Device drivers

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Device drivers

Knecht, David
I am trying to set up a system to work with Micro-Manager: Sutter DG4/Zeiss Axiovert 200M/Uniblitz transmittted shutter and have several questions:
1.  Is there a list of the descriptions of the device properties somewhere?  I don't know what all the labels mean and what they control, so it would make setup much easier if these were detailed somewhere.  If not, I can provide the answers for these devices now that I have played with them if we can establish a repository somewhere.  It would also be nice for this to also list the combinations necessary: for instance I found for the DG4 to turn off and on correctly, you need to select the DG4 shutter state and the DG4 wheel label, even though those two things have no meaning with a DG4 (both are a single galvanometer movement).
2.  The Zeiss Z drive has a group property, but it does not give position feedback as you move the focus.  Is it supposed to?
3.  Can the autoshutter be made to turn something specific (Zeiss fluorescence shutter, etc.) off and on automatically when you go from Live to Stop?
4.  Can the intensity of the Zeiss halogen lamp (as opposed to off/on) be controlled through the software?
(#2 and 4 should work since they can be controlled in Openlab)
Thanks- Dave

Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)



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Re: Device drivers

Nico Stuurman
Administrator

> I am trying to set up a system to work with Micro-Manager: Sutter DG4/Zeiss Axiovert 200M/Uniblitz transmittted shutter and have several questions:
> 1.  Is there a list of the descriptions of the device properties somewhere?  I don't know what all the labels mean and what they control, so it would make setup much easier if these were detailed somewhere.  If not, I can provide the answers for these devices now that I have played with them if we can establish a repository somewhere.  

The Device Adapter wiki ( https://valelab.ucsf.edu/~nico/MMwiki/index.php/Device_Support ) is the place for his information.  We encourage device adapter authors to maintain all possible information about the device and adapter here.  A nice example is the Andor camera adapter ( https://valelab.ucsf.edu/~nico/MMwiki/index.php/Andor ).  

However, note that everyone can make themselves an account (top right corner of the wiki) which gives them to power to edit any of these pages.  Please do go ahead and provide the information you would have found useful at the SutterLambda page.

> 2.  The Zeiss Z drive has a group property, but it does not give position feedback as you move the focus.  Is it supposed to?

I don't know what a group property is, but you will see the actual position of the Z drive listed in the bottom of the main window after pressing the "Refresh" button.

> 3.  Can the autoshutter be made to turn something specific (Zeiss fluorescence shutter, etc.) off and on automatically when you go from Live to Stop?

I probably misunderstand your question, but this is exactly what the AutoShutter checkbox is supposed to do.  It will open the active shutter (the one you select in the shutter dropdown box) before you start live or snap an image and close the shutter when you are done.  

> 4.  Can the intensity of the Zeiss halogen lamp (as opposed to off/on) be controlled through the software?
> (#2 and 4 should work since they can be controlled in Openlab)

Halogen Lamp Intensity is not implemented for the ZeissCAN adapter.  I have always found it much easier to use that button on the front of the microscope than have some kind of slider.

Any particular reason for wanting that control?

Best,

Nico
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Re: Device drivers

Knecht, David

On Feb 12, 2010, at 3:41 PM, Nico Stuurman wrote:

