Channels Tool Freezes on Fiji and MacOS 10.9.5

[Olivier Burri]

Hi all,

We have just had a visit from a user with a big problem using Fiji

Basically when opening any multichannel image, it first is very slow at displaying the image (You actually see the image window's pixels being populated from top to bottom). Then, when using the channel tool to switch from Composite to Single Channel, Fiji partially crashes. The Channel Tool is unresponsive and we cannot quit Fiji normally and must Force Quit the app. Some of the other menus still respond though...

We thought it was due to the 1.50 update so we reverted back to 1.49, no change. Then we also installed JDK1.7 instead of 1.8 to see if this could be fixed. Still nothing. Has anyone experienced this after an update from a couple of days ago? Any hints on where we should keep looking for a possible solution?

MacOS 10.9.5, i7, 8Gb RAM
Java 1.8 and 1.7 x64 versions, managed using jEnv

Thanks for any help regarding this issue

Best
Oli



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[lechristophe]

Did you check if the "use ImageJ2" check box was unchecked in the options?

Christophe
Le 31 juil. 2015 2:24 PM, "Burri Olivier" <[hidden email]> a écrit :

> Hi all,
>
> We have just had a visit from a user with a big problem using Fiji
>
> Basically when opening any multichannel image, it first is very slow at
> displaying the image (You actually see the image window's pixels being
> populated from top to bottom). Then, when using the channel tool to switch
> from Composite to Single Channel, Fiji partially crashes. The Channel Tool
> is unresponsive and we cannot quit Fiji normally and must Force Quit the
> app. Some of the other menus still respond though...
>
> We thought it was due to the 1.50 update so we reverted back to 1.49, no
> change. Then we also installed JDK1.7 instead of 1.8 to see if this could
> be fixed. Still nothing. Has anyone experienced this after an update from a
> couple of days ago? Any hints on where we should keep looking for a
> possible solution?
>
> MacOS 10.9.5, i7, 8Gb RAM
> Java 1.8 and 1.7 x64 versions, managed using jEnv
>
> Thanks for any help regarding this issue
>
> Best
> Oli
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Olivier Burri]

Hi,

Right, sorry, that is also one of the things that we checked.

Unfortunately the problem remains…

Oli



From: [hidden email] [mailto:[hidden email]] On Behalf Of Christophe Leterrier
Sent: Friday, July 31, 2015 15:03
To: [hidden email]
Cc: Burri Olivier <[hidden email]>
Subject: Re: Channels Tool Freezes on Fiji and MacOS 10.9.5


Did you check if the "use ImageJ2" check box was unchecked in the options?

Christophe
Le 31 juil. 2015 2:24 PM, "Burri Olivier" <[hidden email]<mailto:[hidden email]>> a écrit :
Hi all,

We have just had a visit from a user with a big problem using Fiji

Basically when opening any multichannel image, it first is very slow at displaying the image (You actually see the image window's pixels being populated from top to bottom). Then, when using the channel tool to switch from Composite to Single Channel, Fiji partially crashes. The Channel Tool is unresponsive and we cannot quit Fiji normally and must Force Quit the app. Some of the other menus still respond though...

We thought it was due to the 1.50 update so we reverted back to 1.49, no change. Then we also installed JDK1.7 instead of 1.8 to see if this could be fixed. Still nothing. Has anyone experienced this after an update from a couple of days ago? Any hints on where we should keep looking for a possible solution?

MacOS 10.9.5, i7, 8Gb RAM
Java 1.8 and 1.7 x64 versions, managed using jEnv

Thanks for any help regarding this issue

Best
Oli



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

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[Aryeh Weiss]

On 7/31/15 3:21 PM, Burri Olivier wrote:

> Hi all,
>
> We have just had a visit from a user with a big problem using Fiji
>
> Basically when opening any multichannel image, it first is very slow at displaying the image (You actually see the image window's pixels being populated from top to bottom). Then, when using the channel tool to switch from Composite to Single Channel, Fiji partially crashes. The Channel Tool is unresponsive and we cannot quit Fiji normally and must Force Quit the app. Some of the other menus still respond though...
>
> We thought it was due to the 1.50 update so we reverted back to 1.49, no change. Then we also installed JDK1.7 instead of 1.8 to see if this could be fixed. Still nothing. Has anyone experienced this after an update from a couple of days ago? Any hints on where we should keep looking for a possible solution?
>
> MacOS 10.9.5, i7, 8Gb RAM
> Java 1.8 and 1.7 x64 versions, managed using jEnv
>

This seems similar to problems of Java 1.8 + ImageJ + OSX, which we
recently discussed on this list. When I tried Java 1.7, I also has
problems, though I did not test that very much.
I suggest you "fall back" to Java 1.6.

Mark Hiner recently  posted a shell script that will let you run 1.6
even if 1.8 is installed. It should also be in the FAQ. See:
http://fiji.sc/Frequently_Asked_Questions#How_do_I_set_up_Java_6_on_OS_X.3F

--aryeh

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Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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[ctrueden]

Hi everyone,

> Then, when using the channel tool to switch from Composite to Single
> Channel, Fiji partially crashes. The Channel Tool is unresponsive and
> we cannot quit Fiji normally and must Force Quit the app.

