quick movie open help, out of memory

[Laura Lucia Prieto Godino]

Hi!
I am trying to open a quick time movie (not possible to attach to the  
list) with ImageJ. I have updated imageJ, I have downloaded the  
Quicktime opener plug in, and I have set up in the memory option  
1500MB, but still when I try to open it, it says "out of memory, all  
the memory 63MB available has been used.
I am kind of in a hurry so any help would be greatly appreciated!
Thank you!
Lucia

[ctrueden]

Hi Lucia,

I am trying to open a quick time movie (not possible to attach to the list)
> with ImageJ. I have updated imageJ, I have downloaded the Quicktime opener
> plug in, and I have set up in the memory option 1500MB, but still when I try
> to open it, it says "out of memory, all the memory 63MB available has been
> used.
> I am kind of in a hurry so any help would be greatly appreciated!
> Thank you!
>

Have you tried using Fiji (http://fiji.sc/)? And have you tried importing
the data using Bio-Formats (File > Import > Bio-Formats)?

-Curtis

[W. Chan]

Hi Lucia

Looks like ImageJ only saw 63 MB.  Are other processes taking up a lot of memory?

Can you open a smaller/shorter QT movie?  That will let you know if it is a plugin problem or memory problem.

On Thu, 27 Oct 2011, Lucia Prieto Godino wrote:

> Hi!
> I am trying to open a quick time movie (not possible to attach to the list)
> with ImageJ. I have updated imageJ, I have downloaded the Quicktime opener
> plug in, and I have set up in the memory option 1500MB, but still when I try
> to open it, it says "out of memory, all the memory 63MB available has been
> used.
> I am kind of in a hurry so any help would be greatly appreciated!
> Thank you!
> Lucia

--
Pang (Wai Pang Chan, [hidden email], PAB A087, 206-685-1519)
The Biology Imaging Facility (http://depts.washington.edu/if/)

[Walter O'Dell PhD]

no, it is not that other processes are using all but exactly 63Meg; that would be too much of a coincidence.  63Meg is the magic value set as the imageJ default so the problem is that his ImageJ executable is not seeing his memory setting (unless his computer has only 64M of RAM to begin with, but his computer would have to be as old as Wayne R. for that to be the case).

From the ImageJ help pages
http://rsbweb.nih.gov/ij/docs/install/windows.html
you'll note that for your memory option to be read you would have to start ImageJ by clicking the ImageJ desktop icon, rather than running imagej through either an IDE (Netbeans, Xcode, Eclipse) or through the command line ("xxx/bin/java -cp ij.jar", unless you add "-Xmx1500m") or by merely double-clicking on the ij.jar file.

With ImageJ running, once you set the memory under the Options panel, you would of course have to exit ImageJ nicely and then restart ImageJ for it to have an effect.  

But since he said that he just upgraded his ImageJ, I suspect that the problem is that there is confusion with his old ImageJ desktop icon and the new one, that is, after the update, the icon may indeed point to the new ImageJ (or maybe not) but that it's internal links may point to the old ImageJ settings files.  Or perhaps there is a permissions problem such that he cannot write to his ImageJ settings file.  A way to investigate and/or force it to work would be to put the mouse over the desktop icon and right-click to bring up the menu

1. on a mac:  Options->Show in finder  which brings up the actual icon in the imagej folder, then right click over that and select "Show Contents"; go down one folder and open the  info.plist  file there.  At the bottom of that file, under the sub-menu "Java" there is the "VMOptions" tag line that should show "-Xmx1500m" should be seen there.  It if is not there, then you can put it there directly (and I would add "-Xms1500")

2. on a windows PC: select the Properties submenu, and since I do not have a PC handy I forget where it goes from there but it is not too hard to find the java run-time settings, and make sure that  "-Xmx1500m" is in there.

-Walter

On Oct 27, 2011, at 2:27 PM, W. Chan wrote:

> Hi Lucia
>
> Looks like ImageJ only saw 63 MB.  Are other processes taking up a lot of memory?
>
> Can you open a smaller/shorter QT movie?  That will let you know if it is a plugin problem or memory problem.
>
> On Thu, 27 Oct 2011, Lucia Prieto Godino wrote:
>
>> Hi!
>> I am trying to open a quick time movie (not possible to attach to the list)
>> with ImageJ. I have updated imageJ, I have downloaded the Quicktime opener
>> plug in, and I have set up in the memory option 1500MB, but still when I try
>> to open it, it says "out of memory, all the memory 63MB available has been
>> used.
>> I am kind of in a hurry so any help would be greatly appreciated!
>> Thank you!
>> Lucia
>
> --
> Pang (Wai Pang Chan, [hidden email], PAB A087, 206-685-1519)
> The Biology Imaging Facility (http://depts.washington.edu/if/)
>

Walter O'Dell, PhD
Assistant Professor
Dept. Radiation Oncology
2033 Mowry Road Rm 392A
PO Box 100385
Shands Cancer Center, University of Florida
Gainesville, FL 32610
[hidden email]
352-273-9030
http://grove.ufl.edu/~wodell/

[Cammer, Michael]

There's the method of paying the $30 for Quicktime Pro and doing a conversion from there.
-Michael C.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Lucia Prieto Godino
Sent: Thursday, October 27, 2011 12:45 PM
To: [hidden email]
Subject: quick movie open help, out of memory

Hi!
I am trying to open a quick time movie (not possible to attach to the  
list) with ImageJ. I have updated imageJ, I have downloaded the  
Quicktime opener plug in, and I have set up in the memory option  
1500MB, but still when I try to open it, it says "out of memory, all  
the memory 63MB available has been used.
I am kind of in a hurry so any help would be greatly appreciated!
Thank you!
Lucia

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This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================

[Bill Mohler]

Have you tried checking the option for a virtual stack?  That should
solve your problem, if all other things are correctly set up.



