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filter wheel as shutter

Dirk Landgraf
Hi Nico,

I would like to use the filter wheel as a shutter for the fluorescence light path. Basically I am sending 488 nm light in the microscope and direct this light towards the sample by having the GFP filter cube in place. Since I don't have a fluorescence shutter, I would like to stop exposure by moving the filter wheel to an empty position. 

I found an earlier email from you to the micro-manager mailing in which you say that one could use the "State Device Shutter" for such a purpose if I understand you correctly. I installed the "State Device Shutter" from the "Utilities" library but I can't find the property for the "ClosedPosition". Do you have any idea what I might be doing wrong?

I am using Micro-manger 1.3.41 in combination with a Nikon Ti.

Also, can I get the adapter for the Lumencor LED system from you or do I have to contact Lumencor. They state on the company webpage that their LED system offers Micro-manager support. See last page -> "software platforms" of the PDF that you can find here:

Thanks a lot. Greetings, Dirk







Hi Jorge, 


> I am trying to set up a Lambda10-2 filter wheel (there is no shutter 
> available) to capture image sequences keeping the cells without 
> illumination while not getting images. To do this I need to place the 
> wheel in a different position during the loop of acquisition. Going 
> through the setup of options of the group presets I cannot find a way 
> to do this. Where should I look for it? 

To do this, you need to add the virtual "Sate Device Shutter" to your   
configuration.  Go to the Hardware Configuration Wizard, and in step 3   
add the "State Device Shutter" from the "Utilities" library.  After   
saving the configuration, go to the Property Browser (in the Tools   
menu).  Here, you need to select the device controlled by the State   
Device Shutter, so select your 10-2.  Also, you will need to specify   
for your 10-2 what the "ClosedPosition" is.  Once you have this all   
set up correctly, you might want to make this the default on startup   
(see: http://micro-manager.org/documentation.php?object=Configguide#Startup%20Preset  
  ). 

 From now on, the state device shutter should work as any other   
shutter.  You can use the button in the front panel to open and close   
it, check the autoshutter checkbox for the shutter to open   
automatically when you take an image, and also to open automatically   
during a multi-dimensional acquisition ( http://micro-manager.org/documentation.php?object=Userguide#mozTocId402840  
  ). 

This mechanism is not widely used, so you might experience problems.   
If so, please report these back here. 

Best, 

Nico 

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Re: filter wheel as shutter

Nico Stuurman
Administrator
Hi Dirk,

I would like to use the filter wheel as a shutter for the fluorescence light path. Basically I am sending 488 nm light in the microscope and direct this light towards the sample by having the GFP filter cube in place. Since I don't have a fluorescence shutter, I would like to stop exposure by moving the filter wheel to an empty position. 

I found an earlier email from you to the micro-manager mailing in which you say that one could use the "State Device Shutter" for such a purpose if I understand you correctly. I installed the "State Device Shutter" from the "Utilities" library but I can't find the property for the "ClosedPosition". Do you have any idea what I might be doing wrong?

I am using Micro-manger 1.3.41 in combination with a Nikon Ti.

The property "Closed Position" should be implemented by the adapter.  Currently, the Olympus and Leica microscopes, as well as ASIFW1000, and Sutter filter wheels implement this property.  I'll add it to the Nikon TI adapter.


Also, can I get the adapter for the Lumencor LED system from you or do I have to contact Lumencor. They state on the company webpage that their LED system offers Micro-manager support. See last page -> "software platforms" of the PDF that you can find here:
<a href="http://www.lumencor.com/docs/Lumencor LE Brochure.pdf">http://www.lumencor.com/docs/Lumencor%20LE%20Brochure.pdf

Cool if they wrote that code, but this is the first I hear about it.  Best to ask them.

Best,

Nico


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Re: filter wheel as shutter

U. Serdar Tulu
Hi,
 
I had the same issue yesterday that I had to use filter wheel as a shutter. Lambda 10-2 is shuttering our system now. I did it successfully. It was right on time. Thanks Nico and Dirk.
 
My best,
Serdar

Sent: Friday, April 23, 2010 6:52 PM
Subject: Re: [micro-manager-general] filter wheel as shutter

Hi Dirk,

I would like to use the filter wheel as a shutter for the fluorescence light path. Basically I am sending 488 nm light in the microscope and direct this light towards the sample by having the GFP filter cube in place. Since I don't have a fluorescence shutter, I would like to stop exposure by moving the filter wheel to an empty position. 