It would be very helpful if someone who experiences this problem could
attempt to learn more details, as described at:

http://imagej.net/Debugging#Debugging_JVM_hangs

Thanks,
Curtis

On Fri, Jul 31, 2015 at 8:20 AM, Aryeh Weiss <[hidden email]> wrote:

> On 7/31/15 3:21 PM, Burri Olivier wrote:
>
>> Hi all,
>>
>> We have just had a visit from a user with a big problem using Fiji
>>
>> Basically when opening any multichannel image, it first is very slow at
>> displaying the image (You actually see the image window's pixels being
>> populated from top to bottom). Then, when using the channel tool to switch
>> from Composite to Single Channel, Fiji partially crashes. The Channel Tool
>> is unresponsive and we cannot quit Fiji normally and must Force Quit the
>> app. Some of the other menus still respond though...
>>
>> We thought it was due to the 1.50 update so we reverted back to 1.49, no
>> change. Then we also installed JDK1.7 instead of 1.8 to see if this could
>> be fixed. Still nothing. Has anyone experienced this after an update from a
>> couple of days ago? Any hints on where we should keep looking for a
>> possible solution?
>>
>> MacOS 10.9.5, i7, 8Gb RAM
>> Java 1.8 and 1.7 x64 versions, managed using jEnv
>>
>>
> This seems similar to problems of Java 1.8 + ImageJ + OSX, which we
> recently discussed on this list. When I tried Java 1.7, I also has
> problems, though I did not test that very much.
> I suggest you "fall back" to Java 1.6.
>
> Mark Hiner recently  posted a shell script that will let you run 1.6 even
> if 1.8 is installed. It should also be in the FAQ. See:
> http://fiji.sc/Frequently_Asked_Questions#How_do_I_set_up_Java_6_on_OS_X.3F
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Greg]

Hi Curtis,

as I have similar Problems stated in another post, I attach here a Stack dump while maneuvering through a Hyperstack and experiencing laggy behavior. Tell me if you need sth else!

Best,
Gregor

stackdump.stackdump 

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

> On Jul 31, 2015, at 8:21 AM, Burri Olivier <[hidden email]> wrote:
>
> Hi all,
>
> We have just had a visit from a user with a big problem using Fiji
>
> Basically when opening any multichannel image, it first is very slow at displaying the image (You actually see the image window's pixels being populated from top to bottom).

This is a known problem on Mac OS X with Java 7 and 8 prior to Java 1.8.0_45. You can work around the problem by either upgrading to the latest version of Jave (1.8.0_51) or by running Fiji using Jave 6 using the instructions at

    http://fiji.sc/Frequently_Asked_Questions#How_do_I_set_up_Java_6_on_OS_X.3F

> Then, when using the channel tool to switch from Composite to Single Channel, Fiji partially crashes. The Channel Tool is unresponsive and we cannot quit Fiji normally and must Force Quit the app. Some of the other menus still respond though…

You can avoid this Java 8 bug by using the Help>Update ImageJ command to upgrade to the latest version of ImageJ (1.50a) or by running Fiji using Java 6.

-wayne

> We thought it was due to the 1.50 update so we reverted back to 1.49, no change. Then we also installed JDK1.7 instead of 1.8 to see if this could be fixed. Still nothing. Has anyone experienced this after an update from a couple of days ago? Any hints on where we should keep looking for a possible solution?
>
> MacOS 10.9.5, i7, 8Gb RAM
> Java 1.8 and 1.7 x64 versions, managed using jEnv
>
> Thanks for any help regarding this issue
>
> Best
> Oli



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

[Greg]

Hey,

can confirm, after updating JDK to 1.8.0_51 Fiji runs like a charm. Only updating the Java runtime environment via the java panel in Mac OS 10.10. is not sufficient!

Best,
Gregor

[Aryeh Weiss]

On 8/3/15 3:07 PM, Greg wrote:
> Hey,
>
> can confirm, after updating JDK to 1.8.0_51 Fiji runs like a charm. Only
> updating the Java runtime environment via the java panel in Mac OS 10.10. is
> not sufficient!
>
> Best,
> Gregor

I installed jdk 1.8.0_51, and still have the same issues that cause me
to run (when I can) with 1.6.

The two reproducible events are:

1. The Monitor Memory window is blank.

2. After a while the Roi manager Show All checkbox  does not work. If I
open the "About ImageJ" window, it will remain blank.
As soon as i close the Roi Manager , the About ImageJ window immediately
updates itself.

--aryeh

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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

[odedm]

Hi
I also can report the same issues, (running on IOS Yosemite 10.10.4 with Java 8h51)

Roi manager gets stuck,
and
after working for a while, there starts a response delay which is fixed upon restarting FIJI (memory leak?)

any insights would be nice

thanks