Not clear how to open FIJI in Mac

[Guilherme Barbosa]

Hello everyone,

I am not familiar with programing, and so far no instruction was clear to me on how to open FIJI on my mac.

I have OS X Yosemite 10.10.4 updated.

If there is no solution, and I need to use ImageJ, is there something I can do like reinstalling? Installing ImageJ and no FIJI?

Thank you for the help.

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

[Rasband, Wayne (NIH/NIMH) [E]]

> On Jul 9, 2015, at 9:55 AM, Guilherme Barbosa <[hidden email]> wrote:
>
> Hello everyone,
>
> I am not familiar with programing, and so far no instruction was clear to me on how to open FIJI on my mac.
>
> I have OS X Yosemite 10.10.4 updated.
>
> If there is no solution, and I need to use ImageJ, is there something I can do like reinstalling? Installing ImageJ and no FIJI?

Have you installed Java 6? It is available at

   https://support.apple.com/kb/DL1572?locale=en_US

You could also try the version of ImageJ bundled with Java 8, available at

   http://imagej.nih.gov/ij/download.html

Note that Java 8 on OS X has a bug that can cause ImageJ to hang. To reproduce the bug, open the HeLa Cells sample image (File>Open Samples>HeLa Cells), type shift-z (Image>Color>Channels Tool) to open the Channels widget, then try to switch from “Composite” to “Color” mode using the drop down menu.

-wayne





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

[ctrueden]

Hi Guilherme,

> so far no instruction was clear to me on how to open FIJI on my mac.

Did you see this FAQ?
http://imagej.net/FAQ#How_do_I_run_ImageJ_on_Yosemite.3F

Install Java 8 from:
http://www.oracle.com/technetwork/java/javase/downloads/index.html

And then Fiji should work.

Regards,
Curtis

On Thu, Jul 9, 2015 at 8:55 AM, Guilherme Barbosa <[hidden email]>
wrote:

> Hello everyone,
>
> I am not familiar with programing, and so far no instruction was clear to
> me on how to open FIJI on my mac.
>
> I have OS X Yosemite 10.10.4 updated.
>
> If there is no solution, and I need to use ImageJ, is there something I
> can do like reinstalling? Installing ImageJ and no FIJI?
>
> Thank you for the help.
>
> Guilherme
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Guilherme Barbosa]

Thank you Wayne and Curtis,

But I installed Java 6, and it didnt opened FIJI, I updated to java8 downloading the JRE, and still didnt open.

Do I have to follow these steps:

Running

How do I launch ImageJ with a different version of Java?

On Windows

Install Java 7, and delete or rename the ImageJ.app\java and/or ImageJ.app\jre folders, if they exist.

On OS X

Use the --java-home command line option:

/Applications/ImageJ.app/Contents/MacOS/ImageJ-macosx --java-home \
  '/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home'
Note: the --java-home flag does not support Apple Java installations. However, Fiji will fall back to Apple Java if no other Java installations are available.

Specifying Apple Javas with this flag will give an error message about being unable to find lib/server/libjvm.dylib.

On Linux

Use the --java-home command line option:

$HOME/ImageJ.app/ImageJ-linux64 --java-home \
  /usr/lib/jvm/java-7-openjdk-amd64
One downside of doing this is that ImageJ will launch in a separate process, which has some unintuitive side effects. For example, Ubuntu's Unity user interface will not allow you to "Pin to Launcher" in this case...

How do I setup a launcher app for OS X for running with a different JVM version?

Start Automator and select to create an Application. Double-click Run Shell Script in the Library/Utilities folder and replace the text content — cat — with the following:

open -a "Fiji.app" --args --java-home \
 '/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home/'
Save anywhere you like.

To replace this application's icon, Get Info on your real Fiji, click on the icon on the top left, press Cmd-C, Get Info on your Fiji Automator app, click the icon, and press Cmd-V.

You will then see two icons in the dock, the one of the launcher app and the one of Fiji when it's running.

