrí. >> Todo lo que querías saber, y lo que ni imaginabas, >> está en Yahoo! Respuestas (Beta). >> ¡Probalo ya! |
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Hi,
On Fri, 8 Jun 2007, Shawn Mikula wrote: > I tried the ImageJ 3D reconstruction plugin below, and receive the following > error: > Plugin or class not found: "ImageJ_3D_Viewer" > (java.lang.NoClassDefFoundError: > com/sun/j3d/utils/behaviors/mouse/MouseBehaviorCallback). This means that you lack java3d, probably, or that your version is too old. Hth, Dscho |
Re: 3D reconstruction (I need help)
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In reply to this post by Benjamin Schmid-2
Thanks again Benjamin for your reply,
I use a laptop with Windows XP, processor Pentium 1,73 GHz and 512 MB RAM. The graphic card is 915GM/GMS/910GML Express Chipset Family. Please let me know how to start it in a console. Regards Orkun ERSOY -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Benjamin Schmid Sent: Friday, June 08, 2007 7:23 PM To: [hidden email] Subject: Re: 3D reconstruction (I need help) Hi Orkun, can you tell me more about your system? Which computer are you using, which operating system, and which graphics card? It would be also helpful, if you could start it in a console, which would probably provide you with more details about the reason for the crash. If you are interested, I will tell you how to do that once you told me your operating system. Cheers, Benjamin On Jun 8, 2007, at 12:23 PM, Orkun Ersoy wrote: > Hi All, > Thanks Benjamin for your reply to Emilio, > I tried your plugin after installing Java 3D (I can see a rotating > cube) > The plugin opens I used your sample stack in your web page, after > selecting volume mode nad parameters, ImageJ crashes and is shut. > > Any suggestions? > The memory of ImageJ is 1000MB in my settings... > > Orkun ERSOY > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of > Benjamin Schmid > Sent: Friday, June 08, 2007 5:05 PM > To: [hidden email] > Subject: Re: 3D reconstruction (I need help) > > Hi Emilio, > > I would just like to point you to our homepage. We have worked on > plugins regarding segmentation and > 3D reconstruction. Our segmentation tool is mainly made for manual > segmentation, so it may not be what > you are looking for, but we can help you with the 3D reconstruction > of the segmented images. > > Our segmentation editor can be found at > http://132.187.25.13/bene/my/? > category=Download&page=SegmentationEditor > > the 3D reconstruction and visualisation plugin at > http://132.187.25.13/bene/my/?category=Download&page=Viewer3D > > We are working with flies, so all the screenshots you find there are > made from fly brains, but nevertheless > the software is not restricted to that. > > Best wishes, > > Benjamin > > On Jun 7, 2007, at 2:26 PM, Emilio Bedatou wrote: > >> Hello! >> >> I'm new in the list and this is my first message. >> >> I need help to reconstruct in 3D a burrow system that is inside >> of a rock. Yes, its a fossil. It is a complex network of >> interconected burrows. Burrows are not empty, they are filled with >> rock, but slightly different to the enclosing rock. So a difference >> of density is between rock and burrow sufficient for to be detected >> in a tomograph. >> I've scanned the sample in a conventional medical scanner and >> then, I have a lot of images of sections, spaced every 1 mm, of the >> sample. >> >> I need help for >> 1) In every image to select atomatically >> the zones corresponding to burrows and then to eliminate the rest >> of the image; and >> 2) with the resulting series of images of >> "burrows sections" to make a three dimensional reconstruction of >> the burrow system. >> >> My computer skills have been exceeded when I tried to do it alone >> using ImageJ, in fact I never use any other images software than >> Photoshop or similar. >> >> If someone can help me or at least tell me if it is, or not, >> possible of make using ImageJ I will be very grateful. >> >> Also if someone know about other software that can help me, >> please let me know. >> >> Thanks to all of you >> >> Sincerely >> >> Emilio Bedatou >> CONICET-UNLPam >> Av. Uruguay 151 >> Santa Rosa-La Pampa >> Argentina >> >> >> --------------------------------- >> Preguntá. Respondé. Descubrà . >> Todo lo que querà as saber, y lo que ni imaginabas, >> está en Yahoo! Respuestas (Beta). >> ¡Probalo ya! |
Re: 3D reconstruction (I need help)
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In reply to this post by dscho
hi Johannes,
I have the most recent Java3d installed. I think it might be a classpath or environment variable issue. I tried the ImageJ 3D reconstruction plugin again, just now, and received the following error: java.lang.UnsupportedClassVersionError: Bad version number in .class file at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(Unknown Source) at java.lang.ClassLoader.defineClass(Unknown Source) at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:246) at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:209) at ij.IJ.runUserPlugIn(IJ.java:264) at ij.IJ.runPlugIn(IJ.java:120) at ij.Executer.runCommand(Executer.java:95) at ij.Executer.run(Executer.java:49) at java.lang.Thread.run(Unknown Source) Shawn ----- Original Message ----- From: "Johannes Schindelin" <[hidden email]> To: "Shawn Mikula" <[hidden email]> Cc: <[hidden email]> Sent: Friday, June 08, 2007 11:25 AM Subject: Re: 3D reconstruction (I need help) > Hi, > > On Fri, 8 Jun 2007, Shawn Mikula wrote: > >> I tried the ImageJ 3D reconstruction plugin below, and receive the >> following >> error: >> Plugin or class not found: "ImageJ_3D_Viewer" >> (java.lang.NoClassDefFoundError: >> com/sun/j3d/utils/behaviors/mouse/MouseBehaviorCallback). > > This means that you lack java3d, probably, or that your version is too > old. > > Hth, > Dscho > |
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In reply to this post by Orkun Ersoy
Hi,
On Fri, 8 Jun 2007, Orkun Ersoy wrote: > I use a laptop with Windows XP, processor Pentium 1,73 GHz and 512 MB RAM. > The graphic card is 915GM/GMS/910GML Express Chipset Family. > Please let me know how to start it in a console. Run "cmd". Then go to c:/program files/imagej. There, it should be as easy as "java -jar ij.jar". BTW what kind of crash do you experience? Does it show an exception window, or does it close one/all ImageJ windows? Hth, Dscho |
Re: 3D reconstruction (I need help)
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Hi,
It is interesting that when I call ImageJ from "cmd", the plugin worked. Thanks Johannes -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Johannes Schindelin Sent: Friday, June 08, 2007 9:38 PM To: [hidden email] Subject: Re: 3D reconstruction (I need help) Hi, On Fri, 8 Jun 2007, Orkun Ersoy wrote: > I use a laptop with Windows XP, processor Pentium 1,73 GHz and 512 MB RAM. > The graphic card is 915GM/GMS/910GML Express Chipset Family. > Please let me know how to start it in a console. Run "cmd". Then go to c:/program files/imagej. There, it should be as easy as "java -jar ij.jar". BTW what kind of crash do you experience? Does it show an exception window, or does it close one/all ImageJ windows? Hth, Dscho |
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Hi,
On Fri, 8 Jun 2007, Orkun Ersoy wrote: > It is interesting that when I call ImageJ from "cmd", the plugin worked. Probably your ImageJ is installed with its own JRE. Benjamin wrote the Java3D installer plugin for that. You'll find it here: http://132.187.25.13/bene/my/imagej/Install_Java3D.jar This will install Java3D into ImageJ's JRE. Hth, Dscho |
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