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superresolved.com • View topic - Running B3 in parallel on a cluster

Running B3 in parallel on a cluster

Bayesian analysis of blinking and bleaching

Running B3 in parallel on a cluster

Postby ManuelP » Tue Sep 24, 2013 2:37 pm

Hello B3 Team,

I would like to run B3 on multiple nodes in our cluster, and would like to ask for advice on how to do so best.

I would image the following ways to do so

1) subdivide the ROI, calculating each subarea on different nodes, using the same stack of images, and running the same number of iterations
2) use the same ROI for each node, but split the image stack

Am I mistaken about the second one? Can i use both the same time? What reduced computation time more, reducing ROI size, or image stack size?

In any case, I would have the following questions about each method

For 1)
What about the ROI border? Should the ROI's overlap, or be cleanly ( pixel by pixel ) divided? If there is a border, how thick should it be ( in pixels )?
What is the recommended minimal ROI size in pixels?

For 2)
What is the minimal number of frames I should use per node?

Thank you

PS: a very basic question, but what is the unit of measurement used in the result file, indicating the position of possible fluorescence molecules?
ManuelP
 
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Re: Running B3 in parallel on a cluster

Postby edrosten » Fri Sep 27, 2013 1:42 pm

edrosten
 
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Re: Running B3 in parallel on a cluster

Postby dieting » Fri Dec 26, 2014 7:07 am

If your stacks are very much longer than that then you will almost certainly need to split the data up by frames. It is certainly possible to use both at the same time.??
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dieting
 
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