FIJI on Mac OS X

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FIJI on Mac OS X

Jordan T Becker
Hey,

So I'm still have problems using FIJI on Mac OS X. FIJI opens, and will
open an image file (.nd2 and .png). The image opens line by line (slow) and
flipping through three channels is also slow. When I bring up the channels
tool to colorize the grayscale channels, FIJI just freezes. I click the
drop down in the channels tool, its slow to reveal the options, then when I
click color, FIJI no longer responds.

I noticed it a week ago. It doesn't do this with the lifeline version from
November 2014. I have removed all instances of FIJI and downloaded the most
recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and MacOSX
versions. I am running Java 8, so perhaps there are still some bugs there.

I haven't had a hardware problem. With previous FIJI iterations, just a
couple months ago I could use FIJI with multi-GB .nd2 files to process,
analyze, and make movies. Now it won't even change colors on 10MB files.

Anyone else?
Jordan

Sherer Lab
UW-Madison

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Re: FIJI on Mac OS X

ctrueden
Hi Jordan,

> The image opens line by line (slow) and flipping through three
> channels is also slow.

There was a bug in Java with symptoms like this. Have you upgraded to the
latest version of Java? (1.8.0_45 as of this writing)

Regards,
Curtis

On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker <[hidden email]> wrote:

> Hey,
>
> So I'm still have problems using FIJI on Mac OS X. FIJI opens, and will
> open an image file (.nd2 and .png). The image opens line by line (slow) and
> flipping through three channels is also slow. When I bring up the channels
> tool to colorize the grayscale channels, FIJI just freezes. I click the
> drop down in the channels tool, its slow to reveal the options, then when I
> click color, FIJI no longer responds.
>
> I noticed it a week ago. It doesn't do this with the lifeline version from
> November 2014. I have removed all instances of FIJI and downloaded the most
> recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and MacOSX
> versions. I am running Java 8, so perhaps there are still some bugs there.
>
> I haven't had a hardware problem. With previous FIJI iterations, just a
> couple months ago I could use FIJI with multi-GB .nd2 files to process,
> analyze, and make movies. Now it won't even change colors on 10MB files.
>
> Anyone else?
> Jordan
>
> Sherer Lab
> UW-Madison
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: FIJI on Mac OS X

Jordan T Becker
Thanks Curtis,

I saw this bug on either this list or the FIJI specific list. Checking the
Mac OS System Preferences > Java Control Panel > Updates, I am up to date
with _45. Although when FIJI opens it indicates that it's using Java
1.8.0_25.

Cheers,
Jordan

Jordan T. Becker
Research Fellow - Sherer Lab
McArdle Cancer Biology Program
University of Wisconsin - Madison
[hidden email]

Less invasions, more equations. - Hubert J. Farnsworth
Whenever we propose a solution to a problem, we ought to try as hard as we
can to overthrow our solution, rather than defend it. - Karl Popper

On Fri, Jul 3, 2015 at 3:59 PM, Curtis Rueden <[hidden email]> wrote:

> Hi Jordan,
>
> > The image opens line by line (slow) and flipping through three
> > channels is also slow.
>
> There was a bug in Java with symptoms like this. Have you upgraded to the
> latest version of Java? (1.8.0_45 as of this writing)
>
> Regards,
> Curtis
>
> On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker <[hidden email]>
> wrote:
>
> > Hey,
> >
> > So I'm still have problems using FIJI on Mac OS X. FIJI opens, and will
> > open an image file (.nd2 and .png). The image opens line by line (slow)
> and
> > flipping through three channels is also slow. When I bring up the
> channels
> > tool to colorize the grayscale channels, FIJI just freezes. I click the
> > drop down in the channels tool, its slow to reveal the options, then
> when I
> > click color, FIJI no longer responds.
> >
> > I noticed it a week ago. It doesn't do this with the lifeline version
> from
> > November 2014. I have removed all instances of FIJI and downloaded the
> most
> > recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and MacOSX
> > versions. I am running Java 8, so perhaps there are still some bugs
> there.
> >
> > I haven't had a hardware problem. With previous FIJI iterations, just a
> > couple months ago I could use FIJI with multi-GB .nd2 files to process,
> > analyze, and make movies. Now it won't even change colors on 10MB files.
> >
> > Anyone else?
> > Jordan
> >
> > Sherer Lab
> > UW-Madison
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: FIJI on Mac OS X

