Multidimensional acquisition for an infinite time period

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Multidimensional acquisition for an infinite time period

otills
Hi, In addition to my previous post/questions with the Multi-dimensional acquisition feature is it possible to set a loop whereby a sequence over X positions of a multiwell tray are successively imaged for an infinite time period? I know you can capture at various locations but I'm just not sure how to set this to a loop, short of repeating the locations in the XY list.. is there a more elegant way of doing this?

Thanks again, Oli
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Re: Multidimensional acquisition for an infinite time period

Nico Stuurman-4
> Hi, In addition to my previous post/questions with the Multi-
> dimensional acquisition feature is it possible to set a loop whereby  
> a sequence over X positions of a multiwell tray are successively  
> imaged for an infinite time period? I know you can capture at  
> various locations but I'm just not sure how to set this to a loop,  
> short of repeating the locations in the XY list.. is there a more  
> elegant way of doing this?

In Multi-dimensional acquisition window, set Number of of Frames (top  
left of the window) to the desired number (not sure if you really want  
this to go on for infinity, just try an absurdly high number), see:
http://micro-manager.org/documentation.php?object=Userguide#mozTocId402840

Nico



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Re: Multidimensional acquisition for an infinite time period

otills
Hi, OK but if I put a set a large number of frames how do I get the camera to take say 20 frames at each of 4 locations on a plate and then loop round and do the same again for a 2 week period? i.e. the aim is to get a stack of "video" over, for example, two weeks, for each of four locations.

Is this acheivable using the multi-dimensional acquisition window or does it require writing script?

Thanks, Oli

________________________________________
From: Nico Stuurman [[hidden email]]
Sent: 16 January 2010 21:55
To: Micro-Manager General
Subject: Re: [micro-manager-general] Multidimensional acquisition for an        infinite time period

> Hi, In addition to my previous post/questions with the Multi-
> dimensional acquisition feature is it possible to set a loop whereby
> a sequence over X positions of a multiwell tray are successively
> imaged for an infinite time period? I know you can capture at
> various locations but I'm just not sure how to set this to a loop,
> short of repeating the locations in the XY list.. is there a more
> elegant way of doing this?

In Multi-dimensional acquisition window, set Number of of Frames (top
left of the window) to the desired number (not sure if you really want
this to go on for infinity, just try an absurdly high number), see:
http://micro-manager.org/documentation.php?object=Userguide#mozTocId402840

Nico



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Re: Multidimensional acquisition for an infinite time period

Nico Stuurman-4
> Hi, OK but if I put a set a large number of frames how do I get the  
> camera to take say 20 frames at each of 4 locations on a plate and  
> then loop round and do the same again for a 2 week period? i.e. the  
> aim is to get a stack of "video" over, for example, two weeks, for  
> each of four locations.

  Using the GUI you can either take a single frame (which can be a  
single image, z-stack, and/or multi-channel image) at each of the 4  
locations and keep on doing that for as long as you want (time-lapse  
mode), or you can acquire a time-lapse sequence at each of the 4  
locations (multi-field mode).  If you want to repetitively take a time-
lapse sequence at each of the 4 locations, then you will need to write  
a script.

Best,

Nico

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Re: Multidimensional acquisition for an infinite time period

otills
Hi, thanks for this information.

Has anyone written such a script or anything similar? Or is able to offer some wisdom in how to do so?

Thanks, Oli

________________________________________
From: Nico Stuurman [[hidden email]]
Sent: 16 January 2010 23:06
To: Micro-Manager General
Subject: Re: [micro-manager-general] Multidimensional acquisition for   an      infinite time period

> Hi, OK but if I put a set a large number of frames how do I get the
> camera to take say 20 frames at each of 4 locations on a plate and
> then loop round and do the same again for a 2 week period? i.e. the
> aim is to get a stack of "video" over, for example, two weeks, for
> each of four locations.

