Z position in XYZ Time-lapse acquisition order

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Z position in XYZ Time-lapse acquisition order

Paula Sampaio
Hi Nico,

I was testing my new motorized stage and noticed that in
multidimensional acquisition with different positions in XYZ there is a
problem in Z focusing in Time-lapse acquisition order. If I use the
Multi-field order each image is taken at the correct Z, but in
Time-lapse it uses always the same Z, which is the current position at
beginning of the acquisition. This occurs both with PRIOR NanoZ scan or
Zeiss microscope focus. Could be this a bug?  I'm running the MM Studio
version: 1.3.43 MMCore version 2.3.1 Device API version 33, Module API
version 4.

Thank you very much.

Best regards,

Paula


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IBMC - Instituto de Biologia Molecular e Celular
Universidade do Porto
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PORTUGAL

Tel: +351 226074900  Ext: 1606
Fax: +351 226099157
email: [hidden email]
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Re: [micro-manager-general] Z position in XYZ Time-lapse acquisition order

Nico Stuurman-4
Hi Paula,

> I was testing my new motorized stage and noticed that in
> multidimensional acquisition with different positions in XYZ there  
> is a
> problem in Z focusing in Time-lapse acquisition order. If I use the
> Multi-field order each image is taken at the correct Z, but in
> Time-lapse it uses always the same Z, which is the current position at
> beginning of the acquisition. This occurs both with PRIOR NanoZ scan  
> or
> Zeiss microscope focus. Could be this a bug?  I'm running the MM  
> Studio
> version: 1.3.43 MMCore version 2.3.1 Device API version 33, Module API
> version 4.

There have been many tweaks to this part of the code, and I was under  
the impression that it works quite well.  You can try the latest  
nightly build ( http://valelab.ucsf.edu/~MM/nightlyBuilds/1.3 ) to  
check if we happen to have fixed this problem already.

Also, there are many factors that affect the behavior (for instance:  
do you use relative or absolute z in the z-stack section of the MDA  
dialog, do you include the z-drive in the positionlist using the  
checkboxes in the bottom of the position list), and you can give us  
some more insights in how you are setting up the acquisition by  
sending us the acquisition.xml file (save it from the MDA dialog or  
find it with your saved data), nevertheless, since you say the  
behavior is different between multi-field and time-lapse modes it does  
sound like a bug.

In general, we are most helped if you can give us a clear example of a  
bug that makes use of the Demo equipment.  That way, we have the best  
chance of reproducing the problem greatly facilitating fixing it.

Best regards,

Nico


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world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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Re: [micro-manager-general] Z position in XYZ Time-lapse acquisition order

Arthur D. Edelstein
Hi Paula,

I think the bug you report was corrected on Jan 4. The latest nightly
build should contain this correction. Please let us know if you still
find a problem.

http://valelab.ucsf.edu/~MM/nightlyBuilds/1.3

Thanks for reporting this bug!

Best regards,
Arthur



On Wed, Jan 20, 2010 at 8:58 AM, Nico Stuurman <[hidden email]> wrote:

> Hi Paula,
>
>> I was testing my new motorized stage and noticed that in
>> multidimensional acquisition with different positions in XYZ there
>> is a
>> problem in Z focusing in Time-lapse acquisition order. If I use the
>> Multi-field order each image is taken at the correct Z, but in
>> Time-lapse it uses always the same Z, which is the current position at
>> beginning of the acquisition. This occurs both with PRIOR NanoZ scan
>> or
>> Zeiss microscope focus. Could be this a bug?  I'm running the MM
>> Studio
>> version: 1.3.43 MMCore version 2.3.1 Device API version 33, Module API
>> version 4.
>
> There have been many tweaks to this part of the code, and I was under
> the impression that it works quite well.  You can try the latest
> nightly build ( http://valelab.ucsf.edu/~MM/nightlyBuilds/1.3 ) to
> check if we happen to have fixed this problem already.
>
> Also, there are many factors that affect the behavior (for instance:
> do you use relative or absolute z in the z-stack section of the MDA
> dialog, do you include the z-drive in the positionlist using the
> checkboxes in the bottom of the position list), and you can give us
> some more insights in how you are setting up the acquisition by
> sending us the acquisition.xml file (save it from the MDA dialog or
> find it with your saved data), nevertheless, since you say the
> behavior is different between multi-field and time-lapse modes it does
> sound like a bug.
>
> In general, we are most helped if you can give us a clear example of a
> bug that makes use of the Demo equipment.  That way, we have the best
> chance of reproducing the problem greatly facilitating fixing it.
>
> Best regards,
>
> Nico
>
>
> ------------------------------------------------------------------------------
> Throughout its 18-year history, RSA Conference consistently attracts the
> world's best and brightest in the field, creating opportunities for Conference
> attendees to learn about information security's most important issues through
> interactions with peers, luminaries and emerging and established companies.
> http://p.sf.net/sfu/rsaconf-dev2dev
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>

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Re: [micro-manager-general] Z position in XYZ Time-lapse acquisition order

Paula Sampaio
In reply to this post by Paula Sampaio
Hi Nico and Arthur, The lastest nightly build worked fine. Now the z
position is correctly set in both order modes. Thank you very much for
you help. All the best, Paula


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Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
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