Starting MDA from external software

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Starting MDA from external software

Then,Patrick // Leibniz-IPHT

Hello,

 

I have a (potentially trivial) problem with Micro-Manager, to which so far I have not been able to find a satisfying answer.

 

I’m using Micro-Manager for some time now on our home-build microscope setup, mostly for recording of simple image sequences or z-stacks.

Now I’m extending the setup to include a syringe pump and arduino-based stage. To control this parts I’ve written some software (currently in LabView) which is sending various command sequences to the pump and the stage.

After such a sequence is finished, I want to record images on the microscope with the multi-dimensional acquisition tool of Micro-Manager.

For ease of use, I’d prefer to keep those sequences in my own software as opposed to writing some extensive Micro-Manager scripts.

 

What I’d like to do is to start the MDA externally from my own software. The software itself is programmed in LabView, although I wouldn’t mind to rewrite it in Python or to include a call to some small external Python script, if necessary (preferably Python 3.x).

My current solution is to use a small beanshell script in Micro-Manager that is simply listening to the input of an (different) Arduino. Once my software has finished the pumping/stage sequence it puts the input to high and MDA will be triggered.

However, while working in principle, this is a bit inelegant – I would much prefer to directly call the MDA tool from my own software, without the intermittent hardware trigger.

 

I would be grateful for any suggestions on how to do this or to where I can find some further information on the matter.

 

Best regards,

Patrick  

 



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Re: Starting MDA from external software

Stuurman, Nico
Hi Patrick,

> What I’d like to do is to start the MDA externally from my own
> software. The software itself is programmed in LabView, although I
> wouldn’t mind to rewrite it in Python or to include a call to some
> small external Python script, if necessary (preferably Python 3.x).
>
> My current solution is to use a small beanshell script in
> Micro-Manager that is simply listening to the input of an (different)
> Arduino. Once my software has finished the pumping/stage sequence it
> puts the input to high and MDA will be triggered.
>
> However, while working in principle, this is a bit inelegant – I would
> much prefer to directly call the MDA tool from my own software,
> without the intermittent hardware trigger.
>

Henry Pinkard added code to the Micro-Magellan plugin to listen to
commands on a port.  He uses it to send commands from Python and even to
send images into Python for analysis.  He, Bryant Chhun and I will get
together soon to finalize the design of this interface. I think that
should work well for your use case.

Best,


Nico




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Re: Starting MDA from external software

Then,Patrick // Leibniz-IPHT
Hi Nico,

thank you very much for the response.
That plugin does sound interesting indeed, although I wouldn't mind to have a pure software solution for starting MDA or a beanshell script from outside MM (which can be initially running or not).
As I said, maybe that’s even a trivial thing, but I'm new to programming MM and the API documentation is a bit confusing at times...

Best,
Patrick


-----Ursprüngliche Nachricht-----
Von: Nico Stuurman [mailto:[hidden email]]
Gesendet: Dienstag, 14. Januar 2020 19:26
An: Micro-Manager General
Betreff: Re: [micro-manager-general] Starting MDA from external software

Hi Patrick,

> What I’d like to do is to start the MDA externally from my own
> software. The software itself is programmed in LabView, although I
> wouldn’t mind to rewrite it in Python or to include a call to some
> small external Python script, if necessary (preferably Python 3.x).
>
> My current solution is to use a small beanshell script in
> Micro-Manager that is simply listening to the input of an (different)
> Arduino. Once my software has finished the pumping/stage sequence it
> puts the input to high and MDA will be triggered.
>
> However, while working in principle, this is a bit inelegant – I would
> much prefer to directly call the MDA tool from my own software,
> without the intermittent hardware trigger.
>

Henry Pinkard added code to the Micro-Magellan plugin to listen to commands on a port.  He uses it to send commands from Python and even to send images into Python for analysis.  He, Bryant Chhun and I will get together soon to finalize the design of this interface. I think that should work well for your use case.

Best,


Nico




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