Re: ImageJ/Fiji Memory issues - actually an OSX disk image misunderstanding problem

[Daniel James White]

Hi Francie,

On Jul 19, 2010, at 6:01 AM, IMAGEJ automatic digest system wrote:

> Date:    Sun, 18 Jul 2010 20:48:35 -0600
> From:    "Barron, Francie" <[hidden email]>
> Subject: Re: ImageJ/Fuji Memory issues
>
> Hey All,
>
> I've tried to increase the memory available in my FIJI program (via edit --> options --> Memory and Threads) to 1600mb (which is what my ImageJ program has it set for).  I get this error:
>
> Could not write /Volumes/Fiji/Fiji.app/Contents/Info.plist

Very common problem... its a misunderstanding of how diskimages work on OSX:

the problem you see is because you are running Fiji from the mounted disk image that you down loaded.
You should not do that. If you want to change the settings, it tries to write the changes to the disk image, - but that is NOT writable.

What you should do is (common procedure for OSX software):

download the Fiji from the website
OSX will get the disk image and mount it as a disk - and it will appear on your desktop. (if not, you can double click the downloaded .dmg file)
There is an instruction in that finder window for you to drag and drop fiji into your applications folder.
You should do that!

Dont run Fiji from the mounted disk image, but drag and drop (copy)  it into your applications folder,

When its done copying, unmount the disk image ("Eject it - by clicking on the little arrow next to it in a finder window, or by dragging it to the trash)

Now you can also add Fiji to your dock by dragging it there from your applications folder (not from the mounted disk image)

remember to update your fiji often:  Help - update fiji

>
> Anyone know how to fix this issue?  

hope the above fixed the problem in your understanding of disk images....
I have seem many people make the same error - its not really obvious enough, one place where OSX does not  "just work"

> I'm trying to run TrekEM2 in order to do montages.  It has been working fine, but recently has been crashing due to Java running out of memory.

there is no sunstitute for more memory here....
if you machine only has 2GB, you can pretty much forget about dealing with more image dasta than that limit.

you need a workstation with an order of magnitude more RAM to do many jobs at a reasonable speed.


cheers

Dan



>
> Any help would be great.
>
> Thanks!
> ~Francie
>
> NOTE NEW EMAIL ADDRESS:  [hidden email]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net  BioImageXD
http://pacific.mpi-cbg.de                Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk                Dan's Homepages
https://ifn.mpi-cbg.de  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[Barron, Francie]

Hi Daniel,

Thanks for the information.  Yes, I had forgot that I was running from the .dmg/disk image file since I fell prey to the updater bug on OSX and did not realize there was a fix.  I deleted and redownloaded an updated Fiji version and all was fixed!  

Thanks again for the information!
~Francie

NOTE NEW EMAIL ADDRESS:  [hidden email]

***************************************************************

Francie Barron (Hyndman), Graduate Student
Cells Biology, Stem Cells, and Development Program
Dr. David Clouthier lab, Craniofacial Biology

For Correspondence:
University of Colorado, Health Sciences Center
Department of Craniofacial Biology
Mailstop 8120
P.O. Box 6511
Aurora, CO 80045

For Deliveries:
University of Colorado Denver Health Sciences Center
Department of Craniofacial Biology
Building RC1 South, Room 11400B
12801 East 17th Avenue
Aurora, Co 80010

Lab: 303-724-4566
Fax: [phone]

*****************************************************************

________________________________________
From: Daniel James White [[hidden email]]
Sent: Tuesday, July 20, 2010 3:37 AM
To: ImageJ Interest Group
Cc: Barron, Francie
Subject: Re: ImageJ/Fiji Memory issues - actually an OSX  disk image misunderstanding problem

Hi Francie,

On Jul 19, 2010, at 6:01 AM, IMAGEJ automatic digest system wrote:

> Date:    Sun, 18 Jul 2010 20:48:35 -0600
> From:    "Barron, Francie" <[hidden email]>
> Subject: Re: ImageJ/Fuji Memory issues
>
> Hey All,
>
> I've tried to increase the memory available in my FIJI program (via edit --> options --> Memory and Threads) to 1600mb (which is what my ImageJ program has it set for).  I get this error:
>
> Could not write /Volumes/Fiji/Fiji.app/Contents/Info.plist

Very common problem... its a misunderstanding of how diskimages work on OSX:

the problem you see is because you are running Fiji from the mounted disk image that you down loaded.
You should not do that. If you want to change the settings, it tries to write the changes to the disk image, - but that is NOT writable.