I found an earlier email from you to the micro-manager mailing in which you say that one could use the "State Device Shutter" for such a purpose if I understand you correctly. I installed the "State Device Shutter" from the "Utilities" library but I can't find the property for the "ClosedPosition". Do you have any idea what I might be doing wrong?

I am using Micro-manger 1.3.41 in combination with a Nikon Ti.

The property "Closed Position" should be implemented by the adapter.  Currently, the Olympus and Leica microscopes, as well as ASIFW1000, and Sutter filter wheels implement this property.  I'll add it to the Nikon TI adapter.


Also, can I get the adapter for the Lumencor LED system from you or do I have to contact Lumencor. They state on the company webpage that their LED system offers Micro-manager support. See last page -> "software platforms" of the PDF that you can find here:
<A href="http://www.lumencor.com/docs/Lumencor LE Brochure.pdf">http://www.lumencor.com/docs/Lumencor%20LE%20Brochure.pdf

Cool if they wrote that code, but this is the first I hear about it.  Best to ask them.

Best,

Nico


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Re: filter wheel as shutter

tomib
In reply to this post by Nico Stuurman
Hi Nico,
in an older post you wrote:
Nico Stuurman wrote

The property "Closed Position" should be implemented by the adapter.  Currently, the Olympus and Leica microscopes, as well as ASIFW1000, and Sutter filter wheels implement this property.  I'll add it to the Nikon TI adapter.

Best,
Nico
Does that in fact mean, that only special devices or adapter can be used with the 'State Device Shutter'?
I'm asking, because we have a bit weird device, which I can start with the arduino bord eg. pin08 set to 5V and to stop I can just use a 'reset' command, where I just put another pin (eg. pin09) to 5V.

 So I would like to use this with the DeviceShutter and tried to define one as ClosedPosition, but I could not make it to work.

Or do I rather misunderstand the whole concept and there are maybe other (easier) solutions?

Thanks for help

Thomas
--
~~~~~~~~~~~~
Thomas Breitenbach, Post Doc
Dept. of Chemistry, University of Aarhus, Denmark
web: http://www.chem.au.dk/~comi
~~~~~~~~~~~~
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Re: filter wheel as shutter

Nico Stuurman-2
Hi THomas,

> Nico Stuurman wrote
>>
>> The property "Closed Position" should be implemented by the adapter.  Currently, the Olympus and Leica microscopes, as well as ASIFW1000, and Sutter filter wheels implement this property.  I'll add it to the Nikon TI adapter.
>
> Does that in fact mean, that only special devices or adapter can be used with the 'State Device Shutter'?

Correct.  The device needs to implement this feature.

> I'm asking, because we have a bit weird device, which I can start with the arduino bord eg. pin08 set to 5V and to stop I can just use a 'reset' command, where I just put another pin (eg. pin09) to 5V.
>
> So I would like to use this with the DeviceShutter and tried to define one as ClosedPosition, but I could not make it to work.
>
> Or do I rather misunderstand the whole concept and there are maybe other (easier) solutions?

That should indeed work as you planned if the Arduino device adapter supports the "Closed Position" property (which it currently does not).  Let me know if you are interested in adding that yourself.  If you are not a programmer, I can have a look (but that will take a while to get to).

Best,

Nico




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RE: filter wheel as shutter

tomib
This post was updated on .
Dear Nico,
unfortunately, I'm not a programmer, but have some insights.
If it could be done by myself and there's a guidance available, I would love to try, but this seems to be a bit more 'deep-going'. I do not want to cause trouble or work to you guys, which is not necessary.

Could you imagine another possibility to make this work?
It is actually a) an old drug-application-device which is accepting the mentioned 'trigger' from arduino to start and re-set it back from start, b) a home-made motorised grating, which then choose the wavelength towards a PMT by the time the command is on.

Thanks a lot for your help and (in general) for the lot of work you made.

