Multi-dimensional acquisition with laser and fluidics control

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Multi-dimensional acquisition with laser and fluidics control

jonchengw
Hi all, 

I am very new to Micro-Manager and I'd to to seek help on setting up an integrated system with imaging, laser, and fluidics control. 

Equipment:
- Nikon TiE microscope with PFS, Nikon encoded stage: already controlling in MM
- Andor iXon Ultra 888 EMCCD camera 
- FLI 632 filter wheel: TTL or serial control (already controlling in MM)
- Quantum GEM 532 nm laser: can be controlled by serial control
Melles Griot 660 nm laser: can be controlled by serial control
- Luminos 1x2 fiber optics switch: control by TTL / Arduino?
- Third party syringe pump and valve system with serial control : we are able to control already with Micro-Manager using Beanshell scripting.

Here is the desired workflow. The fluidics and imaging just need to be started sequentially with each other. For each workflow cycle, we simply need to turn on the fluidics run and then imaging run sequentially.

for i = 1 : workflow_cycles

% Start Fluidics Module (pump and valve controls)

% Start Imaging Module

* Microscope filter turret will be in a fixed position with a dual-band dichroic mirror 

for j = 1 : num_stage_positions
Switch on 532 nm laser
Go to filter wheel position 1 (Cy3/Cy5 filter)
Snap image and save
Go to filter wheel position 2 (TxR/NIR filter)
Snap image and save
Switch on 660 nm laser
Go to filter wheel position 1 (Cy3/Cy5 filter)
Snap image and save
Go to filter wheel position 2 (TxR/NIR filter)
Snap image and save
Switch off lasers
end
end

I was wondering if someone has done something similar and can give advice to overall integration. I am not sure if I'll need hardware-based triggering for all or some parts talking to each other, or if I can just run almost the whole workflow as a series of serial commands. If the latter, I was concerned about delays. Also wondering about how much of the imaging module I could possibly simply run in the Multi-D Acquisition vs. running as a script. 

Thank you.

Best regards,
Jonathan 




 

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