Re: [micro-manager-general] Burst MD Acquisition

[Nico S. <ni...@cm...>]

Hi Oliver,

> I’m trying to use burst mode in multidimensional  acquisition.
>  
> I’ve tried using Nico’s script (see below), but this doesn’t work for me as produces numerous errors starting at the: console.message (XYStage…..)_ line. 

That script is a tad old and some things changed (slightly).  Have a look at the documentation to the scripting language: https://valelab.ucsf.edu/~nico/MMwiki/index.php/Script_Panel_GUI

Specifically, try changing:
	console.message
to 
	gui.message

and
	gui.fastAcqWin_.start();
to
	gui.runBurstAcquisition().

and
	gui.isBurstAcquisitionRunning();
to
	mmc.isSequenceRunning();

> In this script how do you specify the XY positions and number of frames?

Those are specified in the line:

mmc.setXYPosition(XYStage, startXloc + (i * imageWidth), startYloc);

Apparently, this script moves the stage one image width.  If you know the exact coordinates you want to go to, you could specify those in an array.  Alternatively, you could use the positions specified in the XY position list window.   


Best,

Nico


>  
> Does anyone have a script such as this that they use for the purpose I describe?
>  
> Many thanks,
>  
> Oli
>  
> /*
> * This script takes burst sequences at a set number of sites
> * Written by Nico Stuurman for Andrew Carter, January 2008
> */
>  
> nrLocations = 4;
>  
> XYStage = mmc.getXYStageDevice();
> startXloc = mmc.getXPosition(XYStage);
> startYloc = mmc.getYPosition(XYStage);
> imageWidth = mmc.getImageWidth();
> umPerPixel = mmc.getPixelSizeUm();
>  
> console.message (XYStage + " " + startXloc + " " + startYloc + " " + imageWidth + " " + umPerPixel);
>  
> for (i=0; i < nrLocations; i++) {
>    mmc.setXYPosition(XYStage, startXloc + (i * imageWidth), startYloc);
>    mmc.waitForSystem();
>    // wait an extra 0.5 second for system to settle
>    mmc.sleep(500);
>    // start burst
>    gui.fastAcqWin_.start();
>    console.message("Burst acquisition " + i + " started!");
>    //mmc.sleep(2000);
>    Thread.currentThread().sleep(2000);
>    // poll for burst to end
>    test = gui.isBurstAcquisitionRunning();
>    if (!test)
>       console.message("No Burst running");
>    while (test) {
>      console.message("Still Running");
>       test = gui.isBurstAcquisitionRunning();
>       mmc.sleep(250);
>    }
> }
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