John Minter
On MacOSX I use a starter application (AppleScript application) to start
Fiji. I created it with the script editor and can use any JVM I choose to
program.  Here is the content of mine:

*do shell script* "/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx
-Dpython.cachedir.skip=false --java-home
'/Library/Java/JavaVirtualMachines/jdk1.8.0_45.jdk/Contents/Home' --"

*quit* *me*

It is always a good idea to see what JVMs you actually have installed in
/Library/Java/JavaVirtualMachines


Hope this helps,
John Minter

On Fri, Jul 3, 2015 at 8:14 PM, Jordan T Becker <[hidden email]> wrote:

> Thanks Curtis,
>
> I saw this bug on either this list or the FIJI specific list. Checking the
> Mac OS System Preferences > Java Control Panel > Updates, I am up to date
> with _45. Although when FIJI opens it indicates that it's using Java
> 1.8.0_25.
>
> Cheers,
> Jordan
>
> Jordan T. Becker
> Research Fellow - Sherer Lab
> McArdle Cancer Biology Program
> University of Wisconsin - Madison
> [hidden email]
>
> Less invasions, more equations. - Hubert J. Farnsworth
> Whenever we propose a solution to a problem, we ought to try as hard as we
> can to overthrow our solution, rather than defend it. - Karl Popper
>
> On Fri, Jul 3, 2015 at 3:59 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Jordan,
> >
> > > The image opens line by line (slow) and flipping through three
> > > channels is also slow.
> >
> > There was a bug in Java with symptoms like this. Have you upgraded to the
> > latest version of Java? (1.8.0_45 as of this writing)
> >
> > Regards,
> > Curtis
> >
> > On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker <[hidden email]>
> > wrote:
> >
> > > Hey,
> > >
> > > So I'm still have problems using FIJI on Mac OS X. FIJI opens, and will
> > > open an image file (.nd2 and .png). The image opens line by line (slow)
> > and
> > > flipping through three channels is also slow. When I bring up the
> > channels
> > > tool to colorize the grayscale channels, FIJI just freezes. I click the
> > > drop down in the channels tool, its slow to reveal the options, then
> > when I
> > > click color, FIJI no longer responds.
> > >
> > > I noticed it a week ago. It doesn't do this with the lifeline version
> > from
> > > November 2014. I have removed all instances of FIJI and downloaded the
> > most
> > > recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and MacOSX
> > > versions. I am running Java 8, so perhaps there are still some bugs
> > there.
> > >
> > > I haven't had a hardware problem. With previous FIJI iterations, just a
> > > couple months ago I could use FIJI with multi-GB .nd2 files to process,
> > > analyze, and make movies. Now it won't even change colors on 10MB
> files.
> > >
> > > Anyone else?
> > > Jordan
> > >
> > > Sherer Lab
> > > UW-Madison
> > >
> > > --
> > > 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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Re: FIJI on Mac OS X

ctrueden
In reply to this post by Jordan T Becker
Hi Jordan,

For the moment, Fiji will not use the Java installed into /Library/Internet
Plugins, which is where the java.com installer puts the JRE. This issue
will be fixed later this summer, but for now, please install the JDK from
Oracle's site (linked from imagej.net/FAQ). Make sure Fiji reports 1.8.0_45
in your ImageJ status bar.

