Computer spec for running PALM analysis

[Ann Wheeler]

Hi

We are trying to set up Quick PALM and I'm told the computer isn't co-
operating. We are using a Windows 64 bit processer rather than 32
since we are hoping that it'll run the software faster. Is this
actually a problem, is Quick Palm able to run in a 64 bit environment?
Also how much RAM do you need to run it, at the moment we have 3 GB
which is more than enough for our 3D rendering program but does Quick
PALM need more?

Couldn't see anything about this in Materials and Methods of your
paper but apologies if I havn't read it thoroughly enough.

Thanks

Ann

[Ricardo Henriques]

Hi Ann,

Good question. There are two parts for quickpalm: 

- the laser control software - this one unfortunately to the best of my knowledge only works in WinXP 32-bit

- the ImageJ plugin - the QuickPALM ImageJ plugin works in any system that can support java 32-bit or java 64-bit, actually I more commonly use QuickPALM on a 64-bit WinXP workstation with 48 GB of ram and 8 cores. The most critical factor on a computer running QuickPALM is the memory, you need a lot of it if you're planning to detect a lot of particles. So, I'd say, if you have a 64-bit 3GB RAM machine, make sure that ImageJ is running Java-64bit and that the memory on ImageJ is set to about 75% of the memory of the system (2250 MB in your case). With that amount of memory you should be able to deal with image sequences in the order of 10.000-100.000 (make sure you use virtual-stacks), yielding possibly up to 1 million particles.

Let me know if this helps or if there is anything I can help with.

Cheers,

R

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Ricardo Henriques

Gene Expression and Biophysics Unit  
Institute of Molecular Medicine
Faculty of Medicine, University of Lisbon Av. Prof. Egas Moniz 
1649-028 Lisbon, Portugal 
Phone: + 351 217999503, 
Ext: 47318 
Fax: + 351 217999504 
E-mail: rhenr...@fm.ul.pt
~~ Or ~~ 
Unité de Biochimie Structurale et Cellulaire                          
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