[OpenSPIM] 64-bit Fiji Memory Limit Issue

[Johannes Schindelin]

Hi Tom,

On 2015-04-21 14:28, Roberts, Thomas wrote:

> So, I have mFiji located on my desktop.

Unfortunately I cannot support mFiji. It is unclear from which sources 
it was built/put together, and whether those sources are available to be 
to begin with.

Having said that...

> If I click into the Fiji window it says the following:
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-29/1.49q; Java 1.6.0_31 [64-bit]; 11MB
> of 20000MB (<1%).

Assuming that you use this 64-bit Fiji with the SPIM reconstruction, 
please note that that plugin is a bit wasteful with resources, i.e. it 
does not release memory necessarily as soon as it does not need it 
anymore. I remember that we had problems to reconstruct some data in 
Madison until we moved to a computer with 128GB (!!!).

To verify that this could be the problem, I would suggest to monitor the 
memory consumption by calling Plugins>Utilities>Monitor Memory... before 
starting to process the data. It should be relatively obvious from the 
monitor window and the log which steps in the reconstruction take that 
much memory (if I am correct in my assumption that there is a memory 
pseudo-leak, of course).

Ciao,
Johannes