Regards,
Curtis
 On Jul 3, 2015 7:25 PM, "Jordan T Becker" <[hidden email]> wrote:

> Thanks Curtis,
>
> I saw this bug on either this list or the FIJI specific list. Checking the
> Mac OS System Preferences > Java Control Panel > Updates, I am up to date
> with _45. Although when FIJI opens it indicates that it's using Java
> 1.8.0_25.
>
> Cheers,
> Jordan
>
> Jordan T. Becker
> Research Fellow - Sherer Lab
> McArdle Cancer Biology Program
> University of Wisconsin - Madison
> [hidden email]
>
> Less invasions, more equations. - Hubert J. Farnsworth
> Whenever we propose a solution to a problem, we ought to try as hard as we
> can to overthrow our solution, rather than defend it. - Karl Popper
>
> On Fri, Jul 3, 2015 at 3:59 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Jordan,
> >
> > > The image opens line by line (slow) and flipping through three
> > > channels is also slow.
> >
> > There was a bug in Java with symptoms like this. Have you upgraded to the
> > latest version of Java? (1.8.0_45 as of this writing)
> >
> > Regards,
> > Curtis
> >
> > On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker <[hidden email]>
> > wrote:
> >
> > > Hey,
> > >
> > > So I'm still have problems using FIJI on Mac OS X. FIJI opens, and will
> > > open an image file (.nd2 and .png). The image opens line by line (slow)
> > and
> > > flipping through three channels is also slow. When I bring up the
> > channels
> > > tool to colorize the grayscale channels, FIJI just freezes. I click the
> > > drop down in the channels tool, its slow to reveal the options, then
> > when I
> > > click color, FIJI no longer responds.
> > >
> > > I noticed it a week ago. It doesn't do this with the lifeline version
> > from
> > > November 2014. I have removed all instances of FIJI and downloaded the
> > most
> > > recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and MacOSX
> > > versions. I am running Java 8, so perhaps there are still some bugs
> > there.
> > >
> > > I haven't had a hardware problem. With previous FIJI iterations, just a
> > > couple months ago I could use FIJI with multi-GB .nd2 files to process,
> > > analyze, and make movies. Now it won't even change colors on 10MB
> files.
> > >
> > > Anyone else?
> > > Jordan
> > >
> > > Sherer Lab
> > > UW-Madison
> > >
> > > --
> > > 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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Re: FIJI on Mac OS X

John Minter
In reply to this post by Jordan T Becker
Just a followup. I noticed that when I copied and pasted the text of the
apple script that the commands had been bold and were converted to
markdown. Remove the asterisks around 'do shell script', 'quit', and 'me'.
Sorry for the formatting issues.

I put a screenshot of the launcher code here:

https://github.com/jrminter/OSImageAnalysis/blob/master/images/launcher-applet-code.png


John

On Fri, Jul 3, 2015 at 8:14 PM, Jordan T Becker <[hidden email]> wrote:

