more memory

[Thoralf Seewald]

Hi all,
I have got a powerbook with 4gb. I work with stacks of pictures. One  
stacks needs around 1.8 - 2.2 gb of memory (i know it is a lot).
  With a linux system I can address inside of ImageJ around 3gb for  
this application.
With my book I tried the same, but it didn' work. The max is 2gb.
My question, is there a possibility to reserve more memory for ImageJ?

It would be great, if anybody could help me.


Thanx,

Thoralf.

[Jacqueline Ross]

Hi Thoralf,

Do you use the virtual stack option when opening your stacks? That can
save on memory.

Cheers,

Jacqui

Jacqueline Ross
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/ 

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Thoralf Seewald
Sent: 11 August 2007 05:39
To: [hidden email]
Subject: more memory

Hi all,
I have got a powerbook with 4gb. I work with stacks of pictures. One  
stacks needs around 1.8 - 2.2 gb of memory (i know it is a lot).
  With a linux system I can address inside of ImageJ around 3gb for  
this application.
With my book I tried the same, but it didn' work. The max is 2gb.
My question, is there a possibility to reserve more memory for ImageJ?

It would be great, if anybody could help me.


Thanx,

Thoralf.

[Thoralf Seewald]

Hi Jacqui,

Thank you for responding. Yes, I use this stack opener. But it uses  
the same memory. If I want address more than 2.1 GB, the software  
stops working. There must be another way, like changing something  
inside the java-applications... I am still looking for informations  
at the internet.

Regards,


Thoralf.


Am 13.08.2007 um 01:50 schrieb Jacqui Ross:

> Hi Thoralf,
>
> Do you use the virtual stack option when opening your stacks? That can
> save on memory.
>
> Cheers,
>
> Jacqui
>
> Jacqueline Ross
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland, NEW ZEALAND
>
> Tel: [phone] Ext 87438
> Fax: [phone]
>
> http://www.health.auckland.ac.nz/biru/
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Thoralf Seewald
> Sent: 11 August 2007 05:39
> To: [hidden email]
> Subject: more memory
>
> Hi all,
> I have got a powerbook with 4gb. I work with stacks of pictures. One
> stacks needs around 1.8 - 2.2 gb of memory (i know it is a lot).
>   With a linux system I can address inside of ImageJ around 3gb for
> this application.
> With my book I tried the same, but it didn' work. The max is 2gb.
> My question, is there a possibility to reserve more memory for ImageJ?
>
> It would be great, if anybody could help me.
>
>
> Thanx,
>
> Thoralf.

[Ben.BigHair]

On Aug 25, 2007, at 7:56 AM, Thoralf Seewald wrote:

> Hi Jacqui,
>
> Thank you for responding. Yes, I use this stack opener. But it uses  
> the same memory. If I want address more than 2.1 GB, the software  
> stops working. There must be another way, like changing something  
> inside the java-applications... I am still looking for informations  
> at the internet.

Hi,

This is a little off topic, but I am wondering why a Virtual Stack  
requires the same amount of memory as a regular stack?  I thought the  
purpose of the Virtual Stack is to have only one image in RAM at a  
time and thus reduce the RAM requirements -  all other images in the  
stack would reside on disk (or where ever).  Perhaps I have that  
wrong and if so would love to get some clarity on this issue.  I have  
been alerted by a user that one of my plugins that uses stacks is  
bumping up against memory issues so I am keen to come up with a  
workable fix.

Cheers,
Ben

>
>
> Am 13.08.2007 um 01:50 schrieb Jacqui Ross:
>
>> Hi Thoralf,
>>
>> Do you use the virtual stack option when opening your stacks? That  
>> can
>> save on memory.
>>
>> Cheers,
>>
>> Jacqui
>>
>> Jacqueline Ross
>> Biomedical Imaging Research Unit
>> School of Medical Sciences
>> Faculty of Medical & Health Sciences
>> The University of Auckland
>> Private Bag 92019
>> Auckland, NEW ZEALAND
>>
>> Tel: [phone] Ext 87438
>> Fax: [phone]
>>
>> http://www.health.auckland.ac.nz/biru/
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> Thoralf Seewald
>> Sent: 11 August 2007 05:39
>> To: [hidden email]
>> Subject: more memory
>>
>> Hi all,
>> I have got a powerbook with 4gb. I work with stacks of pictures. One
>> stacks needs around 1.8 - 2.2 gb of memory (i know it is a lot).
>>   With a linux system I can address inside of ImageJ around 3gb for
>> this application.
>> With my book I tried the same, but it didn' work. The max is 2gb.
>> My question, is there a possibility to reserve more memory for  
>> ImageJ?
>>
>> It would be great, if anybody could help me.
>>
>>
>> Thanx,
>>
>> Thoralf.

Ben Tupper
Bigelow Laboratory for Ocean Science
180 McKown Point Road
POB 475
West Boothbay Harbor, ME 04575

[Thoralf Seewald]

Hi Ben,
At my application I am uploading with a selfwritten plug-in the whole  
stack (all nearly 300 images). It is necessary to get the z-values  
out of each image corresponding to the points of the other images.  
Therefore I had to increase the 'memory & threads' option. But image  
works only till 2100MB, if I want to use more, ImageJ doesn´t start  
anymore. Inside of a 32bit-Linux distribution like Fedoracore 5 I  
could use around 2750MB.
A friend told me, that could be an answer inside of the kernel  
structure of the mac-osX. But I am not that familiar and started  
yesterday my search for solutions at the apple-developers website.

Cheers,
Thoralf.