(based on this <http://superuser.com/a/271697> guide)


Guilherme

> On Jul 9, 2015, at 1:39 PM, Curtis Rueden <[hidden email]> wrote:
>
> Hi Guilherme,
>
>> so far no instruction was clear to me on how to open FIJI on my mac.
>
> Did you see this FAQ?
> http://imagej.net/FAQ#How_do_I_run_ImageJ_on_Yosemite.3F
>
> Install Java 8 from:
> http://www.oracle.com/technetwork/java/javase/downloads/index.html
>
> And then Fiji should work.
>
> Regards,
> Curtis
>
> On Thu, Jul 9, 2015 at 8:55 AM, Guilherme Barbosa <[hidden email]>
> wrote:
>
>> Hello everyone,
>>
>> I am not familiar with programing, and so far no instruction was clear to
>> me on how to open FIJI on my mac.
>>
>> I have OS X Yosemite 10.10.4 updated.
>>
>> If there is no solution, and I need to use ImageJ, is there something I
>> can do like reinstalling? Installing ImageJ and no FIJI?
>>
>> Thank you for the help.
>>
>> Guilherme
>> --
>> 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]

For the archives: discussion continues on fiji-devel:
https://groups.google.com/d/msg/fiji-devel/_vGa5ju8JAw/S_oG-kR1O2gJ

On Thu, Jul 9, 2015 at 12:14 PM, Guilherme Barbosa <[hidden email]>
wrote:

> Thank you Wayne and Curtis,
>
> But I installed Java 6, and it didnt opened FIJI, I updated to java8
> downloading the JRE, and still didnt open.
>
> Do I have to follow these steps:
>
> Running
>
> How do I launch ImageJ with a different version of Java?
>
> On Windows
>
> Install Java 7, and delete or rename the ImageJ.app\java and/or
> ImageJ.app\jre folders, if they exist.
>
> On OS X
>
> Use the --java-home command line option:
>
> /Applications/ImageJ.app/Contents/MacOS/ImageJ-macosx --java-home \
>   '/Library/Java/JavaVirtualMachines/jdk1.7.0_45.jdk/Contents/Home'
> Note: the --java-home flag does not support Apple Java installations.
> However, Fiji will fall back to Apple Java if no other Java installations
> are available.
>
> Specifying Apple Javas with this flag will give an error message about
> being unable to find lib/server/libjvm.dylib.
>
> On Linux
>
> Use the --java-home command line option:
>
> $HOME/ImageJ.app/ImageJ-linux64 --java-home \
>   /usr/lib/jvm/java-7-openjdk-amd64
> One downside of doing this is that ImageJ will launch in a separate
> process, which has some unintuitive side effects. For example, Ubuntu's
> Unity user interface will not allow you to "Pin to Launcher" in this case...
>
> How do I setup a launcher app for OS X for running with a different JVM
> version?
>
> Start Automator and select to create an Application. Double-click Run
> Shell Script in the Library/Utilities folder and replace the text content —
> cat — with the following:
>
> open -a "Fiji.app" --args --java-home \
>  '/Library/Java/JavaVirtualMachines/jdk1.7.0_75.jdk/Contents/Home/'
> Save anywhere you like.
>
> To replace this application's icon, Get Info on your real Fiji, click on
> the icon on the top left, press Cmd-C, Get Info on your Fiji Automator app,
> click the icon, and press Cmd-V.
>
> You will then see two icons in the dock, the one of the launcher app and
> the one of Fiji when it's running.
>
> (based on this <http://superuser.com/a/271697> guide)
>
>
> Guilherme
>
> > On Jul 9, 2015, at 1:39 PM, Curtis Rueden <[hidden email]> wrote:
> >
> > Hi Guilherme,
> >
> >> so far no instruction was clear to me on how to open FIJI on my mac.
> >
> > Did you see this FAQ?
> > http://imagej.net/FAQ#How_do_I_run_ImageJ_on_Yosemite.3F
> >
> > Install Java 8 from:
> > http://www.oracle.com/technetwork/java/javase/downloads/index.html
> >
> > And then Fiji should work.
> >
> > Regards,
> > Curtis
> >
> > On Thu, Jul 9, 2015 at 8:55 AM, Guilherme Barbosa <
> [hidden email]>
> > wrote:
> >
> >> Hello everyone,
> >>
> >> I am not familiar with programing, and so far no instruction was clear
> to
> >> me on how to open FIJI on my mac.
> >>
> >> I have OS X Yosemite 10.10.4 updated.
> >>
> >> If there is no solution, and I need to use ImageJ, is there something I
> >> can do like reinstalling? Installing ImageJ and no FIJI?
> >>
> >> Thank you for the help.
> >>
> >> Guilherme
> >> --
> >> 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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html