> Thanks Curtis,
>
> I saw this bug on either this list or the FIJI specific list. Checking the
> Mac OS System Preferences > Java Control Panel > Updates, I am up to date
> with _45. Although when FIJI opens it indicates that it's using Java
> 1.8.0_25.
>
> Cheers,
> Jordan
>
> Jordan T. Becker
> Research Fellow - Sherer Lab
> McArdle Cancer Biology Program
> University of Wisconsin - Madison
> [hidden email]
>
> Less invasions, more equations. - Hubert J. Farnsworth
> Whenever we propose a solution to a problem, we ought to try as hard as we
> can to overthrow our solution, rather than defend it. - Karl Popper
>
> On Fri, Jul 3, 2015 at 3:59 PM, Curtis Rueden <[hidden email]> wrote:
>
> > Hi Jordan,
> >
> > > The image opens line by line (slow) and flipping through three
> > > channels is also slow.
> >
> > There was a bug in Java with symptoms like this. Have you upgraded to the
> > latest version of Java? (1.8.0_45 as of this writing)
> >
> > Regards,
> > Curtis
> >
> > On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker <[hidden email]>
> > wrote:
> >
> > > Hey,
> > >
> > > So I'm still have problems using FIJI on Mac OS X. FIJI opens, and will
> > > open an image file (.nd2 and .png). The image opens line by line (slow)
> > and
> > > flipping through three channels is also slow. When I bring up the
> > channels
> > > tool to colorize the grayscale channels, FIJI just freezes. I click the
> > > drop down in the channels tool, its slow to reveal the options, then
> > when I
> > > click color, FIJI no longer responds.
> > >
> > > I noticed it a week ago. It doesn't do this with the lifeline version
> > from
> > > November 2014. I have removed all instances of FIJI and downloaded the
> > most
> > > recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and MacOSX
> > > versions. I am running Java 8, so perhaps there are still some bugs
> > there.
> > >
> > > I haven't had a hardware problem. With previous FIJI iterations, just a
> > > couple months ago I could use FIJI with multi-GB .nd2 files to process,
> > > analyze, and make movies. Now it won't even change colors on 10MB
> files.
> > >
> > > Anyone else?
> > > Jordan
> > >
> > > Sherer Lab
> > > UW-Madison
> > >
> > > --
> > > 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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Re: FIJI on Mac OS X

Jordan T Becker
Thanks to John, I checked what was actually in the Library/JVM. It was
1.8.0_25 despite the Java Console indicating it was up to date with _45. I
downloaded _45 and FIJI (continuous release - MacOS X dmg) is showing _45
in the status bar. Getting slightly better behavior loading images but the
application still freezes when I switch between color/composite/grayscale.
I can crop, measure, subtract background, adjust B&C, etc. But opening the
channels tool and using that drop down to select color/composite/grayscale
still causes the application to freeze. Very odd. I'll keep testing, the
trouble of course is that the console won't log during a freeze...

Jordan

Jordan T. Becker
Research Fellow - Sherer Lab
McArdle Cancer Biology Program
University of Wisconsin - Madison
[hidden email]

Less invasions, more equations. - Hubert J. Farnsworth