Best

Thomas

--

~~~~~~~~~~
Thomas Breitenbach, PhD, senior research fellow
Dept. of Chemistry, University of Aarhus
Langelandsgade 140, room 1511 - 229
DK- 8000 Aarhus C
--
~~~~~~~~~~~~
Thomas Breitenbach, Post Doc
Dept. of Chemistry, University of Aarhus, Denmark
web: http://www.chem.au.dk/~comi
~~~~~~~~~~~~
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Re: filter wheel as shutter

fjsim
In reply to this post by Nico Stuurman-2
Dear Nico,

I've run into the same problem with a Prior filter wheel which we'd like to use as a shutter on our scope. I don't think the Prior device implements the "Closed Position" property for the filter wheel.

I checked in the source code file at "https://valelab.ucsf.edu/svn/micromanager2/trunk/DeviceAdapters/Prior/Prior.cpp". I couldn't find reference to "Closed position" as I could in "https://valelab.ucsf.edu/svn/micromanager2/trunk/DeviceAdapters/SutterLambda/SutterLambda.cpp" as you mentioned in the old email.

Would the approach be to modify the "Prior.cpp" file to add the Closed Position property to the initialize portion of the wheel and then modify the action handler OnState?

I'm not that familiar with this type of programming but could give it a try.

Cheers,
Fraser
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Re: filter wheel as shutter

Mark Tsuchida-2
Hi Fraser,

On Tue, Aug 18, 2015 at 1:24 PM, fjsim <[hidden email]> wrote:

> I've run into the same problem with a Prior filter wheel which we'd like to
> use as a shutter on our scope. I don't think the Prior device implements the
> "Closed Position" property for the filter wheel.
>
> I checked in the source code file at
> "https://valelab.ucsf.edu/svn/micromanager2/trunk/DeviceAdapters/Prior/Prior.cpp".
> I couldn't find reference to "Closed position" as I could in
> "https://valelab.ucsf.edu/svn/micromanager2/trunk/DeviceAdapters/SutterLambda/SutterLambda.cpp"
> as you mentioned in the old email.
>
> Would the approach be to modify the "Prior.cpp" file to add the Closed
> Position property to the initialize portion of the wheel and then modify the
> action handler OnState?

Yes indeed, and I've made the necessary changes (should be available
in the next (20150818) nightly build). Please let me know if it works!

Best,
Mark

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RE: filter wheel as shutter

fjsim

Hi Mark,

 

I tried it this morning and it works well. I was able to set the closed position and MM can open/close the shutter by moving the filter wheel. The only issue I have run into is that the configuration file doesn’t seem able to set the “State Device” property of the “State Device Shutter” when it loads. I have to manually go in and set it after loading. Even if I then save the configuration it is not stored so that when I launch MM again the property is set to “none”.

 

I think it has something to do with the space being in the name of the property. I have tried putting State Device in “”, with and without a space, using an underscore but to no avail. On loading the config, I get an error message basically says the property name is invalid. If I comment out that line, it loads fine but I need to set the State Device in the property browser. Any ideas?

 

Cheers,

Fraser

 

From: Mark Tsuchida-2 [via Micro-Manager] [mailto:ml-node+[hidden email]]
Sent: Tuesday, August 18, 2015 6:31 PM
To: Sim, Fraser <[hidden email]>
Subject: Re: filter wheel as shutter

 

Hi Fraser,

On Tue, Aug 18, 2015 at 1:24 PM, fjsim <[hidden email]> wrote:


> I've run into the same problem with a Prior filter wheel which we'd like to
> use as a shutter on our scope. I don't think the Prior device implements the
> "Closed Position" property for the filter wheel.
>
> I checked in the source code file at
> "https://valelab.ucsf.edu/svn/micromanager2/trunk/DeviceAdapters/Prior/Prior.cpp".
> I couldn't find reference to "Closed position" as I could in
> "https://valelab.ucsf.edu/svn/micromanager2/trunk/DeviceAdapters/SutterLambda/SutterLambda.cpp"
> as you mentioned in the old email.
>
> Would the approach be to modify the "Prior.cpp" file to add the Closed
> Position property to the initialize portion of the wheel and then modify the
> action handler OnState?


Yes indeed, and I've made the necessary changes (should be available
in the next (20150818) nightly build). Please let me know if it works!

Best,
Mark

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Re: filter wheel as shutter

Mark Tsuchida-2
Hi Fraser,

On Wed, Aug 19, 2015 at 6:40 AM, fjsim <[hidden email]> wrote:
> I tried it this morning and it works well. I was able to set the closed
> position and MM can open/close the shutter by moving the filter wheel. The
> only issue I have run into is that the configuration file doesn’t seem able
> to set the “State Device” property of the “State Device Shutter” when it
> loads. I have to manually go in and set it after loading. Even if I then
> save the configuration it is not stored so that when I launch MM again the
