Re: [micro-manager-general] Matlab Configuration - CMMCore Object

[Kiana Go <gok...@be...>]

Hello Kyle,

    Thanks so much Kyle for the help! I've been stuck on these problems for
days but I've finally moved a step forward with your help! :) In addition,
can you help me figure out if I need to import any other libraries or
anything at all with my code below? Also, if you see anything wrong or
peculiar with how I utilize the functions, please let me know. I am new to
Matlab and Micro-Manager and am still trying to find my way around it. My
goal is to use Matlab's interface with Micro-Manager to control the stage
and microscope. I am aiming to automate the process of moving the stage and
taking image acquisitions with the code below.


*// Install java core and gui object*
*    cd '/Applications/Micro-Manager-1.4'*
*    import org.micromanager.MMStudio;*
*    gui = MMStudio(false);*
*    mmc = gui.getCore;*
*
mmc.loadSystemConfiguration('/Applications/Micro-Manager1.4/MMConfig_automation.cfg')*

*// Load Devices - Stages and Camera*
*    mmc.loadDevice("XYStage", "Prior", "ProScanIII");*
*       throw (CMMError)*
*    mmc.loadDevice("ZStage", "Prior", "ProScanIII");*
*      throw (CMMError)*
*    mmc.loadDevice("Camera", "AndorSDK3", "Andor");*
*      throw (CMMError)*

*//Load Serial Ports if needed*
*     mmc.loadDevice("Port", "SerialManager", "COM1");*

*// Initialize Devices*
*     mmc.initializeAllDevices();*


*//for loops -> until reaches max position of stage (ie. the edge)*
*     for c = z_start :   increment value  : z_max*
*          for a = x_start : increment value  :  x_max*
*                for b = y_start :   increment value   :   y_max*

*                 //Moves stage ; a/b/c = coordinates*
*                 mmc.SetXYPosition("XYStage",a, b);*
*            throw (CMMError)*
*                 mmc.SetPosition("ZStage",c);*
*                   throw (CMMError)*

*                 //makes sure everything has stopped moving*
*                 mmc.waitForSystem();*
*                    throw (CMMError)*

*                 //takes image acquisition*
*                 mmc.snapImage();*
*                    throw (CMMError)*

*                //gets image acquired from snapImage*
*                img=mmc.getImage();*
*                    throw (CMMError)*

*                //save image with coordinates as name*
*               a/b/c = img*

*                //add image to Album *
*               gui.addToAlbum(a/b/c);*
*                    throw (org.micromanager.utils.MMScriptException)*
*            end*
*      end *
*end*


*gui.showMessage('Acquisitions completed ')*


Thanks so much for the help again Kyle!!!


Much Appreciated,
Kiana Go


On Wed, Jun 27, 2018 at 11:55 PM, Kyle Douglass <kyl...@gm...>
wrote:

> Hi Kiana Go,
>
> On Wed, Jun 27, 2018 at 8:03 PM, Kiana Go <gok...@be...> wrote:
>
>> Hi Kyle,
>>
>>    Thank you so much! That makes so much sense! In addition, I cannot
>> find StartMMStudio.m. Is this for Windows?
>>
>
> Whoops. Yes I think that this script is only included with the Windows
> nightly builds. You may need to download and install MM on a Windows
> computer and copy the script from the installation directory to your Mac.
> It's not necessary to use this script, but it does reduce some of the work
> you need to do when using Micro-Manager in MATLAB.
>
>
>> In addition, I am following Matlab and the Micro-Manager GUI
>> <https://micro-manager.org/wiki/Matlab_and_the_Micro-Manager_GUI> guide
>> and stumbled upon the error below. However, after gui = MMStudio(false); ,
>> Micro-Manager pops up. Do I need gui.show; ? Can I just skip it?
>>
>> >> cd '/Applications/Micro-Manager1.4'
>> >> import org.micromanager.MMStudio;
>> >> gui = MMStudio(false);
>> >> gui.show;
>>      Undefined function 'show' for input arguments of type
>> 'org.micromanager.MMStudio'.
>>
>
> I haven't used Micro-Manager in MATLAB for a while now, but I don't recall
> using this method. I would say that if everything else works without it,
> then by all means just skip the call to gui.show :)
>
> Kyle
>
>
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