BoneJ crashing

[TimFeinstein]

Hello,

Has anyone else noticed that the BoneJ plugin has become unstable?  I use
the Threshold tool all the time and suddenly it causes Fiji to crash
without an error.  I tried it on two computers (OSX 10.10.5 and 10.11.3)
with the same result.  The most recent Fiji lifeline version (2015
December 22) seems to work with no problem.

Thanks!


Tim

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

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[TimFeinstein]

Correction: I meant the Thickness feature, not Threshold.


T

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





On 9/28/16, 10:32 AM, "ImageJ Interest Group on behalf of Feinstein,
Timothy N" <[hidden email] on behalf of [hidden email]> wrote:

>This sender failed our fraud detection checks and may not be who they
>appear to be. Learn about spoofing at http://aka.ms/LearnAboutSpoofing
>
>Hello,
>
>Has anyone else noticed that the BoneJ plugin has become unstable?  I use
>the Threshold tool all the time and suddenly it causes Fiji to crash
>without an error.  I tried it on two computers (OSX 10.10.5 and 10.11.3)
>with the same result.  The most recent Fiji lifeline version (2015
>December 22) seems to work with no problem.
>
>Thanks!
>
>
>Tim
>
>Timothy Feinstein, Ph.D.
>Research Scientist
>University of Pittsburgh Department of Developmental Biology
>
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>ImageJ mailing list:
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>.gov%2Fij%2Flist.html&data=01%7C01%7Ctnf8%40pitt.edu%7Cd9ea753f6ea14e2a548
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>%2FDuCxp0R2NRSbqHGNGFGMH22Txg3Lc%3D&reserved=0

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[Michael Doube-4]

Hi Tim,

BoneJ1 has just been updated to v1.4.2, which is only a minor update since the previous one in 2015, so I don't expect that this is the cause of your problem. Because BoneJ1 has to be installed manually, you would soon know whether it was the act of updating that caused the instability!

It's instead likely that "something changed" in your Fiji or JRE which caused the instability.

In general, if you are using BoneJ1, you need to stick with 'old' Fiji and Java 6, without turning on the Java 8 update site, as discussed at length on the Forum:
http://forum.imagej.net/t/java3d-issue-bonej-with-latest-fiji-version-problem-solved/1151/6

I run BoneJ1 in vanilla ImageJ (v1.51c) & Java 6 for my routine image processing tasks.

BoneJ2 will be fully integrated with the ImageJ2 / Fiji updater and plugin ecosystem, and work is going on actively, though we are some way away from a user-ready release. Watch this space...

Michael


On 28/09/16 15:32, Feinstein, Timothy N wrote:

> Hello,
>
> Has anyone else noticed that the BoneJ plugin has become unstable?  I use
> the Threshold tool all the time and suddenly it causes Fiji to crash
> without an error.  I tried it on two computers (OSX 10.10.5 and 10.11.3)
> with the same result.  The most recent Fiji lifeline version (2015
> December 22) seems to work with no problem.
>
> Thanks!
>
>
> Tim
>
> Timothy Feinstein, Ph.D.
> Research Scientist
> University of Pittsburgh Department of Developmental Biology
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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
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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 (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.

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[TimFeinstein]

Thanks Michael!  I am using BoneJ as part of a rather large macro in Fiji,
so I will use the lifeline version until v2 comes out.  Thank you again
for developing such a useful program!


Tim  

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





On 9/28/16, 11:37 AM, "ImageJ Interest Group on behalf of Michael Doube"
<[hidden email] on behalf of [hidden email]> wrote:

>Hi Tim,
>
>BoneJ1 has just been updated to v1.4.2, which is only a minor update
>since the previous one in 2015, so I don't expect that this is the cause
>of your problem. Because BoneJ1 has to be installed manually, you would
>soon know whether it was the act of updating that caused the instability!
>
>It's instead likely that "something changed" in your Fiji or JRE which
>caused the instability.
>
>In general, if you are using BoneJ1, you need to stick with 'old' Fiji
>and Java 6, without turning on the Java 8 update site, as discussed at
>length on the Forum:
>https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fforum.imag
>ej.net%2Ft%2Fjava3d-issue-bonej-with-latest-fiji-version-problem-solved%2F
>1151%2F6&data=01%7C01%7Ctnf8%40pitt.edu%7C2c9c56ea827644fbeef608d3e7b56c4f
>%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=rHNZByOiDJyf8ULHeNj613hATALb
>Azm9xOxvFQiD66c%3D&reserved=0
>
>I run BoneJ1 in vanilla ImageJ (v1.51c) & Java 6 for my routine image
>processing tasks.
>
>BoneJ2 will be fully integrated with the ImageJ2 / Fiji updater and
>plugin ecosystem, and work is going on actively, though we are some way
>away from a user-ready release. Watch this space...
>
>Michael
>
>
>On 28/09/16 15:32, Feinstein, Timothy N wrote:
>> Hello,
>>
>> Has anyone else noticed that the BoneJ plugin has become unstable?  I
>>use
>> the Threshold tool all the time and suddenly it causes Fiji to crash
>> without an error.  I tried it on two computers (OSX 10.10.5 and 10.11.3)
>> with the same result.  The most recent Fiji lifeline version (2015
>> December 22) seems to work with no problem.
>>
>> Thanks!
>>
>>
>> Tim
>>
>> Timothy Feinstein, Ph.D.
>> Research Scientist
>> University of Pittsburgh Department of Developmental Biology
>>
>> --
>> ImageJ mailing list:
>>https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.ni
>>h.gov%2Fij%2Flist.html&data=01%7C01%7Ctnf8%40pitt.edu%7C2c9c56ea827644fbe
>>ef608d3e7b56c4f%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1&sdata=3Y7j8xJWi7Gp
>>pUKJMnxhhKuHi8BJlMod9QYu9y4VbGc%3D&reserved=0
>>
>
>--
>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)
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