BoneJ and Java3D

[TimFeinstein]

Hi folks,

When I try to run various features in the BoneJ plugin, it tells me that I need to get Java3D via the 3D Viewer plugin.  The viewer runs, more or less, but if I try to re-size the viewer window I get a complex error message in the Log window and Fiji freezes completely.  3D viewer also does not fix my Java3D problem.  I am using Fiji with the latest updates; ImageJ 1.5.1t; OSX 10.13.1.

I tried installing the May 30, 2017 version of Fiji following the thread below, but BoneJ still did not acknowledge Java#D.  The 3D Viewer help menu seems to think that I have the correct Java3D installed.

http://forum.imagej.net/t/bonej-issue-volume-fraction-or-3d-viewer-problem/6823

Any ideas?


Tim

Timothy Feinstein, Ph.D.
Research Scientist
Department of Developmental Biology
University of Pittsburgh



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[Swayne, Theresa C.]

Hi Tim,

I tried to do this too (OS X 10.12), and had similar issues.

However, I was able to use a Windows 7 machine to run BoneJ with Java 6 Fiji.

And I’ve started looking at the pre-release BoneJ2:
https://github.com/bonej-org/BoneJ2/wiki/Installing-BoneJ2

It runs on my Mac (using up-to-date, Java 8 Fiji), and it successfully generates a thickness map from a sample image, but I haven’t tested it extensively.

Hope this helps.


------------------------------------
Theresa Swayne, Ph.D.
Associate Research Scientist
Manager, Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>

Herbert Irving Comprehensive Cancer Center
Columbia University Medical Center
1130 St. Nicholas Ave., Room 222A
New York, NY 10032
Phone: [phone]
[hidden email]<mailto:[hidden email]>



From: ImageJ Interest Group <[hidden email]> on behalf of "Feinstein, Timothy N" <[hidden email]>
Reply-To: "[hidden email]" <[hidden email]>
Date: Friday, January 5, 2018 at 12:45 PM
To: "[hidden email]" <[hidden email]>
Subject: BoneJ and Java3D

Hi folks,

When I try to run various features in the BoneJ plugin, it tells me that I need to get Java3D via the 3D Viewer plugin.  The viewer runs, more or less, but if I try to re-size the viewer window I get a complex error message in the Log window and Fiji freezes completely.  3D viewer also does not fix my Java3D problem.  I am using Fiji with the latest updates; ImageJ 1.5.1t; OSX 10.13.1.

I tried installing the May 30, 2017 version of Fiji following the thread below, but BoneJ still did not acknowledge Java#D.  The 3D Viewer help menu seems to think that I have the correct Java3D installed.

http://forum.imagej.net/t/bonej-issue-volume-fraction-or-3d-viewer-problem/6823

Any ideas?


Tim

Timothy Feinstein, Ph.D.
Research Scientist
Department of Developmental Biology
University of Pittsburgh



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[Michael Doube-4]

Hi Tim, Theresa,

Please have a go with the BoneJ2 preview. It's not complete, but will do a lot of the main analyses.

We're aware of issues with BoneJ1 and new versions of Mac OS
http://forum.imagej.net/t/java3d-issue-bonej-with-latest-fiji-version-problem-solved/1151/54

If you have access to an older Mac or a Windows or Linux machine (I use Ubuntu most of the time), then try Richard's instructions in the forum post above, and feed back to us there.

Michael

On 05/01/18 19:30, Swayne, Theresa C. wrote:

>
> Hi Tim,
>
> I tried to do this too (OS X 10.12), and had similar issues.
>
> However, I was able to use a Windows 7 machine to run BoneJ with Java 6 Fiji.
>
> And I’ve started looking at the pre-release BoneJ2:
> https://github.com/bonej-org/BoneJ2/wiki/Installing-BoneJ2
>
> It runs on my Mac (using up-to-date, Java 8 Fiji), and it successfully generates a thickness map from a sample image, but I haven’t tested it extensively.
>
> Hope this helps.
>
>
> ------------------------------------
> Theresa Swayne, Ph.D.
> Associate Research Scientist
> Manager, Confocal and Specialized Microscopy Shared Resource<http://hiccc.columbia.edu/research/sharedresources/confocal>
>
> Herbert Irving Comprehensive Cancer Center
> Columbia University Medical Center
> 1130 St. Nicholas Ave., Room 222A
> New York, NY 10032
> Phone: [phone]
> [hidden email]<mailto:[hidden email]>
>
>
>
> From: ImageJ Interest Group <[hidden email]> on behalf of "Feinstein, Timothy N" <[hidden email]>
> Reply-To: "[hidden email]" <[hidden email]>
> Date: Friday, January 5, 2018 at 12:45 PM
> To: "[hidden email]" <[hidden email]>
> Subject: BoneJ and Java3D
>
> Hi folks,
>
> When I try to run various features in the BoneJ plugin, it tells me that I need to get Java3D via the 3D Viewer plugin.  The viewer runs, more or less, but if I try to re-size the viewer window I get a complex error message in the Log window and Fiji freezes completely.  3D viewer also does not fix my Java3D problem.  I am using Fiji with the latest updates; ImageJ 1.5.1t; OSX 10.13.1.
>
> I tried installing the May 30, 2017 version of Fiji following the thread below, but BoneJ still did not acknowledge Java#D.  The 3D Viewer help menu seems to think that I have the correct Java3D installed.
>
> http://forum.imagej.net/t/bonej-issue-volume-fraction-or-3d-viewer-problem/6823
>
> Any ideas?
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> Research Scientist
> Department of Developmental Biology
> University of Pittsburgh
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Michael Doube, PhD
Lecturer, Comparative Biomedical Sciences
The Royal Veterinary College, University of London
Royal College Street
London NW1 0TU
United Kingdom

[phone] (Internal: 5503)
@mdoube

<http://www.rvc.ac.uk>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College.

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