Help with time series imaging

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Help with time series imaging

Dawn Nagel
Hello,
I've just installed micromanager to run my old ORCA Hammamatsu camera. My plan is to use this for luciferase imaging in plants. I'm trying to set up a protocol to take an image every 2.5 hr for 5 days with an exposure time of 20 mins. Can you help guide me on how to accomplish this if possible.

Thanks.

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Re: Help with time series imaging

Jones, Matthew A
Hi Dawn,

We drive an Andor camera using MicroManager and an Arduino for this purpose. The core loop we use is;

for (i=0; i < nrFrames; i++) {
j = i + 1;
gui.clearMessageWindow();
Calendar cal = Calendar.getInstance();
loopTime = cal.getTime();
print(startText);
gui.message("In acquisition loop- LEDs on");
gui.message("Loop " + j + " of " + nrFrames + " at:" + "\n" + loopTime);
mmc.sleep(5700000); // Wait for next acquisition cycle (currently 95min)
mmc.setShutterOpen(false); //Turn off LEDs
mmc.setProperty("Arduino-Switch", "State", "0"); //Set LEDs to off
Calendar cal = Calendar.getInstance();
expTime = cal.getTime();
gui.message("Exposure started at:" + "\n" + expTime);
gui.message("Exposure in progress");
gui.snapAndAddImage(acqName, i, 0, 0, 0); 
mmc.deviceBusy("Andor"); //Safety call to wait for exposure to finish
gui.message("Image acquired");
mmc.sleep(4000); //"Safety" pause after exposure
mmc.setProperty("Arduino-Switch", "State", colourLed); //Set LEDs to chosen colour
mmc.setShutterOpen(true); //Turn on LEDs
gui.message("LEDs on");
}

gui.closeAcquisition(acqName);
}

You’ll need to make modifications to use an ORCA- if you want to chat in more detail you can contact me off list; matthew.jones {@} essex.ac.uk

Matt

Matt Jones PhD FHEA
Lecturer in Molecular Biology
University of Essex


On Jul 18, 2017, at 5:25 PM, Dawn Nagel <[hidden email]> wrote:

Hello,
I've just installed micromanager to run my old ORCA Hammamatsu camera. My plan is to use this for luciferase imaging in plants. I'm trying to set up a protocol to take an image every 2.5 hr for 5 days with an exposure time of 20 mins. Can you help guide me on how to accomplish this if possible.

Thanks.
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Re: Help with time series imaging

julou
In reply to this post by Dawn Nagel
Hi,

What you want to do is called a "Multi Dimensional Acquisition" aka MDA in micro-manager.
This is documented here (for MM1.4) and here (for MM2).

I've no experience with using very long exposure but somehow remember that there can be a limitation on how long one can expose (to prevent damaging CCD I guess). I couldn't find it anymore, maybe in the properties of your camera?

Best,
Thomas
Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
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Re: Help with time series imaging

Dawn Nagel
In reply to this post by Jones, Matthew A
Thanks Matt. I will try this and let you know if it works or have questions. I appreciate it.
Best,
Dawn

On Wed, Jul 19, 2017 at 12:11 AM, Jones, Matthew A <[hidden email]> wrote:
Hi Dawn,

We drive an Andor camera using MicroManager and an Arduino for this purpose. The core loop we use is;

for (i=0; i < nrFrames; i++) {
j = i + 1;
gui.clearMessageWindow();
Calendar cal = Calendar.getInstance();
loopTime = cal.getTime();
print(startText);
gui.message("In acquisition loop- LEDs on");
gui.message("Loop " + j + " of " + nrFrames + " at:" + "\n" + loopTime);
mmc.sleep(5700000); // Wait for next acquisition cycle (currently 95min)
mmc.setShutterOpen(false); //Turn off LEDs
mmc.setProperty("Arduino-Switch", "State", "0"); //Set LEDs to off
Calendar cal = Calendar.getInstance();
expTime = cal.getTime();
gui.message("Exposure started at:" + "\n" + expTime);
gui.message("Exposure in progress");
gui.snapAndAddImage(acqName, i, 0, 0, 0); 
mmc.deviceBusy("Andor"); //Safety call to wait for exposure to finish
gui.message("Image acquired");
mmc.sleep(4000); //"Safety" pause after exposure
mmc.setProperty("Arduino-Switch", "State", colourLed); //Set LEDs to chosen colour
mmc.setShutterOpen(true); //Turn on LEDs
gui.message("LEDs on");
}

gui.closeAcquisition(acqName);
}

You’ll need to make modifications to use an ORCA- if you want to chat in more detail you can contact me off list; matthew.jones {@} essex.ac.uk

Matt

Matt Jones PhD FHEA
Lecturer in Molecular Biology
University of Essex


On Jul 18, 2017, at 5:25 PM, Dawn Nagel <[hidden email]> wrote:

Hello,
I've just installed micromanager to run my old ORCA Hammamatsu camera. My plan is to use this for luciferase imaging in plants. I'm trying to set up a protocol to take an image every 2.5 hr for 5 days with an exposure time of 20 mins. Can you help guide me on how to accomplish this if possible.

Thanks.
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Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot_______________________________________________
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