odd inensity shift over time

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mcammer mcammer
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odd inensity shift over time

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Dear confocalers,
We would appreciate help identifying (and remedying) a problem we have not encountered before.
One of our users reported that the laser intensity of the confocal was dropping off during each of her imaging sessions.   Today I put a mirror on the confocal and imaged for 4 1/2 hours in the reflectance mode with the slits to detect over than 20 nm open.  During that time the intensities at 488, 543, and 633 nm rose to a peak between 15 and 60 minutes and then fell off at a slower rate (graph posted at http://www.flickr.com/photos/mcammer/6512342071/ ).
Has anyone seen this pattern before and could help us identify the cause?  Is it a laser issue (with three different lasers?), an AOTF issue, a detectors issue, a drifting out of alignment issue (although in this last case the resolution in fluorescent imaging continues to look fine)?
Also, this is not a focus drift issue.

The microscope is a Zeiss 710 with three spectral detectors.

Any help identifying this greatly appreciated.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270

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Craig Brideau Craig Brideau
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Re: odd inensity shift over time

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Is the temperature in the room holding steady over this time period?

Craig


On Wed, Dec 14, 2011 at 1:44 PM, Cammer, Michael <[hidden email]
> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear confocalers,
> We would appreciate help identifying (and remedying) a problem we have not
> encountered before.
> One of our users reported that the laser intensity of the confocal was
> dropping off during each of her imaging sessions.   Today I put a mirror on
> the confocal and imaged for 4 1/2 hours in the reflectance mode with the
> slits to detect over than 20 nm open.  During that time the intensities at
> 488, 543, and 633 nm rose to a peak between 15 and 60 minutes and then fell
> off at a slower rate (graph posted at
> http://www.flickr.com/photos/mcammer/6512342071/ ).
> Has anyone seen this pattern before and could help us identify the cause?
>  Is it a laser issue (with three different lasers?), an AOTF issue, a
> detectors issue, a drifting out of alignment issue (although in this last
> case the resolution in fluorescent imaging continues to look fine)?
> Also, this is not a focus drift issue.
>
> The microscope is a Zeiss 710 with three spectral detectors.
>
> Any help identifying this greatly appreciated.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: (212) 263-3208  Cell: (914) 309-3270
>
> </PRE>
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Vladimir Ghukasyan-2 Vladimir Ghukasyan-2
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Re: odd inensity shift over time

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Michael,

Does this happen when you run imaging with a single laser at a time?

Vladimir


On Wed, Dec 14, 2011 at 3:44 PM, Cammer, Michael
<[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear confocalers,
> We would appreciate help identifying (and remedying) a problem we have not encountered before.
> One of our users reported that the laser intensity of the confocal was dropping off during each of her imaging sessions.   Today I put a mirror on the confocal and imaged for 4 1/2 hours in the reflectance mode with the slits to detect over than 20 nm open.  During that time the intensities at 488, 543, and 633 nm rose to a peak between 15 and 60 minutes and then fell off at a slower rate (graph posted at http://www.flickr.com/photos/mcammer/6512342071/ ).
> Has anyone seen this pattern before and could help us identify the cause?  Is it a laser issue (with three different lasers?), an AOTF issue, a detectors issue, a drifting out of alignment issue (although in this last case the resolution in fluorescent imaging continues to look fine)?
> Also, this is not a focus drift issue.
>
> The microscope is a Zeiss 710 with three spectral detectors.
>
> Any help identifying this greatly appreciated.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: (212) 263-3208  Cell: (914) 309-3270
>
> </PRE>
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Csúcs  Gábor Csúcs Gábor
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Re: odd inensity shift over time

In reply to this post by mcammer
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Dear Michael,

I could imagine that it I the temperature stabilization/control of the
AOTF that creates the observed phenomenon. You could relatively easily
test this if you would do an intensity measurement directly on the laser
(before the AOTF) and then do the same thing after the AOTF (but before
the fibre).

