Vincent D3 shutter

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Vincent D3 shutter

Dirk Landgraf
Hi Nico,

we got a Vincent D3 shutter to independently control 3 laser lines  
with our Nikon Ti. Micro-manager recognizes the Vincent shutter and we  
are able to open and close all three channels by changing the property  
"Vincent-D3-Channel #" in the property browser to either 1, 2, 3 or all.

Now, we would like to define different presets (e.g. acquisition with  
488 laser or acquisition with 405 laser) that allow us to e.g. open  
shutter 1 or only shutter 2 that control the different lasers but I  
can't select the property "Vincent-D3-Channel #" when using the Preset  
editor. The only Vincent option the Preset editor has, is "Vincent-D3-
Command" open/close. This would be enough for controlling one line but  
not all three.

Is it possible to change this? It would be very useful if the property  
"Vincent-D3-Channel #" would also be included in the Preset editor  
otherwise it would be impossible to use the three channels of the  
Vincent shutter (i.e. the three laser lines) in e.g. a time-lapse  
experiment.

I know how to workaround this problem in Matlab but we would like to  
have this working Micro-manager. Do you have any idea how to change  
this?

Thanks a lot. Dirk






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Re: Vincent D3 shutter

Nico Stuurman-4
Hi Rick,

> we got a Vincent D3 shutter to independently control 3 laser lines
> with our Nikon Ti. Micro-manager recognizes the Vincent shutter and we
> are able to open and close all three channels by changing the property
> "Vincent-D3-Channel #" in the property browser to either 1, 2, 3 or  
> all.
>
> Is it possible to change this? It would be very useful if the property
> "Vincent-D3-Channel #" would also be included in the Preset editor
> otherwise it would be impossible to use the three channels of the
> Vincent shutter (i.e. the three laser lines) in e.g. a time-lapse
> experiment.

I think that the rational for this approach was to make multiple  
shutters, one for each "channel".  Let me know if that works,  
otherwise I'll make this a normal property (in which case you should  
let mw know - off-list - what OS you use so that I can send you an  
adapter to test).

Best,

Nico



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Re: Vincent D3 shutter

Nico Stuurman-4
In reply to this post by Dirk Landgraf
Hi Dirk,

> thanks a lot for this suggestion. It worked great.

Good to hear!  I added this to the Wiki.

> I have one more question. I am trying to do very fast z stacks with  
> our Nikon Ti (13 planes, 0.2 um steps, 100 ms exposure and 2x2  
> binning) and I was able to reduce the time for the whole z-stack to  
> 7-8 seconds (without using a Piezo stage insert).
>
> The only problem now is that moving the z position by 0.2 um can  
> take very long (up to 800 ms) or be very fast (70 ms). This  
> variability is small problem for my experiment. I figured out that  
> the z stepper motor of the Nikon Ti is the culprit. Is there a way  
> to make the z motor more reliable without compromising speed? It  
> should be easy to always make it wait 1 second but thats not what I  
> want.

Are you certain that the Z-drive is the culprit?  You could use a  
Beanshell script to time the movements of the Z-drive.  There are some  
examples in the scripts directory.  Especially the scripts names  
mm_test_* should be helpful to time different aspects of the  
acquisition.

Once we have our TI working, I'll do some testing here as well.

Best,

Nico

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xy-stage calibration

Dirk Landgraf
In reply to this post by Nico Stuurman-4
Hi Nico,

I have a question about calibration of the XY stage in micro-manager.  
If I tell micro-manager to move the XY stage by e.g. 10 micron, the  
stage moves by ~ 5.4 micron. What is the correct procedure to  
calibrate the XY stage in micro-manager?

Thanks a lot. Dirk




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Re: xy-stage calibration

Nico Stuurman-4
Hi Dirk,

> I have a question about calibration of the XY stage in micro-manager.
> If I tell micro-manager to move the XY stage by e.g. 10 micron, the
> stage moves by ~ 5.4 micron. What is the correct procedure to
> calibrate the XY stage in micro-manager?

There is no procedure for distance calibration in Micro-Manager.  The  
Micro-Manager adapter for you stage should take care of this.  
Apparently, it does not do so properly.  Some adapters have properties  
that affect the relation between stepsize and micrometers.  Others  
have settings in the controller itself that might influence that same  
property.  What stage are you using?

Best,

Nico



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Re: xy-stage calibration

Dirk Landgraf
Hi Nico,

I am using the inverted BioPrecision2 stage (99S106-LE2, http://www.ludl.com/Default.aspx?tabid=91)
  from Ludl.

Thanks, Dirk



On Dec 16, 2009, at 2:57 PM, Nico Stuurman wrote:

> Hi Dirk,
>
>> I have a question about calibration of the XY stage in micro-manager.
>> If I tell micro-manager to move the XY stage by e.g. 10 micron, the
>> stage moves by ~ 5.4 micron. What is the correct procedure to
>> calibrate the XY stage in micro-manager?
>
> There is no procedure for distance calibration in Micro-Manager.  The
> Micro-Manager adapter for you stage should take care of this.
> Apparently, it does not do so properly.  Some adapters have properties
> that affect the relation between stepsize and micrometers.  Others
> have settings in the controller itself that might influence that same
> property.  What stage are you using?
>
> Best,
>
> Nico
>
>
>
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Re: xy-stage calibration

Nico Stuurman
Administrator
Hi Dirk,

> I am using the inverted BioPrecision2 stage (99S106-LE2, http://www.ludl.com/Default.aspx?tabid=91)
>  from Ludl.

The Ludl Micro-Manager XYStage adapter has the "StepSize" property.  It is set by default at 0.1 um.  You can change it so that it matches what you expect (presumably, you'll need to set it to 0.054 um).  You can set this value on Micro-Manager startup by including it in the System->Startup group.  Alternatively, you can set the Microsteps per revolution in your controller (this is done with dipswitches in the Mac5000 controller).  

Best,

Nico


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