Whenever we propose a solution to a problem, we ought to try as hard as we
can to overthrow our solution, rather than defend it. - Karl Popper

On Fri, Jul 3, 2015 at 8:08 PM, John Minter <[hidden email]> wrote:

> Just a followup. I noticed that when I copied and pasted the text of the
> apple script that the commands had been bold and were converted to
> markdown. Remove the asterisks around 'do shell script', 'quit', and 'me'.
> Sorry for the formatting issues.
>
> I put a screenshot of the launcher code here:
>
>
> https://github.com/jrminter/OSImageAnalysis/blob/master/images/launcher-applet-code.png
>
>
> John
>
> On Fri, Jul 3, 2015 at 8:14 PM, Jordan T Becker <[hidden email]>
> wrote:
>
> > Thanks Curtis,
> >
> > I saw this bug on either this list or the FIJI specific list. Checking
> the
> > Mac OS System Preferences > Java Control Panel > Updates, I am up to date
> > with _45. Although when FIJI opens it indicates that it's using Java
> > 1.8.0_25.
> >
> > Cheers,
> > Jordan
> >
> > Jordan T. Becker
> > Research Fellow - Sherer Lab
> > McArdle Cancer Biology Program
> > University of Wisconsin - Madison
> > [hidden email]
> >
> > Less invasions, more equations. - Hubert J. Farnsworth
> > Whenever we propose a solution to a problem, we ought to try as hard as
> we
> > can to overthrow our solution, rather than defend it. - Karl Popper
> >
> > On Fri, Jul 3, 2015 at 3:59 PM, Curtis Rueden <[hidden email]> wrote:
> >
> > > Hi Jordan,
> > >
> > > > The image opens line by line (slow) and flipping through three
> > > > channels is also slow.
> > >
> > > There was a bug in Java with symptoms like this. Have you upgraded to
> the
> > > latest version of Java? (1.8.0_45 as of this writing)
> > >
> > > Regards,
> > > Curtis
> > >
> > > On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker <[hidden email]>
> > > wrote:
> > >
> > > > Hey,
> > > >
> > > > So I'm still have problems using FIJI on Mac OS X. FIJI opens, and
> will
> > > > open an image file (.nd2 and .png). The image opens line by line
> (slow)
> > > and
> > > > flipping through three channels is also slow. When I bring up the
> > > channels
> > > > tool to colorize the grayscale channels, FIJI just freezes. I click
> the
> > > > drop down in the channels tool, its slow to reveal the options, then
> > > when I
> > > > click color, FIJI no longer responds.
> > > >
> > > > I noticed it a week ago. It doesn't do this with the lifeline version
> > > from
> > > > November 2014. I have removed all instances of FIJI and downloaded
> the
> > > most
> > > > recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and
> MacOSX
> > > > versions. I am running Java 8, so perhaps there are still some bugs
> > > there.
> > > >
> > > > I haven't had a hardware problem. With previous FIJI iterations,
> just a
> > > > couple months ago I could use FIJI with multi-GB .nd2 files to
> process,
> > > > analyze, and make movies. Now it won't even change colors on 10MB
> > files.
> > > >
> > > > Anyone else?
> > > > Jordan
> > > >
> > > > Sherer Lab
> > > > UW-Madison
> > > >
> > > > --
> > > > 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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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Re: FIJI on Mac OS X

