Troubleshooting LeicaDMI 6000B shutter behavior for multidimensional acquisition

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Troubleshooting LeicaDMI 6000B shutter behavior for multidimensional acquisition

Aofei Liu
Hi all,

Our lab has been trying to set up micro-manager with one of our LeicaDMI 6000B microscopes (equipped with a pco.edge sCMOS camera, a Lumencor Sola SE2 lightbox and a Prior XY stage). 

We've managed to get the software to run smoothly with the microscope for taking single snapshots and single-channel multi-timepoint acquisitions, but we are running into some problems with multi-channel acquisition. When more than one channel is selected, the shutter stays open after the last channel in between time points (e.g. if we selected both TXR and GFP for acquisition every 10 seconds, the software will take a TXR image followed by a GFP image, then the filter cube will shift back to TXR and the shutter will stay open for the 10 second interval until the next image, so the sample is illuminated with green light for the entire duration). 

We've tried to play around with the group settings for our channels, but nothing seems to have fixed the problem so far. We've found some similar queries on online forums but none of them had a resolution. Attached is our current config file, do you have any recommendations?

Best,
Aofei


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2020-02-06 leica2.cfg (6K) Download Attachment
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Re: Troubleshooting LeicaDMI 6000B shutter behavior for multidimensional acquisition

Cammer, Michael-2

We have a similar issue with an old Zeiss Axioplan which has no shutters.  The filter turret turns and the halogen lamp may be turned on/off by computer control.

 

We defined five presets with five filter turret positions.

Green

Red

Blue

No light (filter cube position with light blocked to serve as a shutter)

Transmitted (no filter cube position)

Transmitted setup (to use for a dummy image while the lamp turns on).

 

In multi dimensional acquisition we take five images:

3 fluorescent channels

Transmitted seetup channel to account for the time it takes for the halogen lamp to turn on and allow time for user to slide in polarizing filter for Nomarksi

Transmitted

 

Then we run a macro to open the image stack, delete the fourth slice, convert to hyperstack with channels, update LUTs, and resave.

 

So it sounds like you could add a blank position with image snap to the beginning or end  of each of your sequences to make sure the light is off.

 

Cheers-

 

Michael Cammer, Sr Research Scientist, DART Microscopy Laboratory

NYU Langone Health, 540 First Avenue, SK2 Microscopy Suite, New York, NY  10016

Office: 646-501-0567 Cell: 914-309-3270  [hidden email] 

http://nyulmc.org/micros  http://microscopynotes.com/

 

 

 

 

 

From: Aofei Liu <[hidden email]>
Sent: Monday, February 10, 2020 3:16 PM
To: [hidden email]
Cc: Taylor E Jones IV <[hidden email]>
Subject: [micro-manager-general] Troubleshooting LeicaDMI 6000B shutter behavior for multidimensional acquisition

 

[EXTERNAL]

Hi all,

 

Our lab has been trying to set up micro-manager with one of our LeicaDMI 6000B microscopes (equipped with a pco.edge sCMOS camera, a Lumencor Sola SE2 lightbox and a Prior XY stage). 

 

We've managed to get the software to run smoothly with the microscope for taking single snapshots and single-channel multi-timepoint acquisitions, but we are running into some problems with multi-channel acquisition. When more than one channel is selected, the shutter stays open after the last channel in between time points (e.g. if we selected both TXR and GFP for acquisition every 10 seconds, the software will take a TXR image followed by a GFP image, then the filter cube will shift back to TXR and the shutter will stay open for the 10 second interval until the next image, so the sample is illuminated with green light for the entire duration). 

 

We've tried to play around with the group settings for our channels, but nothing seems to have fixed the problem so far. We've found some similar queries on online forums but none of them had a resolution. Attached is our current config file, do you have any recommendations?

 

Best,

Aofei



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