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

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

Hi Kyle,

   I just realized / is a right division operator. I want to name the image
using the X, Y, Z coordinates. Thus, instead of



*a/b/c = img*
  would

  *a,b,c = img*

  work correctly and assign the coordinates as the name of the image?

Thanks!
Kiana Go

On Thu, Jun 28, 2018 at 2:05 PM, Kiana Go <gok...@be...> wrote:

> 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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>>
>
>
> --
> Class of 2021
>



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Class of 2021