  Using the GUI you can either take a single frame (which can be a
single image, z-stack, and/or multi-channel image) at each of the 4
locations and keep on doing that for as long as you want (time-lapse
mode), or you can acquire a time-lapse sequence at each of the 4
locations (multi-field mode).  If you want to repetitively take a time-
lapse sequence at each of the 4 locations, then you will need to write
a script.

Best,

Nico

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Re: Multidimensional acquisition for an infinite time period

Nico Stuurman-4
> Has anyone written such a script or anything similar? Or is able to  
> offer some wisdom in how to do so?

The script can look as follows:

while (true) {
   acq.acquire();
   Thread.sleep(60000);
}

That is all.  Make sure that you set up the acquisition parameters as  
desired (Multi-field, 20 frames, desired interval, etc.), save image  
files, display in single window.

For more details on scripting, see: http://valelab.ucsf.edu/~nico/MMwiki/index.php/Script_Panel_GUI

Bst,

Nico


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Re: [micro-manager-general] Multidimensional acquisition for an infinite time period

otills
Thanks for this script, however it doesn't seem to "loop". After following the instructions of the MD window nothing seems to happen, although in trying to do anything else with the camera I'm told acquisition is still underway. Am I missing something or is there something I need to add to this script to make it repeat the MD window's instructions "x" times?

________________________________________
From: Nico Stuurman [[hidden email]]
Sent: 19 January 2010 04:54
To: Micro-Manager General
Subject: Re: [micro-manager-general] Multidimensional acquisition       for     an      infinite time period

> Has anyone written such a script or anything similar? Or is able to
> offer some wisdom in how to do so?

The script can look as follows:

while (true) {
   acq.acquire();
   Thread.sleep(60000);
}

That is all.  Make sure that you set up the acquisition parameters as
desired (Multi-field, 20 frames, desired interval, etc.), save image
files, display in single window.

For more details on scripting, see: http://valelab.ucsf.edu/~nico/MMwiki/index.php/Script_Panel_GUI

Bst,

Nico


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Re: [micro-manager-general] Multidimensional acquisition for an infinite time period

Nico Stuurman
Administrator

> Thanks for this script, however it doesn't seem to "loop". After following the instructions of the MD window nothing seems to happen, although in trying to do anything else with the camera I'm told acquisition is still underway.

Sounds like your MDA acquisition is not terminating properly.  Look in your Corelog.txt (in debug mode) for errors.  Can you start MDA twice in a row manually (guess not, this is really doing the same thing)?  The script works fine here, repeats itself every 60 seconds.

Best,

Nico


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Re: [micro-manager-general] Multidimensional acquisition for an infinite time period

otills
Hi Nico,

Thanks I'll look at this when in the lab tomorrow.

Just for clarification.. does this script just continue to repeat the MDA every 60 seconds until you terminate the acquisition? i.e. has the potential to continue indefinitely?

________________________________________
From: Nico Stuurman [[hidden email]]
Sent: 20 January 2010 21:37
To: Micro-Manager General
Subject: Re: [micro-manager-general] Multidimensional   acquisition     for     an      infinite time period

> Thanks for this script, however it doesn't seem to "loop". After following the instructions of the MD window nothing seems to happen, although in trying to do anything else with the camera I'm told acquisition is still underway.

Sounds like your MDA acquisition is not terminating properly.  Look in your Corelog.txt (in debug mode) for errors.  Can you start MDA twice in a row manually (guess not, this is really doing the same thing)?  The script works fine here, repeats itself every 60 seconds.

Best,

Nico


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Re: [micro-manager-general] Multidimensional acquisition for an infinite time period

Nico Stuurman
Administrator
> Thanks I'll look at this when in the lab tomorrow.
>
> Just for clarification.. does this script just continue to repeat the MDA every 60 seconds until you terminate the acquisition? i.e. has the potential to continue indefinitely?

It keeps running until you stop the script.  Why don't you experiment using the demo configuration?

best,

Nico


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