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Fiji freezes after update

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Avital Steinberg
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Fiji freezes after update

Avital Steinberg
Hi,
I'm using a mac version 10.9.5 - I've recently updated Fiji, and ever since
then, it either freezes completely, in which case I have to force quit
Fiji, or it runs extremely slowly, both with the graphical user interface
and the scripts.

The version of ImageJ which is giving me a hard time is: 2.0.0-rc-43/1.50e,
build: 49b667f9aa, Date: 2015-11-20.

I also get warning messages from the console:

[INFO] Reading IFDs
[INFO] Populating metadata
[INFO] Checking comment style
[WARNING] Expected positive value for PhysicalSizeX; got 0.0
[WARNING] Expected positive value for PhysicalSizeY; got 0.0
[WARNING] Expected positive value for PhysicalSizeX; got 0.0
[WARNING] Expected positive value for PhysicalSizeY; got 0.0

What can I do in order to be able to work with Fiji again?

Thanks,
Avital

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ctrueden
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Re: Fiji freezes after update

ctrueden
Hi Avital,

Which version of Java are you using?
http://imagej.net/Troubleshooting#Checking_the_Java_version

You could try to gather some information about the freezes:
http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs

But first make sure you are running either:
A) Apple Java 6 (i.e.: 1.6.0_65); or
B) The newest available Oracle Java 8 (i.e.: 1.8.0_66)

Regards,
Curtis

On Tue, Dec 1, 2015 at 11:49 AM, Avital Steinberg <[hidden email]
> wrote:

> Hi,
> I'm using a mac version 10.9.5 - I've recently updated Fiji, and ever since
> then, it either freezes completely, in which case I have to force quit
> Fiji, or it runs extremely slowly, both with the graphical user interface
> and the scripts.
>
> The version of ImageJ which is giving me a hard time is: 2.0.0-rc-43/1.50e,
> build: 49b667f9aa, Date: 2015-11-20.
>
> I also get warning messages from the console:
>
> [INFO] Reading IFDs
> [INFO] Populating metadata
> [INFO] Checking comment style
> [WARNING] Expected positive value for PhysicalSizeX; got 0.0
> [WARNING] Expected positive value for PhysicalSizeY; got 0.0
> [WARNING] Expected positive value for PhysicalSizeX; got 0.0
> [WARNING] Expected positive value for PhysicalSizeY; got 0.0
>
> What can I do in order to be able to work with Fiji again?
>
> Thanks,
> Avital
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Avital Steinberg
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Re: Fiji freezes after update

Avital Steinberg
Hi Curtis,
I'm running Java 1.7.0_71[64-bit] . Is running Java 7 a problem?

Thanks,
Avital

On Tue, Dec 1, 2015 at 7:55 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Avital,
>
> Which version of Java are you using?
> http://imagej.net/Troubleshooting#Checking_the_Java_version
>
> You could try to gather some information about the freezes:
> http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs
>
> But first make sure you are running either:
> A) Apple Java 6 (i.e.: 1.6.0_65); or
> B) The newest available Oracle Java 8 (i.e.: 1.8.0_66)
>
> Regards,
> Curtis
>
> On Tue, Dec 1, 2015 at 11:49 AM, Avital Steinberg <
> [hidden email]
> > wrote:
>
> > Hi,
> > I'm using a mac version 10.9.5 - I've recently updated Fiji, and ever
> since
> > then, it either freezes completely, in which case I have to force quit
> > Fiji, or it runs extremely slowly, both with the graphical user interface
> > and the scripts.
> >
> > The version of ImageJ which is giving me a hard time is:
> 2.0.0-rc-43/1.50e,
> > build: 49b667f9aa, Date: 2015-11-20.
> >
> > I also get warning messages from the console:
> >
> > [INFO] Reading IFDs
> > [INFO] Populating metadata
> > [INFO] Checking comment style
> > [WARNING] Expected positive value for PhysicalSizeX; got 0.0
> > [WARNING] Expected positive value for PhysicalSizeY; got 0.0
> > [WARNING] Expected positive value for PhysicalSizeX; got 0.0
> > [WARNING] Expected positive value for PhysicalSizeY; got 0.0
> >
> > What can I do in order to be able to work with Fiji again?
> >
> > Thanks,
> > Avital
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
ctrueden
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Re: Fiji freezes after update

ctrueden
Hi Avital,

> Is running Java 7 a problem?

Yes, Java 7 has critical painting bugs on OS X that will never be fixed.
Please use Java 8 instead.

See also:
* https://github.com/imagej/imagej/issues/135
* http://imagej.net/2015-06-15_-_Major_updates_in_the_works

Note that the ImageJ Launcher still has problems selecting the latest
installed version of Java, when multiple versions are installed. So even if
you install Java 8, it may still launch ImageJ with Java 7 by default.

You can either uninstall Java 7, or force ImageJ to use your preferred Java
version [1].

See also:
http://imagej.net/FAQ#How_do_I_run_ImageJ_on_El_Capitan.3F

Regards,
Curtis

[1]
http://imagej.net/FAQ#How_do_I_launch_ImageJ_with_a_different_version_of_Java.3F

On Tue, Dec 1, 2015 at 12:20 PM, Avital Steinberg <[hidden email]
> wrote:

> Hi Curtis,
> I'm running Java 1.7.0_71[64-bit] . Is running Java 7 a problem?
>
> Thanks,
> Avital
>
> On Tue, Dec 1, 2015 at 7:55 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Avital,
> >
> > Which version of Java are you using?
> > http://imagej.net/Troubleshooting#Checking_the_Java_version
> >
> > You could try to gather some information about the freezes:
> > http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs
> >
> > But first make sure you are running either:
> > A) Apple Java 6 (i.e.: 1.6.0_65); or
> > B) The newest available Oracle Java 8 (i.e.: 1.8.0_66)
> >
> > Regards,
> > Curtis
> >
> > On Tue, Dec 1, 2015 at 11:49 AM, Avital Steinberg <
> > [hidden email]
> > > wrote:
> >
> > > Hi,
> > > I'm using a mac version 10.9.5 - I've recently updated Fiji, and ever
> > since
> > > then, it either freezes completely, in which case I have to force quit
> > > Fiji, or it runs extremely slowly, both with the graphical user
> interface
> > > and the scripts.
> > >
> > > The version of ImageJ which is giving me a hard time is:
> > 2.0.0-rc-43/1.50e,
> > > build: 49b667f9aa, Date: 2015-11-20.
> > >
> > > I also get warning messages from the console:
> > >
> > > [INFO] Reading IFDs
> > > [INFO] Populating metadata
> > > [INFO] Checking comment style
> > > [WARNING] Expected positive value for PhysicalSizeX; got 0.0
> > > [WARNING] Expected positive value for PhysicalSizeY; got 0.0
> > > [WARNING] Expected positive value for PhysicalSizeX; got 0.0
> > > [WARNING] Expected positive value for PhysicalSizeY; got 0.0
> > >
> > > What can I do in order to be able to work with Fiji again?
> > >
> > > Thanks,
> > > Avital
> > >
> > > --
> > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Avital Steinberg
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Re: Fiji freezes after update

Avital Steinberg
Thanks, Curtis - I uninstalled Java 7, installed the latest version of
Java, installed a new version of Fiji, and now it's working well. It
selected Java 6, but I don't want to change anything, because everything is
back to normal now :-)

Avital

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