What you should do is (common procedure for OSX software):

download the Fiji from the website
OSX will get the disk image and mount it as a disk - and it will appear on your desktop. (if not, you can double click the downloaded .dmg file)
There is an instruction in that finder window for you to drag and drop fiji into your applications folder.
You should do that!

Dont run Fiji from the mounted disk image, but drag and drop (copy)  it into your applications folder,

When its done copying, unmount the disk image ("Eject it - by clicking on the little arrow next to it in a finder window, or by dragging it to the trash)

Now you can also add Fiji to your dock by dragging it there from your applications folder (not from the mounted disk image)

remember to update your fiji often:  Help - update fiji

>
> Anyone know how to fix this issue?

hope the above fixed the problem in your understanding of disk images....
I have seem many people make the same error - its not really obvious enough, one place where OSX does not  "just work"

> I'm trying to run TrekEM2 in order to do montages.  It has been working fine, but recently has been crashing due to Java running out of memory.

there is no sunstitute for more memory here....
if you machine only has 2GB, you can pretty much forget about dealing with more image dasta than that limit.

you need a workstation with an order of magnitude more RAM to do many jobs at a reasonable speed.


cheers

Dan



>
> Any help would be great.
>
> Thanks!
> ~Francie
>
> NOTE NEW EMAIL ADDRESS:  [hidden email]

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

[phone] (German Mobile)
[phone] (Work phone at MPI-CBG)
[phone] (Fax MPI-CBG LMF)

http://www.bioimagexd.net       BioImageXD
http://pacific.mpi-cbg.de               Fiji -  is just ImageJ (Batteries Included)
http://www.chalkie.org.uk               Dan's Homepages
https://ifn.mpi-cbg.de                  Dresden Imaging Facility Network
dan (at) chalkie.org.uk
( white (at) mpi-cbg.de )

[dscho]

Hi,

On Tue, 20 Jul 2010, Barron, Francie wrote:

> Thanks for the information.  Yes, I had forgot that I was running from
> the .dmg/disk image file since I fell prey to the updater bug on OSX and
> did not realize there was a fix.  I deleted and redownloaded an updated
> Fiji version and all was fixed!

Well, there is a prominently featured fix for the updater bug. And I fail
to see how the .dmg issue and the updater bug and the deletion and
redownloading are related.

Ciao,
Johannes

[Barron, Francie]

I first downloaded Fiji prior to the updater bug fix.  When I updated, I couldn't reopen the program.  I found that I could run it via the disk image, and didn't seem to have a problem with function.  It was only until much later that I had some memory issues and couldn't increase the memory due to the problem that started this whole thread.  I had forgot that I was running it off the disk image as I made an alias for my doc for ease in opening the program. When people suggested that my issue was the disk image, I remembered what I had done.  I did try to run the updater bug fix downloaded from the Fiji website, but for some reason encountered an error.  In frustration, I deleted Fiji and decided to start from scratch (a "if all else fails delete and reload drivers" sort of philosophy).  I then appropriately loaded the program into my applications file, and was able to properly edit the Memory to allow function (it had been previously set for 300mb -- my RAM is 2GB, so an increase in allocation was definitely possible).  I hope that clarifies my logic and relation to some degree!

Again, thanks everyone for the help.  I appreciate the patience for the neophytes.

Best,
~Francie

NOTE NEW EMAIL ADDRESS:  [hidden email]

***************************************************************

Francie Barron (Hyndman), Graduate Student
Cells Biology, Stem Cells, and Development Program
Dr. David Clouthier lab, Craniofacial Biology

For Correspondence:
University of Colorado, Health Sciences Center
Department of Craniofacial Biology
Mailstop 8120
P.O. Box 6511
Aurora, CO 80045

For Deliveries:
University of Colorado Denver Health Sciences Center
Department of Craniofacial Biology
Building RC1 South, Room 11400B
12801 East 17th Avenue
Aurora, Co 80010

Lab: 303-724-4566
Fax: [phone]

*****************************************************************

________________________________________
From: Johannes Schindelin [[hidden email]]
Sent: Tuesday, July 20, 2010 4:09 PM
To: Barron, Francie
Cc: [hidden email]
Subject: Re: ImageJ/Fiji Memory issues - actually an OSX  disk image misunderstanding problem

Hi,

On Tue, 20 Jul 2010, Barron, Francie wrote:

> Thanks for the information.  Yes, I had forgot that I was running from
> the .dmg/disk image file since I fell prey to the updater bug on OSX and
> did not realize there was a fix.  I deleted and redownloaded an updated
> Fiji version and all was fixed!

Well, there is a prominently featured fix for the updater bug. And I fail
to see how the .dmg issue and the updater bug and the deletion and
redownloading are related.

Ciao,
Johannes