Guilherme Barbosa
I got confused.

I coud not make Fiji work in my mac.

Yes there a way I can do that?

Guilherme


> On Jul 3, 2015, at 11:53 PM, Jordan T Becker <[hidden email]> wrote:
>
> Thanks to John, I checked what was actually in the Library/JVM. It was
> 1.8.0_25 despite the Java Console indicating it was up to date with _45. I
> downloaded _45 and FIJI (continuous release - MacOS X dmg) is showing _45
> in the status bar. Getting slightly better behavior loading images but the
> application still freezes when I switch between color/composite/grayscale.
> I can crop, measure, subtract background, adjust B&C, etc. But opening the
> channels tool and using that drop down to select color/composite/grayscale
> still causes the application to freeze. Very odd. I'll keep testing, the
> trouble of course is that the console won't log during a freeze...
>
> Jordan
>
> Jordan T. Becker
> Research Fellow - Sherer Lab
> McArdle Cancer Biology Program
> University of Wisconsin - Madison
> [hidden email]
>
> Less invasions, more equations. - Hubert J. Farnsworth
> Whenever we propose a solution to a problem, we ought to try as hard as we
> can to overthrow our solution, rather than defend it. - Karl Popper
>
> On Fri, Jul 3, 2015 at 8:08 PM, John Minter <[hidden email]> wrote:
>
>> Just a followup. I noticed that when I copied and pasted the text of the
>> apple script that the commands had been bold and were converted to
>> markdown. Remove the asterisks around 'do shell script', 'quit', and 'me'.
>> Sorry for the formatting issues.
>>
>> I put a screenshot of the launcher code here:
>>
>>
>> https://github.com/jrminter/OSImageAnalysis/blob/master/images/launcher-applet-code.png
>>
>>
>> John
>>
>> On Fri, Jul 3, 2015 at 8:14 PM, Jordan T Becker <[hidden email]>
>> wrote:
>>
>>> Thanks Curtis,
>>>
>>> I saw this bug on either this list or the FIJI specific list. Checking
>> the
>>> Mac OS System Preferences > Java Control Panel > Updates, I am up to date
>>> with _45. Although when FIJI opens it indicates that it's using Java
>>> 1.8.0_25.
>>>
>>> Cheers,
>>> Jordan
>>>
>>> Jordan T. Becker
>>> Research Fellow - Sherer Lab
>>> McArdle Cancer Biology Program
>>> University of Wisconsin - Madison
>>> [hidden email]
>>>
>>> Less invasions, more equations. - Hubert J. Farnsworth
>>> Whenever we propose a solution to a problem, we ought to try as hard as
>> we
>>> can to overthrow our solution, rather than defend it. - Karl Popper
>>>
>>> On Fri, Jul 3, 2015 at 3:59 PM, Curtis Rueden <[hidden email]> wrote:
>>>
>>>> Hi Jordan,
>>>>
>>>>> The image opens line by line (slow) and flipping through three
>>>>> channels is also slow.
>>>>
>>>> There was a bug in Java with symptoms like this. Have you upgraded to
>> the
>>>> latest version of Java? (1.8.0_45 as of this writing)
>>>>
>>>> Regards,
>>>> Curtis
>>>>
>>>> On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker <[hidden email]>
>>>> wrote:
>>>>
>>>>> Hey,
>>>>>
>>>>> So I'm still have problems using FIJI on Mac OS X. FIJI opens, and
>> will
>>>>> open an image file (.nd2 and .png). The image opens line by line
>> (slow)
>>>> and
>>>>> flipping through three channels is also slow. When I bring up the
>>>> channels
>>>>> tool to colorize the grayscale channels, FIJI just freezes. I click
>> the
>>>>> drop down in the channels tool, its slow to reveal the options, then
>>>> when I
>>>>> click color, FIJI no longer responds.
>>>>>
>>>>> I noticed it a week ago. It doesn't do this with the lifeline version
>>>> from
>>>>> November 2014. I have removed all instances of FIJI and downloaded
>> the
>>>> most
>>>>> recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and
>> MacOSX
>>>>> versions. I am running Java 8, so perhaps there are still some bugs
>>>> there.
>>>>>
>>>>> I haven't had a hardware problem. With previous FIJI iterations,
>> just a
>>>>> couple months ago I could use FIJI with multi-GB .nd2 files to
>> process,
>>>>> analyze, and make movies. Now it won't even change colors on 10MB
>>> files.
>>>>>
>>>>> Anyone else?
>>>>> Jordan
>>>>>
>>>>> Sherer Lab
>>>>> UW-Madison
>>>>>
>>>>> --
>>>>> 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
>>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: FIJI on Mac OS X

