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    Shalin Shah
    @shalinshah1993
    hello, I have 7500 frames of diffraction limited data. After localization i want to apply RCC drift correction. However, it runs out of memory if I put in 75 bins.
    I also get this exception sometime while performing localization
    Exception in thread "pool-2-thread-2" java.lang.NullPointerException
    at cz.cuni.lf1.lge.ThunderSTORM.estimators.PSF.MoleculeDescriptor.getParamColumn(MoleculeDescriptor.java:227)
    at cz.cuni.lf1.lge.ThunderSTORM.estimators.PSF.Molecule.getParamUnits(Molecule.java:217)
    at cz.cuni.lf1.lge.ThunderSTORM.estimators.PSF.Molecule.getParam(Molecule.java:142)
    at cz.cuni.lf1.lge.ThunderSTORM.rendering.AbstractRendering.addToImage(AbstractRendering.java:273)
    at cz.cuni.lf1.lge.ThunderSTORM.rendering.RenderingQueue$RenTask.run(RenderingQueue.java:91)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
    at java.lang.Thread.run(Thread.java:745)
    Shalin Shah
    @shalinshah1993
    The error while drift correction using RCC

    (Fiji Is Just) ImageJ 2.0.0-rc-61/1.51n; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 5139MB of 12179MB (42%)

    java.util.concurrent.ExecutionException: org.apache.commons.math3.exception.NotFiniteNumberException: � is not a finite number
    at java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.util.concurrent.FutureTask.get(FutureTask.java:192)
    at javax.swing.SwingWorker.get(SwingWorker.java:602)
    at cz.cuni.lf1.lge.ThunderSTORM.util.WorkerThread$1.done(WorkerThread.java:49)
    at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
    at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
    at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
    at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
    at javax.swing.Timer.fireActionPerformed(Timer.java:313)
    at javax.swing.Timer$DoPostEvent.run(Timer.java:245)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
    at java.awt.EventQueue.access$500(EventQueue.java:97)
    at java.awt.EventQueue$3.run(EventQueue.java:709)
    at java.awt.EventQueue$3.run(EventQueue.java:703)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

    Martin Ovesny
    @zitmen
    Hi, I'll look at the exception, but I don't think I can help you with memory much. You can buy more memory or don't oversample the image too much or use less bins. You don't usually need that many, especially when the drift is nearly linear.
    Shalin Shah
    @shalinshah1993
    oh so you think it is because i am oversampling? I did 25x magnification
    i think drift wasn't linear.
    Martin Ovesny
    @zitmen
    I would try 5x, that is standard and worked on our data
    You can use higher if it fits your memory
    Shalin Shah
    @shalinshah1993
    okay and what about number of bins for drift correction using RCC?
    I am trying to resolve spots that are about 70 and 50 nm away
    Shalin Shah
    @shalinshah1993
    I collected 8000 frames so I was trying about 80 bins but it gives out of memory heap exception or the one i showed above
    Martin Ovesny
    @zitmen
    Well, it's really hard to say like that. Try 10 bins with higher sampling, try 80 with lower sampling, try just subsequence of the 8000 frames. Then see how it fits together and what makes sense. If you data is sparse, you might be fine with 10 samples and higher sampling might give you wrong results when the correlation fixes on a wrong feature. You will have to figure it out, it can't always work automagically :)
    Shalin Shah
    @shalinshah1993
    Yes fiddling around does seem to work for drift. However, the question is how do i know whether the drift correction is correct or not? That RCC is not stuck in wrong place
    Martin Ovesny
    @zitmen
    Just look at your data, I dont know how to answer this. If you have something on background you would see or track a bead, (sub)structure, etc.
    NicoKiaru
    @NicoKiaru
    Hi everybody! Sorry for my naive question, but I haven't started yet to play with the plugin. So: is there a possibility to have GPU acceleration in Thunderstorm ? Thanks!