Time Series: Why do you need to load the WHOLE time-lapse?
Shouldn't you process (deconvolve) one time point at a time?
The deconvolution itself is frame by frame, but the pre and post processing <br>
isn't. The preprocessing consists of bleaching correction and background <br>
estimation. In the Pro there is also the possibility to apply a time or full 4D <br>
prefilter. In the postprocessing the Z-drift is corrected over time. (See Zdrift Correction). <br>
Most of these operations work on multiple adjacent frames, so working on a file <br>
by files bases would be awkward and limiting the current and future processing <br>
possibilities.
For us, one time-point is only 15MBytes,, a rather small size. <br>
But we have 50 of those now, and for the real EXPERIMENT WE MIGHT HAVE 1000. <br>
You are saying that we can never do deconvolution of such a series?
It is not an absolute necessity to have the complete 4D image all in RAM. <br>
Also in the case you have many, say 1000, time frames to process you can deconvolve the stack. <br>
Provided the swap space is large enough most of it can be swapped out. <br>
In fact, paging out means that the processed data is written in raw form back to disk. <br>
This will slow down the preprocessing operations, but presumably having the data paged out as necessary by the OS is faster than 'manually' <br>
writing to files. <br>
The deconvolution speed would hardly be impeded, paging being only necessary between frames.
A second possibility is to use a script to process the frames individually. <br>
Because the cmle and qmle deconvolution methods allow you to specify a <br>
background as a percentage of the estimated background that would handle varying <br>
backgrounds also nicely. <br>
You could use our example batch processing script for this. <br>
That has the additional feature that it can distribute deconvolution jobs over processors.
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Keywords: time series lapse scripting z-drift<br>
Categories: Faq Deconvolution, Huygens Faq, Imported Faqs<br>
Platforms: Irix Linux<br>
Related products: Hu Ess Hu Pro Hu Script<br>
