handling large stacks

[Franklin Shaffer-2]

I have sequences of 50,000 images of particle motion from a high speed camera.  
I need to process the images, all 50,000 of them, in ImageJ.  But I can only load about 3000 of the images before ImageJ
runs out of memory.  
 
I'm using Windows XP Professional.  I did change the ImageJ.cfg file to increase the memory to 1500.
 
Is there a way to get ImageJ to handle a sequence of 50,000 images?
 
Thank you,
Frank Shaffer
 
 
Franklin Shaffer, Senior Engineer
USDOE National Energy Technology Laboratory
Office of Research & Development
Computational Science Division
Mail Stop 84-202
626 Cochrans Mill Road
Pittsburgh, PA  15236
[hidden email]
Office: 412-386-5964
Cell: 412-833-3849

[David Hovis]

Use the Virtual Stack option.

--David

On Mar 11, 2008, at 8:56 AM, Franklin Shaffer wrote:

> I have sequences of 50,000 images of particle motion from a high  
> speed camera.
> I need to process the images, all 50,000 of them, in ImageJ.  But I  
> can only load about 3000 of the images before ImageJ
> runs out of memory.
>
> I'm using Windows XP Professional.  I did change the ImageJ.cfg file  
> to increase the memory to 1500.
>
> Is there a way to get ImageJ to handle a sequence of 50,000 images?
>
> Thank you,
> Frank Shaffer
>
>
> Franklin Shaffer, Senior Engineer
> USDOE National Energy Technology Laboratory
> Office of Research & Development
> Computational Science Division
> Mail Stop 84-202
> 626 Cochrans Mill Road
> Pittsburgh, PA  15236
> [hidden email]
> Office: 412-386-5964
> Cell: 412-833-3849
> <Franklin Shaffer.vcf>

[Wayne Rasband]

On Mar 11, 2008, at 8:56 AM, Franklin Shaffer wrote:

> I have sequences of 50,000 images of particle motion from a high speed
> camera.
> I need to process the images, all 50,000 of them, in ImageJ.  But I
> can only load about 3000 of the images before ImageJ
> runs out of memory.
>
> I'm using Windows XP Professional.  I did change the ImageJ.cfg file
> to increase the memory to 1500.
>
> Is there a way to get ImageJ to handle a sequence of 50,000 images?

Open the sequence as a virtual stack by enabling "Use Virtual Stack" in
the File>Import>Image Sequence Dialog box. Process the virtual stack
using a macro such as the one at

     http://rsb.info.nih.gov/ij/macros/Process_Virtual_Stack.txt

-wayne

[Franklin Shaffer-2]

I have an application where I'm using a high speed camera and an endoscope to track the motion of small particles in a flow field.  
I'm doing frame-to-frame tracking.
 
I've looked through all of the cell/particle tracking plugins I could find on the internet for ImageJ (Manual Tracking, MultiTracker, MTrack2, MTrackJ, ParticleTracker, SpotTracker), but none use information from the flow field, for example, using the range of possible velocities to guess the next location of a particle image.
 
Before I start writing my own plugin from scratch, I would like to know if anyone knows of cell/particle tracking code for ImageJ that assumes cell/particles are in a flow field?
 
Thanks,
Frank
 
 
Franklin Shaffer, Senior Engineer
USDOE National Energy Technology Laboratory
Office of Research & Development
Computational Science Division
Mail Stop 84-202
626 Cochrans Mill Road
Pittsburgh, PA  15236
[hidden email]
Office: 412-386-5964
Cell: 412-833-3849