_______________
Hightech-Research Center Basel

University Hospital Basel
Department for Cranio-Maxillofacial Surgery
Spitalstrasse 21
CH-4051 Basel
Switzerland

Am 25.08.2007 um 15:11 schrieb Ben Tupper:

Hi,

This is a little off topic, but I am wondering why a Virtual Stack  
requires the same amount of memory as a regular stack?  I thought the  
purpose of the Virtual Stack is to have only one image in RAM at a  
time and thus reduce the RAM requirements -  all other images in the  
stack would reside on disk (or where ever).  Perhaps I have that  
wrong and if so would love to get some clarity on this issue.  I have  
been alerted by a user that one of my plugins that uses stacks is  
bumping up against memory issues so I am keen to come up with a  
workable fix.

Cheers,
Ben

[Gabriel Landini]

On Sunday 26 August 2007, Thoralf Seewald wrote:
> At my application I am uploading with a selfwritten plug-in the whole
> stack (all nearly 300 images). It is necessary to get the z-values
> out of each image corresponding to the points of the other images.
> Therefore I had to increase the 'memory & threads' option. But image
> works only till 2100MB, if I want to use more, ImageJ doesn´t start
> anymore. Inside of a 32bit-Linux distribution like Fedoracore 5 I
> could use around 2750MB.

Hi,
I have the feeling that there is some misunderstanding of the previous
suggestions given earlier, but I may be wrong.

There is a plugin that is called "Virtual Stack Opener".
http://rsbweb.nih.gov/ij/plugins/virtual-opener.html
which now is included in IJ in the File>Import>Image Sequence
(you check: Use Virtual Stack).

This loads one slice at a time from disk, so you would not need to load the
whole stack (and therefore would allow you to use stacks which are much
larger than your memory).

In a previous mail, you said that the virtual opener takes the same amount of
memory than loading whole the stack. Can you verify this? This should not be
the case because at any one time there is a single slice on memory.

But now you say that you are using a self-written plugin that loads the whole
stack, so this is not the virtual stack opener...

Here is all the information on how to increase the memory available for IJ:

http://imagejdocu.tudor.lu/imagej-documentation-wiki/faq/how-do-i-increase-the-memory-in-imagej
http://imagejdocu.tudor.lu/imagej-documentation-wiki/faq/can-i-use-more-than-4-gb-of-memory

I hope it helps.
Cheers,

Gabriel

[Thoralf Seewald]

Hi Gabriel,
I was sick at home, therefore I am answering so late - sorry.

To clean up the missunderstanding:  Yes we use a selfwritten stack  
opener - it is based on our experimental setup. This VIVA reader  
opens a stack - the size differs between 1.7 and 2.5 GB -  into the  
memory:  each image is loaded. This is absolutely necessary to get a  
3d extraction out of this stack.
On a Linux-based workstation (32bit system, Fedora Core 5, Siemens,  
4GB memory) I pushed the usable memory for ImageJ V1.36 inside the  
command line up to 2670MB - enough for our application.

Now  I am using a MacBook Pro (OsX 10.4, 4 GB memory) and ImageJ  
1.38x, where I can change the usable memory inside of the program  
(edit > options > memory & threads). But if I want to use more than  
2100MB, ImageJ doesn´t start anymore.

This is my question: why can I use around 2.8GB on a Linux 32bit  
distribution, but get on boarders with a Mac OsX system (also linux  
based)

I used the compile & run option to start the virtual stack opener  
(the same you mean), but it gaves me only wrong slides (only 48 of  
315 images in wrong color).

I looked at the webpages you gave me, but it couldn´t solve the  
problem. As I sayed, I guess, it is inside of the OsX Kernel, but I  
have no idea how to get this problem (isn´t it science? ;) ) - I am  
looking foreward.

Thank you
Thoralf.


Am 26.08.2007 um 14:47 schrieb Gabriel Landini:

> On Sunday 26 August 2007, Thoralf Seewald wrote:
>> At my application I am uploading with a selfwritten plug-in the whole
>> stack (all nearly 300 images). It is necessary to get the z-values
>> out of each image corresponding to the points of the other images.
>> Therefore I had to increase the 'memory & threads' option. But image
>> works only till 2100MB, if I want to use more, ImageJ doesn´t start
>> anymore. Inside of a 32bit-Linux distribution like Fedoracore 5 I
>> could use around 2750MB.
>
> Hi,
> I have the feeling that there is some misunderstanding of the previous
> suggestions given earlier, but I may be wrong.
>
> There is a plugin that is called "Virtual Stack Opener".
> http://rsbweb.nih.gov/ij/plugins/virtual-opener.html
> which now is included in IJ in the File>Import>Image Sequence
> (you check: Use Virtual Stack).
>
> This loads one slice at a time from disk, so you would not need to  
> load the
> whole stack (and therefore would allow you to use stacks which are  
> much
> larger than your memory).
>
> In a previous mail, you said that the virtual opener takes the same  
> amount of
> memory than loading whole the stack. Can you verify this? This  
> should not be
> the case because at any one time there is a single slice on memory.
>
> But now you say that you are using a self-written plugin that loads  
> the whole
> stack, so this is not the virtual stack opener...
>
> Here is all the information on how to increase the memory available  
> for IJ:
>
> http://imagejdocu.tudor.lu/imagej-documentation-wiki/faq/how-do-i- 
> increase-the-memory-in-imagej
> http://imagejdocu.tudor.lu/imagej-documentation-wiki/faq/can-i-use- 
> more-than-4-gb-of-memory
>
> I hope it helps.
> Cheers,
>
> Gabriel