> property is set to “none”.

Great, thanks for confirming.

To automatically set the closed position property, it is best to use
the System-Startup configuration preset method.

Create a configuration group named "System" (exactly), and add the
closed position property (and at least one other property that you
want to set at startup time -- it works best when you have at least
two properties). Then name the first preset "Startup" (exactly), and
set the correct values.

This specially named config group and preset are recognized by MM and
applied after loading the hardware configuration.

> I think it has something to do with the space being in the name of the
> property. I have tried putting State Device in “”, with and without a space,
> using an underscore but to no avail. On loading the config, I get an error
> message basically says the property name is invalid. If I comment out that
> line, it loads fine but I need to set the State Device in the property
> browser. Any ideas?

Do you mean you are manually editing the config file? If so I would
need to see the file (or at least where and what line you added) to
tell what's going on. But hopefully the above method will eliminate
the need to manually edit the config file.

Best,
Mark

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RE: filter wheel as shutter

fjsim

Thanks. That fix worked. Using the System>Startup configuration group worked great. Cheers, Fraser

 

From: Mark Tsuchida-2 [via Micro-Manager] [mailto:ml-node+[hidden email]]
Sent: Wednesday, August 19, 2015 2:11 PM
To: Sim, Fraser <[hidden email]>
Subject: Re: filter wheel as shutter

 

Hi Fraser,

On Wed, Aug 19, 2015 at 6:40 AM, fjsim <[hidden email]> wrote:
> I tried it this morning and it works well. I was able to set the closed
> position and MM can open/close the shutter by moving the filter wheel. The
> only issue I have run into is that the configuration file doesn’t seem able
> to set the “State Device” property of the “State Device Shutter” when it
> loads. I have to manually go in and set it after loading. Even if I then
> save the configuration it is not stored so that when I launch MM again the
> property is set to “none”.

Great, thanks for confirming.

To automatically set the closed position property, it is best to use
the System-Startup configuration preset method.

Create a configuration group named "System" (exactly), and add the
closed position property (and at least one other property that you
want to set at startup time -- it works best when you have at least
two properties). Then name the first preset "Startup" (exactly), and
set the correct values.

This specially named config group and preset are recognized by MM and
applied after loading the hardware configuration.

> I think it has something to do with the space being in the name of the
> property. I have tried putting State Device in “”, with and without a space,
> using an underscore but to no avail. On loading the config, I get an error
> message basically says the property name is invalid. If I comment out that
> line, it loads fine but I need to set the State Device in the property
> browser. Any ideas?

Do you mean you are manually editing the config file? If so I would
need to see the file (or at least where and what line you added) to
tell what's going on. But hopefully the above method will eliminate
the need to manually edit the config file.

Best,
Mark

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Re: filter wheel as shutter

Konstanz
In reply to this post by Dirk Landgraf
Hi,
I still didn't resolve the issue with filter wheel "Closed Position".
I have also a Lambda10-2 filter wheel. I'm recording a time series in Muliti-D Acq mode.
Actually, I have an option "Closed Position". However, the filter doesn't switch to close position and cells are still illuminated till the end of experiment.

I don't have any other shutters, I can't find "State Device Shutter" & yes, I'm not the programmer.

Any suggestion?
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Re: filter wheel as shutter

Nico Stuurman-2
On 3/29/2017 7:13 AM, Konstanz wrote:
> I still didn't resolve the issue with filter wheel "Closed Position".
>
> Actually, I have an option "Closed Position". However, the filter doesn't
> switch to close position and cells are still illuminated till the end of
> experiment.
>
> I don't have any other shutters, I can't find "State Device Shutter" & yes,

That is the key question.  In step 2 of the Hardware Configuration
Wizard, (under the Tools menu in 1.4 or the Config menu in 2.0), find
the "Utilities" module.  That module contains the "State Device
Shutter".  You will also need to set the property "State Device Shutter
- State Device" to the wheel that you want to use as a shutter.  Best to
add that to your System-Startup group, so that you do not need to do
that every time.

Best,

Nico


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