>
>> I am trying to set up a system to work with Micro-Manager: Sutter DG4/Zeiss Axiovert 200M/Uniblitz transmittted shutter and have several questions:
>> 1.  Is there a list of the descriptions of the device properties somewhere?  I don't know what all the labels mean and what they control, so it would make setup much easier if these were detailed somewhere.  If not, I can provide the answers for these devices now that I have played with them if we can establish a repository somewhere.  
>
> The Device Adapter wiki ( https://valelab.ucsf.edu/~nico/MMwiki/index.php/Device_Support ) is the place for his information.  We encourage device adapter authors to maintain all possible information about the device and adapter here.  A nice example is the Andor camera adapter ( https://valelab.ucsf.edu/~nico/MMwiki/index.php/Andor ).  
>
> However, note that everyone can make themselves an account (top right corner of the wiki) which gives them to power to edit any of these pages.  Please do go ahead and provide the information you would have found useful at the SutterLambda page.
>
>> 2.  The Zeiss Z drive has a group property, but it does not give position feedback as you move the focus.  Is it supposed to?
>
> I don't know what a group property is, but you will see the actual position of the Z drive listed in the bottom of the main window after pressing the "Refresh" button.
Yes, that works sometimes.  NOt sure yet why not always.  In Openlab you can control the Z position and get continuous readout of position with teh Serial interface so I presumed it would be the same here. Not a big deal as long as the position is recorded with metadata.
>
>> 3.  Can the autoshutter be made to turn something specific (Zeiss fluorescence shutter, etc.) off and on automatically when you go from Live to Stop?
>
> I probably misunderstand your question, but this is exactly what the AutoShutter checkbox is supposed to do.  It will open the active shutter (the one you select in the shutter dropdown box) before you start live or snap an image and close the shutter when you are done.  
You understood.  I did not realize that the Shutter pull down tab was linked to the Autoshutter control.  So now I am unsure how to set up the shutters. I have a Vincent D1 controlling transmitted, an internal Zeiss fluorescence shutter, and the DG4 has something called a shutter even though there is no shutter (it just blanks the light).  What is the relationship between the Core shutter device and the other shutters in terms of setting up the group?  In my channels group, do I activate the Core, Zeiss, Vincent and DG4?  WHen I did this, the autoshutter for the Vincent ceased to work.  Another complication is that the Zeiss automatically opens its fluorescence shutter when you switch the reflector turret to a fluorescence cube, so perhaps that shutter does not need to be part of the channel group?  Can I automatically switch what autoshutter is controlling when I choose  a channel and when you switch between fluorescence and transmitted modes and go live?
>
>> 4.  Can the intensity of the Zeiss halogen lamp (as opposed to off/on) be controlled through the software?
>> (#2 and 4 should work since they can be controlled in Openlab)
>
> Halogen Lamp Intensity is not implemented for the ZeissCAN adapter.  I have always found it much easier to use that button on the front of the microscope than have some kind of slider.
Openlab can control this through serial.  I had presumed the drivers were the same, but perhaps not.  Not a big deal- I agree the microscope button is easy to use.

>
> Any particular reason for wanting that control?
>
> Best,
>
> Nico
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> SOLARIS 10 is the OS for Data Centers - provides features such as DTrace,
> Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)



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Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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Re: Device drivers

Nico Stuurman-4
>>> 3.  Can the autoshutter be made to turn something specific (Zeiss  
>>> fluorescence shutter, etc.) off and on automatically when you go  
>>> from Live to Stop?
>>
>> I probably misunderstand your question, but this is exactly what  
>> the AutoShutter checkbox is supposed to do.  It will open the  
>> active shutter (the one you select in the shutter dropdown box)  
>> before you start live or snap an image and close the shutter when  
>> you are done.
> You understood.  I did not realize that the Shutter pull down tab  
> was linked to the Autoshutter control.

The logic is as follows: Micro-Manager knows about one shutter only  
(Core-Shutter).  You can set this (active) shutter with the shutter  
drop-down box or by directly manipulating the Core-Shutter property  
(which you might be doing in your Configuration Presets).  The  
Autoshutter functionality will open the Core-Shutter before exposure  
and close it afterwards.

> So now I am unsure how to set up the shutters. I have a Vincent D1  
> controlling transmitted, an internal Zeiss fluorescence shutter, and  
> the DG4 has something called a shutter even though there is no  
> shutter (it just blanks the light).  What is the relationship  
> between the Core shutter device and the other shutters in terms of  
> setting up the group?  In my channels group, do I activate the Core,  
> Zeiss, Vincent and DG4?

What do you mean with activating the "Core"?  I assume that you have a  
"Core-Shutter" property in you "Channels" group which you set to  
either your Zeiss, Vincent or DG4 shutter.

> WHen I did this, the autoshutter for the Vincent ceased to work.

What did you do?  Set Core-Shutter back to Vincent, and it will be  
auto-shuttered.

> Another complication is that the Zeiss automatically opens its  
> fluorescence shutter when you switch the reflector turret to a  
> fluorescence cube, so perhaps that shutter does not need to be part  
> of the channel group?

If I am not mistaken, this functionality is caused by the microscope's  
"LightManager".  The Zeiss LightManager might be nice for interactive  
work with the microscope, but it really complicates things when  
controlling the microscope from a computer (there are too many  semi-
intelligent entities at work) and I always switch off the  
LightManager.  You can either do this using some mysterious key-
presses on the microscope itself (see the manual), or there might be a  
LightManager property with one of the ZeissCAN devices.

> Can I automatically switch what autoshutter is controlling when I  
> choose  a channel and when you switch between fluorescence and  
> transmitted modes and go live?

Absolutely!  AutoShutter always controls the Core-Shutter, and nothing  
else.


Best,

Nico


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