FIJI won't open with new update

[Taylor Jaraczewski]

Hello

Thanks for all the work being done on FIJI, it's truly changed the way I do
research!

I recently had an automatic update on FIJI and now the program will not
open. I use a MacBook Pro OSX 10.9.3.  I'm assuming it's an issue with the
launcher, but do not know how to fix it.

Thanks!

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

[dscho]

Hi Taylor,

On Sat, 21 Jun 2014, Taylor Jaraczewski wrote:

> Thanks for all the work being done on FIJI, it's truly changed the way I
> do research!

Thank you for the positive feedback!

I guess at some time we have to provide a way for users to leave such
messages for funding agencies to read. That might make it easier to
finally get a grant dedicated to developing and maintaining Fiji.

> I recently had an automatic update on FIJI and now the program will not
> open. I use a MacBook Pro OSX 10.9.3.  I'm assuming it's an issue with
> the launcher, but do not know how to fix it.

First of all: sorry to hear that it broke! I tried very hard to prevent
such a situation, but unfortunatel my crystal ball malfunctioned ;-)

To fix things quickly on your side, I would like to suggest the following
strategy:

- open the directory containing Fiji in your Finder (typically, you will
  have installed Fiji into /Applications/)

- Ctrl+click on the Fiji icon to open the context menu and select "Show
  Package Contents"

- in the newly opened window, open the jars/ folder by double-clicking it

- locate the ij.jar file (it will have a version number, i.e. read
  something like ij-1.49b.jar) and double-click it.

- in the just opened pure ImageJ 1.x, call File>Import>URL... and open the
  URL http://update.imagej.net/bootstrap.js

- after a while, the updater will open and you can install any updates.

If this does not bring you back to a working version (i.e. when no file is
marked for update), you most likely have an update site activated with
slightly inconsistent files (such as TrackMate-dev, totally my fault
because I missed a crucial bug in the script that keeps it up-to-date).

In that case, I would like to suggest to open the "Manage update sites"
dialog in the updater and uncheck the update site for now.

I will hopefully be able to fix the TrackMate-dev update site very soon,
so if it is the culprit, let me know so I can keep you in the loop.

Ciao,
Johannes

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[dscho]

Hi Taylor,

On Sun, 22 Jun 2014, Taylor Jaraczewski wrote:

> The first suggestion worked!

Good.

> However, I can't open FIJI through the desktop
> icon. I can only open ImageJ through the applications.

That's bad, because it actually did not fix anything.

> It doesn't seem to have a negative effect, but figured I'd tell you.

Basically, you run a plain ImageJ 1.x without updater, editor, without the
option to run modern plugins, i.e. pretty much lacking all the benefits
that Fiji would actually bring to your table. In fact, all the plugins
should be missing (unless my tests are different than yours).

So unfortunately, my suggestion did not bring you back to a working state.

FWIW I just fixed the TrackMate-dev site (I still do not know whether you
activated that update site or not).

Could you go through the steps to run the updater via the bootstrap.js
again and verify that you have only the ImageJ and Fiji update sites
enabled?

Ciao,
Johannes

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

[dscho]

Hi Taylor,

please keep the mailing list Cc:ed. I will work privately for you if you
want, but only if you pay me to do so. In all other cases, Open Source
should be discussed openly.

On Sun, 22 Jun 2014, Taylor Jaraczewski wrote:

> I used the updater fiat the bootstrap.js again; however, I still cannot
> open FIJI. How exactly to you verify that ImageJ and Fiji are the only
> updated sites?

There is a button called "Manage update sites" in the lower left of the
updater GUI.

Also, regarding your startup problems, it would be good to follow
http://fiji.sc/Command-Line_Debugging and paste the console output to give
me -- and others -- a chance to diagnose the issue.

Ciao,
Johannes

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

[Taylor Jaraczewski]

Yep sure thing, sorry about that.

Just an update, I ended up downloading a fresh version of FIJI and it works
completely fine after I restarted my computer.

I will report the bug now.

Thanks
Taylor


On Mon, Jun 23, 2014 at 11:12 AM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Taylor,
>
> please keep the mailing list Cc:ed. I will work privately for you if you
> want, but only if you pay me to do so. In all other cases, Open Source
> should be discussed openly.
>
> On Sun, 22 Jun 2014, Taylor Jaraczewski wrote:
>
> > I used the updater fiat the bootstrap.js again; however, I still cannot
> > open FIJI. How exactly to you verify that ImageJ and Fiji are the only
> > updated sites?
>
> There is a button called "Manage update sites" in the lower left of the
> updater GUI.
>
> Also, regarding your startup problems, it would be good to follow
> http://fiji.sc/Command-Line_Debugging and paste the console output to give
> me -- and others -- a chance to diagnose the issue.
>
> Ciao,
> Johannes
>

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[Rojitas]

Hi there,

I was reading all this posts. I am in a similar situation. Cannot open FIJI since my last update. I just followed all the directions previously posted with no success. In contrast to perhaps the other users, I get the following notice every time I try to open FIJI.