TimFeinstein
Aha, so that is what happened to me today.  I tried merging a composite and had to hard-reboot my Mac.  Fiji/ImageJ never froze like that before.  Oddly it seemed like an isolated incident, as I did a lot of other work with LUTs and composites today.  

If it happens again I will try going to the download site (http://fiji.sc/Downloads) to replace my current Fiji with the continuous release there.  Guilherme, I do not know enough about your situation to say whether that will help you as well but it looks like something to try.  

All the best,


Tim

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

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Guilherme Barbosa
Sent: Tuesday, July 07, 2015 9:10 PM
To: [hidden email]
Subject: Re: FIJI on Mac OS X

I got confused.

I coud not make Fiji work in my mac.

Yes there a way I can do that?

Guilherme


> On Jul 3, 2015, at 11:53 PM, Jordan T Becker <[hidden email]> wrote:
>
> Thanks to John, I checked what was actually in the Library/JVM. It was
> 1.8.0_25 despite the Java Console indicating it was up to date with
> _45. I downloaded _45 and FIJI (continuous release - MacOS X dmg) is
> showing _45 in the status bar. Getting slightly better behavior
> loading images but the application still freezes when I switch between color/composite/grayscale.
> I can crop, measure, subtract background, adjust B&C, etc. But opening
> the channels tool and using that drop down to select
> color/composite/grayscale still causes the application to freeze. Very
> odd. I'll keep testing, the trouble of course is that the console won't log during a freeze...
>
> Jordan
>
> Jordan T. Becker
> Research Fellow - Sherer Lab
> McArdle Cancer Biology Program
> University of Wisconsin - Madison
> [hidden email]
>
> Less invasions, more equations. - Hubert J. Farnsworth Whenever we
> propose a solution to a problem, we ought to try as hard as we can to
> overthrow our solution, rather than defend it. - Karl Popper
>
> On Fri, Jul 3, 2015 at 8:08 PM, John Minter <[hidden email]> wrote:
>
>> Just a followup. I noticed that when I copied and pasted the text of
>> the apple script that the commands had been bold and were converted
>> to markdown. Remove the asterisks around 'do shell script', 'quit', and 'me'.
>> Sorry for the formatting issues.
>>
>> I put a screenshot of the launcher code here:
>>
>>
>> https://github.com/jrminter/OSImageAnalysis/blob/master/images/launch
>> er-applet-code.png
>>
>>
>> John
>>
>> On Fri, Jul 3, 2015 at 8:14 PM, Jordan T Becker <[hidden email]>
>> wrote:
>>
>>> Thanks Curtis,
>>>
>>> I saw this bug on either this list or the FIJI specific list.
>>> Checking
>> the
>>> Mac OS System Preferences > Java Control Panel > Updates, I am up to
>>> date with _45. Although when FIJI opens it indicates that it's using
>>> Java 1.8.0_25.
>>>
>>> Cheers,
>>> Jordan
>>>
>>> Jordan T. Becker
>>> Research Fellow - Sherer Lab
>>> McArdle Cancer Biology Program
>>> University of Wisconsin - Madison
>>> [hidden email]
>>>
>>> Less invasions, more equations. - Hubert J. Farnsworth Whenever we
>>> propose a solution to a problem, we ought to try as hard as
>> we
>>> can to overthrow our solution, rather than defend it. - Karl Popper
>>>
>>> On Fri, Jul 3, 2015 at 3:59 PM, Curtis Rueden <[hidden email]> wrote:
>>>
>>>> Hi Jordan,
>>>>
>>>>> The image opens line by line (slow) and flipping through three
>>>>> channels is also slow.
>>>>
>>>> There was a bug in Java with symptoms like this. Have you upgraded
>>>> to
>> the
>>>> latest version of Java? (1.8.0_45 as of this writing)
>>>>
>>>> Regards,
>>>> Curtis
>>>>
>>>> On Fri, Jul 3, 2015 at 10:58 AM, Jordan T Becker
>>>> <[hidden email]>
>>>> wrote:
>>>>
>>>>> Hey,
>>>>>
>>>>> So I'm still have problems using FIJI on Mac OS X. FIJI opens, and
>> will
>>>>> open an image file (.nd2 and .png). The image opens line by line
>> (slow)
>>>> and
>>>>> flipping through three channels is also slow. When I bring up the
>>>> channels
>>>>> tool to colorize the grayscale channels, FIJI just freezes. I
>>>>> click
>> the
>>>>> drop down in the channels tool, its slow to reveal the options,
>>>>> then
>>>> when I
>>>>> click color, FIJI no longer responds.
>>>>>
>>>>> I noticed it a week ago. It doesn't do this with the lifeline
>>>>> version
>>>> from
>>>>> November 2014. I have removed all instances of FIJI and downloaded
>> the
>>>> most
>>>>> recent FIJI with ImageJ2.0.31. I've tried both the "no JRE" and
>> MacOSX
>>>>> versions. I am running Java 8, so perhaps there are still some
>>>>> bugs
>>>> there.
>>>>>
>>>>> I haven't had a hardware problem. With previous FIJI iterations,
>> just a
>>>>> couple months ago I could use FIJI with multi-GB .nd2 files to
>> process,
>>>>> analyze, and make movies. Now it won't even change colors on 10MB
>>> files.
>>>>>
>>>>> Anyone else?
>>>>> Jordan
>>>>>
>>>>> Sherer Lab
>>>>> UW-Madison
>>>>>
>>>>> --
>>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>>
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>
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>>>
>>
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