issue in Stage Control plugin: rounding up to 5 um steps

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issue in Stage Control plugin: rounding up to 5 um steps

Nikita Vladimirov

Dear MM community,

I am testing the generic plugin from Plugins > Device Control > Stage control, and found that it does not allow to increment in less than 5 micron steps.

For example, when I set z-step to 2.5 um and increment one step, it shows the new z-position + 5 um, and the stage actually moves + 5 um.

Is this a bug or a feature? Any particular purpose for this rounding?

Should I dive into the source code and fix it?

Thank you!

Nikita Vladimirov


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Nikita Vladimirov, PhD

Preibisch Lab
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Max Delbrück Center for Molecular Medicine (MDC)
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Re: issue in Stage Control plugin: rounding up to 5 um steps

JonD
Administrator
Hi Nikita,


Nikita Vladimirov wrote
> I am testing the generic plugin from *Plugins > Device Control > Stage
> control*, and found that it does not allow to increment in less than 5
> micron steps.
>
> For example, when I set z-step to 2.5 um and increment one step, it
> shows the new z-position + 5 um, and the stage actually moves + 5 um.
>
> Is this a bug or a feature? Any particular purpose for this rounding?

I suspect it's a bug or feature of your stage and/or stage device adapter,
not the stage control plugin.  With the demo config it works just fine to
deal in 0.1um increments including with 2.5um step size.

Jon

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Applied Scientific Instrumentation
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Re: issue in Stage Control plugin: rounding up to 5 um steps

m.losen
Hi Nikita,
I checked yesterday: with our Ludl stage z-drive, I can use 0.1 um increments in the 'Stage control' menu.
Which stage are you using?
Could the rounding be related to a number formatting problem related to computer settings of decimal point or comma, maybe?
Greetings,
Mario


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Re: issue in Stage Control plugin: rounding up to 5 um steps

Dhananjay
I have a related problem with Prior H117 stage. The hardware is capable of moving at 0.01um steps, but with micronamanger software, I see it going at much bigger, 1um steps. Is there a way to improve this?

D.



On Fri, Nov 23, 2018, 4:52 AM Losen, M (NP) <[hidden email]> wrote:
Hi Nikita,
I checked yesterday: with our Ludl stage z-drive, I can use 0.1 um increments in the 'Stage control' menu.
Which stage are you using?
Could the rounding be related to a number formatting problem related to computer settings of decimal point or comma, maybe?
Greetings,
Mario


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Office: 3129 Shelby, 3154 MSB
Lab: 3160 MSB
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Re: issue in Stage Control plugin: rounding up to 5 um steps

Nikita Vladimirov
In reply to this post by Nikita Vladimirov
Hi, Jon, Mario, and others,
I am using RAMPS stage controller (Arduino). Indeed, the problem was in the device adapter code, it specified the minimum z-step (5 um).
I will create a pull request once I fix the bug.
Thanks for your feedback,
Nikita Vladimirov


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Re: issue in Stage Control plugin: rounding up to 5 um steps

Nikita Vladimirov
In reply to this post by Nikita Vladimirov

Hi, Dhananjay,

I went ahead and changed the C++ code of my device adapter (RAMPS), then recompiled it to DLL file for Micromanager. In particular, I changed the internal variable 'stepSize_um_' to 0.025 um. You can find my case here.

Good luck,

Nikita Vladimirov

I have a related problem with Prior H117 stage. The hardware is capable of moving at 0.01um steps, but with micronamanger software, I see it going at much bigger, 1um steps. Is there a way to improve this?

D.



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Re: issue in Stage Control plugin: rounding up to 5 um steps

Dhananjay
Thank you, Nikita. I am assuming that this is the only way to get smaller step size. I.e., no Beanshell means to do this. In that case, I will follow your lead and do the same for the Prior Stage.

Appreciate you sharing the solution.

With kind regards,
Dhananjay.



On Sun, Nov 25, 2018, 4:19 PM Nikita Vladimirov <[hidden email]> wrote:

Hi, Dhananjay,

I went ahead and changed the C++ code of my device adapter (RAMPS), then recompiled it to DLL file for Micromanager. In particular, I changed the internal variable 'stepSize_um_' to 0.025 um. You can find my case here.

Good luck,

Nikita Vladimirov

I have a related problem with Prior H117 stage. The hardware is capable of moving at 0.01um steps, but with micronamanger software, I see it going at much bigger, 1um steps. Is there a way to improve this?

D.

_______________________________________________
micro-manager-general mailing list
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--
Dhananjay T. Tambe, Ph.D.
Department of Mechanical Engineering,
Department of Pharmacology,
Center for Lung Biology,
University of South Alabama,
Mobile, AL 36688-0002

Office: 3129 Shelby, 3154 MSB
Lab: 3160 MSB
<a href="tel:%28251%29%20461-1980" value="+12514611980" target="_blank">(251) 461-1980 or <a href="tel:%28251%29%20461-1685" value="+12514611685" target="_blank">(251) 461-1685
<a href="tel:%28251%29%20460-6549" value="+12514606549" target="_blank">(251) 460-6549 (Fax)



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Re: issue in Stage Control plugin: rounding up to 5 um steps

Stuurman, Nico

I have a related problem with Prior H117 stage. The hardware is capable of moving at 0.01um steps, but with micronamanger software, I see it going at much bigger, 1um steps. Is there a way to improve this?

The Prior adapter code shows that it asks the controller for its step size. You can see what happens by enabling logging of the serial port communication (this is a serial port property).  However, the following lines in the GetResolution function indicate trouble:

   // This is a little unclear in the manual, it is possible that this works onsome controllers, not others
   const char* commandX="RES,s";
   //const char* commandY="RES,Y";

Nevertheless, if the code gets the step size wrong, then asking it to move by (for instance) 10 micron will result in a stage movement by a different distance.  So, do you get the correct movement from Micro-Manager (best to check with a stage micrometer)?

Best,

Nico





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Re: issue in Stage Control plugin: rounding up to 5 um steps

Nikita Vladimirov
In reply to this post by Nikita Vladimirov

Hi, Dhananjay,

You can change this property in Beanshell or using Tools > Device Property Browser, if is this property is made "public". Check the Device Property Browser, you may find it there.

Nikita

On 26/11/2018 13:04, [hidden email] wrote:
Thank you, Nikita. I am assuming that this is the only way to get smaller step size. I.e., no Beanshell means to do this. In that case, I will follow your lead and do the same for the Prior Stage.

-- 
Nikita Vladimirov, PhD

Preibisch Lab
Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrück Center for Molecular Medicine (MDC)
Robert-Rössle-Str. 10
Bld. 89, room 1.08
13125 Berlin
twitter.com/nvladimus
github.com/nvladimus


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