To open "Fiji" you need to install the legacy Java SE 6 runtime.

I have however installed the JAVA 8. Is this the problem? Do you have any suggestions?

Thanks!

[ctrueden]

Hi Rojitas,

> I get the following notice every time I try to open FIJI.
>
> To open "Fiji" you need to install the legacy Java SE 6 runtime.
>
> I have however installed the JAVA 8. Is this the problem? Do you have
> any suggestions?

There is a fix in testing. Please see:

http://imagej.net/FAQ#How_do_I_run_ImageJ_on_Yosemite.3F

We would love to have feedback from users whether this fix actually
addresses the problem for you. Once we hear back about whether the fix is
working, we will push the update to everyone.

Regards,
Curtis

On Thu, Feb 19, 2015 at 8:56 AM, Rojitas <[hidden email]> wrote:

> Hi there,
>
> I was reading all this posts. I am in a similar situation. Cannot open FIJI
> since my last update. I just followed all the directions previously posted
> with no success. In contrast to perhaps the other users, I get the
> following
> notice every time I try to open FIJI.
>
> To open "Fiji" you need to install the legacy Java SE 6 runtime.
>
> I have however installed the JAVA 8. Is this the problem? Do you have any
> suggestions?
>
> Thanks!
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/FIJI-won-t-open-with-new-update-tp5008360p5011693.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Rojitas]

Dear Curtis,

So I am not sure how to replace the Fiji.app/Contents/MacOS/ImageJ-macosx file with an updated version

I downloaded the updated version and tried to put in the folder MacOs but id did not make any difference. Could you tell me what to do exactly,

Tanks a lot!

[Kota Miura]

Hi Curtis,

I'm not sure if it becomes redundant, but I filed the Fiji.app
behavior@java8 in bugzilla to report details. If it's redundant, I will
comment a pointer to it and close the issue.

http://fiji.sc/bugzilla/show_bug.cgi?id=1008

I tried replacing ImageJ-maxosx with imagej-launcher and the above
behaviors were same.

Cheers,
Kota

On Thu, Feb 19, 2015 at 5:58 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Rojitas,
>
> > I get the following notice every time I try to open FIJI.
> >
> > To open "Fiji" you need to install the legacy Java SE 6 runtime.
> >
> > I have however installed the JAVA 8. Is this the problem? Do you have
> > any suggestions?
>
> There is a fix in testing. Please see:
>
> http://imagej.net/FAQ#How_do_I_run_ImageJ_on_Yosemite.3F
>
> We would love to have feedback from users whether this fix actually
> addresses the problem for you. Once we hear back about whether the fix is
> working, we will push the update to everyone.
>
> Regards,
> Curtis
>
> On Thu, Feb 19, 2015 at 8:56 AM, Rojitas <[hidden email]> wrote:
>
> > Hi there,
> >
> > I was reading all this posts. I am in a similar situation. Cannot open
> FIJI
> > since my last update. I just followed all the directions previously
> posted
> > with no success. In contrast to perhaps the other users, I get the
> > following
> > notice every time I try to open FIJI.
> >
> > To open "Fiji" you need to install the legacy Java SE 6 runtime.
> >
> > I have however installed the JAVA 8. Is this the problem? Do you have any
> > suggestions?
> >
> > Thanks!
> >
> >
> >
> >
> > --
> > View this message in context:
> >
> http://imagej.1557.x6.nabble.com/FIJI-won-t-open-with-new-update-tp5008360p5011693.html
> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--

-------------------------------------------------------------
Dr. Kota Miura <[hidden email]>

Senior Image Analyst / NINS Research Administrator
European Molecular Biology Laboratory
Meyerhofstr. 1, 69117 Heidelberg, GERMANY
Tel [phone]
Mobile [phone]http://cmci.embl.de
++++++++++++++++++

Dr. Kota Miura  <[hidden email]>
Project Associate Professor
National Institutes of Natural Sciences (NINS), Japan
Bonn Office: Ahrstr. 58, 53175 Bonn, Germany
Tel: [phone]http://www.nins.jp/english/
-------------------------------------------------------------

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