On 10/27/11 3:53 PM, Cammer, Michael wrote:

> There's the method of paying the $30 for Quicktime Pro and doing a conversion from there.
> -Michael C.
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Lucia Prieto Godino
> Sent: Thursday, October 27, 2011 12:45 PM
> To: [hidden email]
> Subject: quick movie open help, out of memory
>
> Hi!
> I am trying to open a quick time movie (not possible to attach to the
> list) with ImageJ. I have updated imageJ, I have downloaded the
> Quicktime opener plug in, and I have set up in the memory option
> 1500MB, but still when I try to open it, it says "out of memory, all
> the memory 63MB available has been used.
> I am kind of in a hurry so any help would be greatly appreciated!
> Thank you!
> Lucia
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
> =================================
>

[Philip Ershler]

What are the sizes of the files you are trying to open? What OS are you using on what kind of machine? And finally, how much RAM is installed on your system?

Oh, and which version of ImageJ 32 or 64 bit? The QT_Movie_Opener only works with the 32 bit version, but the plugin should warn you if you are trying to run this with 64 bit ImageJ?

Phil

On Oct 27, 2011, at 2:03 PM, Bill Mohler <[hidden email]> wrote:

> Have you tried checking the option for a virtual stack?  That should solve your problem, if all other things are correctly set up.
>
>
>
> On 10/27/11 3:53 PM, Cammer, Michael wrote:
>> There's the method of paying the $30 for Quicktime Pro and doing a conversion from there.
>> -Michael C.
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Lucia Prieto Godino
>> Sent: Thursday, October 27, 2011 12:45 PM
>> To: [hidden email]
>> Subject: quick movie open help, out of memory
>>
>> Hi!
>> I am trying to open a quick time movie (not possible to attach to the
>> list) with ImageJ. I have updated imageJ, I have downloaded the
>> Quicktime opener plug in, and I have set up in the memory option
>> 1500MB, but still when I try to open it, it says "out of memory, all
>> the memory 63MB available has been used.
>> I am kind of in a hurry so any help would be greatly appreciated!
>> Thank you!
>> Lucia
>>
>> ------------------------------------------------------------
>> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
>> =================================
>>

[Jimena Berni]

Hola Lucia,

you can convert/compress your movies with the free software MPEG  
streamclip. You can as well decrease the number of frames to make your  
movies smaller or cut it in peaces there.
Sometimes even when you have the memory increased it doesn't open the  
movies (i don't know why) but the software offers several options when  
opening the files among them is virtual stack, click there and it  
should work.

Good luck
Jimena


------------
Dr. Jimena Berni
Henslow Research Fellow
Downing College
Department of Zoology
University of Cambridge
Downing Street
CB2 3EJ
Cambridge, UK

Tel.: (++44) 1223 336635
Fax.: (++44) 1223 336676
[hidden email]








On 27 Oct 2011, at 17:45, Lucia Prieto Godino wrote:

> Hi!
> I am trying to open a quick time movie (not possible to attach to  
> the list) with ImageJ. I have updated imageJ, I have downloaded the  
> Quicktime opener plug in, and I have set up in the memory option  
> 1500MB, but still when I try to open it, it says "out of memory, all  
> the memory 63MB available has been used.
> I am kind of in a hurry so any help would be greatly appreciated!
> Thank you!
> Lucia

[Herbert M. Geller]

Dear Friends,

I am rotating an image an arbitrary number of degreees.  The rotation
works fine, but there is a single pixel line around the newly rotated
areas.  Is there a way to eliminate this line?

Thanks.


--
--------------------------------------
Herbert M. Geller, Ph.D.
Developmental Neurobiology Section
National Heart Lung and Blood Institute, NIH
10 Center Drive MSC 1754
Bldg 10, Room 6D18
Bethesda, MD  20892-1754
Tel: [phone]; Fax: [phone]
e-mail: [hidden email]
Web: http://dir.nhlbi.nih.gov/labs/ldn/index.asp
---------------------------------------

[Laura Lucia Prieto Godino]

Thank you for all your answers! Transforming them with jpeg, and then  
importing them with import image sequence and downsampling it by 10 by  
using "increment" it was not the best way but it worked, but I think  
in the future I will use some of the other things you suggested. I  
will have a look at all the options and choose the easiest! Thank you!


On 28 Oct 2011, at 10:06, Jimena Berni wrote:

> Hola Lucia,
>
> you can convert/compress your movies with the free software MPEG  
> streamclip. You can as well decrease the number of frames to make  
> your movies smaller or cut it in peaces there.
> Sometimes even when you have the memory increased it doesn't open  
> the movies (i don't know why) but the software offers several  
> options when opening the files among them is virtual stack, click  
> there and it should work.
>
> Good luck
> Jimena
>
>
> ------------
> Dr. Jimena Berni
> Henslow Research Fellow
> Downing College
> Department of Zoology
> University of Cambridge
> Downing Street
> CB2 3EJ
> Cambridge, UK
>
> Tel.: (++44) 1223 336635
> Fax.: (++44) 1223 336676
> [hidden email]
>
>
>
>
>
>
>
>
> On 27 Oct 2011, at 17:45, Lucia Prieto Godino wrote:
>
>> Hi!
>> I am trying to open a quick time movie (not possible to attach to  
>> the list) with ImageJ. I have updated imageJ, I have downloaded the  
>> Quicktime opener plug in, and I have set up in the memory option  
>> 1500MB, but still when I try to open it, it says "out of memory,  
>> all the memory 63MB available has been used.
>> I am kind of in a hurry so any help would be greatly appreciated!
>> Thank you!
>> Lucia