Strange Out of Memory errors

[Harry Parker]

Help, please.  I'm running out of memory when I use above 127MB, even though I've set the amount of memory to use at 512MB.
 
  I'm running the current version of ImageJ (1.35h) under Java 1.5.0 on Windows XP SP2.
 
  After opening a few 5 MP images (14.4MB BMP files) I get the error:
  >>>>>>>>>>>>>>>>>>>>>>>>>>>
  <Out of memory>
  <All available memory (127MB) has been>
  <used. Instructions for making more>
  <available can be found in the "Memory" >
  <sections of the installation notes at>
  <http://rsb.info.nih.gov/ij/docs/install/>
  >>>>>>>>>>>>>>>>>>>>>>>>>>>
 
  The properties, the info box, and the memory monitor all show that I  have 512MB, but soon after I go above 120MB, I get the above  error.  Any ideas?
 
  Hopefully,
  Harry
 
 
 


--  
Harry Parker  
Systems Engineer  
Imaging Systems Division  
Dialog Semiconductor, Inc.
               
---------------------------------
 Yahoo! FareChase - Search multiple travel sites in one click.  

[Justin Murdock-2]

I am calculating volumes of various size cells from stacks of confocal
microscope images with '3D objects counter'. Some stacks are rather
large and I have to reduce the original size to avoid the out of memory
error. My problem is that when I rescale the file to half size (i.e.
1024x1024 to 512x512, voxels go from .45x.45x4.5 to .9x.9x4.5) I get
very different total volume and number of particles counted.  When
measuring xy distances with the measure command I get the same on both
images so it appears to keep the pixel calibration.  I assume the
thresholding part of the 3D counter is part of the problem but can't
quite figure it out.

Thanks,
Justin



Justin Murdock
Kansas State University
Division of Biology
232 Ackert Hall
Manhattan, KS 66506

[Albert Cardona]

Justin,

Instead of resizing the images, use the virtual stack opener plugin
from Wayne,
at http://rsb.info.nih.gov/ij/plugins/ or some variation of it that
fits your need.

The virtual stack will operate as a normal stack but under the curtains
it is loading/unloading each image file in a sequence one by one, thus
avoiding the out of memory problems.

Albert

[Pedro Ramos]

Have you tried what it is said in the error message?  if you go to
http://rsb.info.nih.gov/ij/docs/install you can find how to increase the
memory used by imageJ. For windows it is easy; open imageJ and select from
the menu:

Edit >> Options >> Memory

change to the value you wools like to use and re-start imageJ.

If you have already tried this, then forget about this message.


Pedro

[Sarria J.-C. Floyd]

Hi!

"Edit >> Options >> Memory"

I've tried when using the VOLUMEJ plug-in, and it is impossible to increase
the memory by this way....
Is it possible to change the memory size with VolumeJ?
Furthermore we need a lot of ram for 3D applications........

Any comment?

Floyd

-------------------------------------------------
Sarria Juan-Carlos, Floyd
Swiss Federal Institute of Technology (EPFL) - Lausanne School of
Life Sciences
BIOIMAGING CENTER Image Processing & Analysis Office
EPFL/20000 FSV/AI-2206
CH-1015 Lausanne, Switzerland

Phone : [phone]
Fax:    [phone]
Mobile: [phone]
Email:  [hidden email]
URL:    http://sv.epfl.ch

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Pedro
Ramos
Sent: jeudi, 17. novembre 2005 09:25
To: [hidden email]
Subject: Re: Strange Out of Memory errors

Have you tried what it is said in the error message?  if you go to
http://rsb.info.nih.gov/ij/docs/install you can find how to increase the
memory used by imageJ. For windows it is easy; open imageJ and select from
the menu:


change to the value you wools like to use and re-start imageJ.

If you have already tried this, then forget about this message.


Pedro