Re: help with 3D segmentation

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Re: help with 3D segmentation

Aryeh Weiss
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]> 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:


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

On Nov 1, 2015, at 8:06 AM, Aryeh Weiss <[hidden email]> wrote:

I have been asked to do a 3D segmentation of a DAPI stained image, such as the image stack available at:
https://drive.google.com/open?id=0B9hvIdSL8kGyY0NiRzRkaXlINmM

I find that I can do very well in 2D by blurring the image and doing peak detection, or gray-scale watershed.
Gabriel Landini's domes followed by a peak detection or thresholding step also works nicely.
However, I have not succeeded in extending this to 3D, using the 3D morphological segmentation tools.

A 3D-domes would be nice, but I have not found that.
I tried peak detection or 2D-domes and then 3D object counting, but there is still too much overlap in the Z-direction, so that nuclei which
overlap vertically are counted as one object.

So I seek to tap into the knowledge available on this list, because I am sure someone has already done this type of segmentation.

Thanks in advance
--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


-- 
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051



-- 
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051



-- 
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051




--


-- 
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

--
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