http://imagej.273.s1.nabble.com/help-with-3D-segmentation-tp5014798p5014817.html
forum. Somehow, you still had permission to post (along with some others),
mails. Albert is not the person responsible for maintaining the 3D Viewer.
Which should work correctly with Java 8. (Feedback welcome!)
> Hi Albert,
>
> Thank you again for your reply.
>
> On 02/11/2015 3:59 PM, Albert Cardona wrote:
>
> Last I remember, when the 3D Viewer fails to run because java3D is not
> installed, it should automatically prompt the user to allow an automatic
> installation.
>
> Albert
>
> That is not happening -- I only get the error in the console. My
> hypothesis is that some part of java3D is installed, and this makes the
> system think that it is there. Alternatively, it could be yet another java
> 1.8 issue.
>
> I found that in my Java 1.6 , the 3D viewer works, so I must have java3D
> there. Unfortunately, using java 1.6, I just started getting
> another problem -- the pop-up windows do not display text. This just
> started, and I have not had a chance yet to characterize it, so I have not
> yet formally reported this.
>
> How can I install java3D manually, or through the updater?
>
> Best regards
> --aryeh
>
>
>
>
> 2015-11-01 23:52 GMT-05:00 Aryeh Weiss <
[hidden email]>:
>
>> On 01/11/2015 11:33 PM, Albert Cardona wrote:
>>
>> Search in the command finder for the plugin that installs java3d
>> automatically.
>>
>>
>>
>> I found TestJava3D in teh command finder (and that fails, as expected).
>> I could not find anything that installs it, although I found the file in
>> the updater.
>>
>> Which command will do this?
>>
>>
>> Best regards
>> --aryeh
>>
>>
>>
>> On Nov 1, 2015, at 2:30 PM, Aryeh Weiss < <
[hidden email]>
>>
[hidden email]> wrote:
>>
>> On 01/11/2015 9:15 PM, Albert Cardona wrote:
>>
>> Works for me. Do you have java3d installed? Please open tbh 3D viewer
>> which will offer to install it automatically if not there yet.
>>
>> Albert
>>
>>
>>
>> When I open the 3D viewer, the following shows up in the Console:
>>
>> Exception in thread "J3D-Renderer-1" java.lang.UnsatisfiedLinkError: no
>> jogl in java.library.path
>> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864)
>> at java.lang.Runtime.loadLibrary0(Runtime.java:870)
>> at java.lang.System.loadLibrary(System.java:1122)
>> at
>> com.sun.opengl.impl.NativeLibLoader.loadLibraryInternal(NativeLibLoader.java:189)
>> at
>> com.sun.opengl.impl.NativeLibLoader.access$000(NativeLibLoader.java:49)
>> at
>> com.sun.opengl.impl.NativeLibLoader$DefaultAction.loadLibrary(NativeLibLoader.java:80)
>> at
>> com.sun.opengl.impl.NativeLibLoader.loadLibrary(NativeLibLoader.java:103)
>> at
>> com.sun.opengl.impl.NativeLibLoader.access$200(NativeLibLoader.java:49)
>> at com.sun.opengl.impl.NativeLibLoader$1.run(NativeLibLoader.java:111)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at
>> com.sun.opengl.impl.NativeLibLoader.loadCore(NativeLibLoader.java:109)
>> at
>> com.sun.opengl.impl.macosx.MacOSXGLDrawableFactory.<clinit>(MacOSXGLDrawableFactory.java:53)
>> at java.lang.Class.forName0(Native Method)
>> at java.lang.Class.forName(Class.java:264)
>> at
>> javax.media.opengl.GLDrawableFactory.getFactory(GLDrawableFactory.java:108)
>> at
>> javax.media.j3d.JoglPipeline$QueryCanvas.<init>(JoglPipeline.java:9010)
>> at
>> javax.media.j3d.JoglPipeline.getBestConfiguration(JoglPipeline.java:8774)
>> at javax.media.j3d.Renderer.doWork(Renderer.java:495)
>> at javax.media.j3d.J3dThread.run(J3dThread.java:256)
>>
>> so I guess that something which Java3D needs is broken
>>
>> best regards
>> --aryeh
>>
>>
>> On Nov 1, 2015, at 10:42 AM, Aryeh Weiss <
[hidden email]> wrote:
>>
>> On 01/11/2015 4:22 PM, Albert Cardona wrote:
>>
>>
>> Try this:
>>
>>
https://www.ini.uzh.ch/~acardona/fiji-tutorial/#find-peaks>>
>> Works with difference of gaussian to find peaks, in nd (the example is in
>> 3D just like in your data).
>>
>> The key in DoG is to determine the two sigmas. A bit of experimentation
>> will take you there.
>>
>> Albert
>>
>>
>>
>> Thank you for your reply. I think you are referring to:
>>
>> Find cells in an 3D image stack by Difference of Gaussian, count them,
>> and show them in 3D as spheres.
>>
>> I cut and paste this into my interpreter, with the modifications:
>> imp = IJ.getImage()
>>
>> and
>>
>> iso = Compute.inFloats(Scale2D(ImgLib.wrap(imp), scale2D))
>>
>> since I am not working on a color image.
>>
>> This produces a list of peaks.
>> Each peak is of the form:
>> array('f', [152.0, 123.0, 1.0])
>> so I assume that I can access the coordinates and do something with them.
>>
>> However, the script hangs (with no error - I can kill it)
>> when it gets to:
>>
>> # Show the peaks as spheres in 3D, along with orthoslices:
>> univ = Image3DUniverse(512, 512)
>> print type(univ)
>> univ.addIcospheres(ps, Color3f(1, 0, 0), 2, cell_diameter/2,
>> "Cells").setLocked(True)
>> univ.addOrthoslice(imp).setLocked(True)
>> univ.show()
>>
>> So I have not yet seen the objects.
>>
>> I will continue working on it, but I dont know how to use imagelib, so I
>> have to learn that.
>>
>> It looks promising.
>>
>> Best regards
>> --aryeh
>>
>>