Taking multi images at different z

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Taking multi images at different z

Cecile Cottin-Bizonne
Hello,

I am using MM with a microscope LEICA a piezo PI and a camera Hamamatsu
ORCA.
I can finely recognize each of those devices, but I do not manage to
make a multiacquisition in the following way:
- Take N (N beeing equal to 10 for instance) images at a given z position
- Move to the next z position, take another N images
and so on...

Could anyone help me on how to do this multi-image z stack acquisition ?
If a script is required, it would be nice to get an example.
Thanks for your help !

cecile

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Re: Taking multi images at different z

Nico Stuurman-4
> I am using MM with a microscope LEICA a piezo PI and a camera  
> Hamamatsu
> ORCA.
> I can finely recognize each of those devices, but I do not manage to
> make a multiacquisition in the following way:
> - Take N (N beeing equal to 10 for instance) images at a given z  
> position
> - Move to the next z position, take another N images
> and so on...

Why do you want to do this?

> Could anyone help me on how to do this multi-image z stack  
> acquisition ?

You could set up your z-positions in the Position List.  To so,  
uncheck the XY stage in the bottom of the list, and click mark for  
each Z-position.  To move between z-positions write the one line script:
        mmc.setRelativePosition(mmc.getFocusDevice(), 1);
And change "1" to whatever you want the distance between the slices to  
be.  Then set up your desired time points, uncheck z-stack, set up  
your Acquisition Order as "Time First" (be sure to save your images  
somewhere).

Best,

Nico

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Re: Taking multi images at different z

Cecile Cottin-Bizonne
In reply to this post by Cecile Cottin-Bizonne
Thanks for your answer,
I tried what you suggested but I still have few issues.

With your solution, if I want to take N images at each P positions, the
way it works is that it takes one image at each Position and then redo
this N times. What I would like to do is make N images at one position
AND move at the next position and take again N images, and move again at
the next position and take N images and this till the last P position.
Any idea of how I could do this ?

FYI I do this to study sedimentation profiles of colloids.

Thanks a lot for your help!

cecile

 > I am using MM with a microscope LEICA a piezo PI and a camera
 > Hamamatsu
 > ORCA.
 > I can finely recognize each of those devices, but I do not manage to
 > make a multiacquisition in the following way:
 > - Take N (N beeing equal to 10 for instance) images at a given z
 > position
 > - Move to the next z position, take another N images
 > and so on...

Why do you want to do this?

 > Could anyone help me on how to do this multi-image z stack
 > acquisition ?

You could set up your z-positions in the Position List. To so,
uncheck the XY stage in the bottom of the list, and click mark for
each Z-position. To move between z-positions write the one line script:
mmc.setRelativePosition(mmc.getFocusDevice(), 1);
And change "1" to whatever you want the distance between the slices to
be. Then set up your desired time points, uncheck z-stack, set up
your Acquisition Order as "Time First" (be sure to save your images
somewhere).

Best,

Nico

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Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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Re: Taking multi images at different z

Philippe GENDRE
Hello Cécile,

Try this basic attached script (I have tested it with democamera).

Copy it into the "scripts" folder of Micro-Manager and run it from Tools>Script Panel.

Don't forget to enter the right values for the size and bit depth of your live picture (for imgStack initialization).

Best regards,

Philippe

2010/2/17 Cecile Cottin-Bizonne <[hidden email]>
Thanks for your answer,
I tried what you suggested but I still have few issues.

With your solution, if I want to take N images at each P positions, the
way it works is that it takes one image at each Position and then redo
this N times. What I would like to do is make N images at one position
AND move at the next position and take again N images, and move again at
the next position and take N images and this till the last P position.
Any idea of how I could do this ?

FYI I do this to study sedimentation profiles of colloids.

Thanks a lot for your help!

cecile

 > I am using MM with a microscope LEICA a piezo PI and a camera
 > Hamamatsu
 > ORCA.
 > I can finely recognize each of those devices, but I do not manage to
 > make a multiacquisition in the following way:
 > - Take N (N beeing equal to 10 for instance) images at a given z
 > position
 > - Move to the next z position, take another N images
 > and so on...

Why do you want to do this?

 > Could anyone help me on how to do this multi-image z stack
 > acquisition ?

You could set up your z-positions in the Position List. To so,
uncheck the XY stage in the bottom of the list, and click mark for
each Z-position. To move between z-positions write the one line script:
mmc.setRelativePosition(mmc.getFocusDevice(), 1);
And change "1" to whatever you want the distance between the slices to
be. Then set up your desired time points, uncheck z-stack, set up
your Acquisition Order as "Time First" (be sure to save your images
somewhere).

Best,

Nico

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Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW
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Re: Taking multi images at different z

Nico Stuurman-4
In reply to this post by Cecile Cottin-Bizonne
> With your solution, if I want to take N images at each P positions,  
> the
> way it works is that it takes one image at each Position and then redo
> this N times. What I would like to do is make N images at one position
> AND move at the next position and take again N images, and move  
> again at
> the next position and take N images and this till the last P position.
> Any idea of how I could do this ?

Did you set the Acquisition Order drop-down to "Time first"?  With  
that setting, the acquisition behaves as you desire.

Best,

Nico

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