micromanager plugin development help for beginner

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micromanager plugin development help for beginner

SaralaT

Hello!


I am new to micromanager and want to develop a plugin which is able to identify the camera and piezo stage and then perform a feed back loop with the following format;


  1. Load the equipment (Camera, Piezo stages, Lasers)
  2. Then the iteration program
    1. Snapshot (save snap)
    2. Analyze the width ratio of the psf of the particle
    3. Check with calibration curve and decide on stage movement step and direction
    4. Move stage
    5. Snapshot (save snap)
    6. and so on till the particle is lost in which event it must exit the loop and stop acquisition
I am very very new to this sort of work, and would be very grateful if someone could point me on a good start as to how to get about this. 


Thanks a lot in advance!


Best Regards,

Sarala


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Re: micromanager plugin development help for beginner

JonD
Administrator
Hello Sarala,

Sarala Neomi Tantirimudalige wrote
I am new to micromanager and want to develop a plugin which is able to identify the camera and piezo stage and then perform a feed back loop with the following format;


  1.  Load the equipment (Camera, Piezo stages, Lasers)
  2.  Then the iteration program
     *   Snapshot (save snap)
     *   Analyze the width ratio of the psf of the particle
     *   Check with calibration curve and decide on stage movement step and direction
     *   Move stage
     *   Snapshot (save snap)
     *   and so on till the particle is lost in which event it must exit the loop and stop acquisition

I am very very new to this sort of work, and would be very grateful if someone could point me on a good start as to how to get about this.
Here are some thoughts, hopefully others can add.

* Consider writing a Beanshell script instead of a plugin, at least to start.  I don't see anything here requiring a full-blown plugin.

* Using the selected camera/stage/shutter is easy, use the Core and/or GUI APIs (corresponding to MMCore's C++ layer and the Micro-manager's Java layer) which are linked at the bottom of the sidebar at https://micro-manager.org/wiki/Micro-Manager_Programming%20Guide.  There are also guides to scripting and plugin writing linked there.

* Once you have a script it's straightforward to convert to a plugin, you will just be using the equivalent of the mmc and gui objects automatically available in the scripting environment.

* Refer to the links above  and the listserv archives about snapping images from a script.

* You're doing some image analysis which you could either offload to an ImageJ macro entirely or embed the macro code into your script/plugin.

Jon

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Jon Daniels
Applied Scientific Instrumentation
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
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