Cheers     Gabor



On 12/14/11 9:44 PM, "Cammer, Michael" <[hidden email]> wrote:

>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>Dear confocalers,
>We would appreciate help identifying (and remedying) a problem we have
>not encountered before.
>One of our users reported that the laser intensity of the confocal was
>dropping off during each of her imaging sessions.   Today I put a mirror
>on the confocal and imaged for 4 1/2 hours in the reflectance mode with
>the slits to detect over than 20 nm open.  During that time the
>intensities at 488, 543, and 633 nm rose to a peak between 15 and 60
>minutes and then fell off at a slower rate (graph posted at
>http://www.flickr.com/photos/mcammer/6512342071/ ).
>Has anyone seen this pattern before and could help us identify the cause?
> Is it a laser issue (with three different lasers?), an AOTF issue, a
>detectors issue, a drifting out of alignment issue (although in this last
>case the resolution in fluorescent imaging continues to look fine)?
>Also, this is not a focus drift issue.
>
>The microscope is a Zeiss 710 with three spectral detectors.
>
>Any help identifying this greatly appreciated.
>________________________________________________________
>Michael Cammer, Assistant Research Scientist
>Skirball Institute of Biomolecular Medicine
>Lab: (212) 263-3208  Cell: (914) 309-3270
>
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mmodel mmodel
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Re: odd inensity shift over time

In reply to this post by mcammer
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I would first check what's going on in the transmitted detector.
Mike

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, December 14, 2011 3:44 PM
To: [hidden email]
Subject: odd inensity shift over time

*****
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Dear confocalers,
We would appreciate help identifying (and remedying) a problem we have not encountered before.
One of our users reported that the laser intensity of the confocal was dropping off during each of her imaging sessions.   Today I put a mirror on the confocal and imaged for 4 1/2 hours in the reflectance mode with the slits to detect over than 20 nm open.  During that time the intensities at 488, 543, and 633 nm rose to a peak between 15 and 60 minutes and then fell off at a slower rate (graph posted at http://www.flickr.com/photos/mcammer/6512342071/ ).
Has anyone seen this pattern before and could help us identify the cause?  Is it a laser issue (with three different lasers?), an AOTF issue, a detectors issue, a drifting out of alignment issue (although in this last case the resolution in fluorescent imaging continues to look fine)?
Also, this is not a focus drift issue.

The microscope is a Zeiss 710 with three spectral detectors.

Any help identifying this greatly appreciated.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270

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Boswell, Carl A - (cboswell) Boswell, Carl A - (cboswell)
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Re: odd inensity shift over time

My first guess would be the AOTF, notwithstanding the differences in spectral changes.  Does Zeiss have any comment?

C


Carl A. Boswell
520-954-7053

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of MODEL, MICHAEL
Sent: Wednesday, December 14, 2011 2:25 PM
To: [hidden email]
Subject: Re: odd inensity shift over time

*****
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I would first check what's going on in the transmitted detector.
Mike

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, December 14, 2011 3:44 PM
To: [hidden email]
Subject: odd inensity shift over time

*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear confocalers,
We would appreciate help identifying (and remedying) a problem we have not encountered before.
One of our users reported that the laser intensity of the confocal was dropping off during each of her imaging sessions.   Today I put a mirror on the confocal and imaged for 4 1/2 hours in the reflectance mode with the slits to detect over than 20 nm open.  During that time the intensities at 488, 543, and 633 nm rose to a peak between 15 and 60 minutes and then fell off at a slower rate (graph posted at http://www.flickr.com/photos/mcammer/6512342071/ ).
Has anyone seen this pattern before and could help us identify the cause?  Is it a laser issue (with three different lasers?), an AOTF issue, a detectors issue, a drifting out of alignment issue (although in this last case the resolution in fluorescent imaging continues to look fine)?
Also, this is not a focus drift issue.

The microscope is a Zeiss 710 with three spectral detectors.

Any help identifying this greatly appreciated.
________________________________________________________
Michael Cammer, Assistant Research Scientist Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270

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Zac Arrac Atelaz Zac Arrac Atelaz
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Re: odd inensity shift over time

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Michael: Some things come to my mind, not sure they are what you are looking for, but use them as reference: 1. Change on the ambient temperature, It would be great having an adjacent graph with the room and laser area temp on side of this one, gas laser is making a blinking, fast enough so you cannot notice, changes in temp would make this faster or slower, and also affect the efficiency of the light emitting properties of the device. 2. If you want to check, there is a laser stabilization function which is basically a feedback info going to the AOTF, I am sure Olympus have this on the FV1000, but you have to check if Zeiss can retrofit something like this to your system. gas laser is on a continuos fluctuation, which might be corrected with this feedback function. Hope this helps Gabriel OH
  > Date: Wed, 14 Dec 2011 15:44:15 -0500

> From: [hidden email]
> Subject: odd inensity shift over time
> To: [hidden email]
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Dear confocalers,
> We would appreciate help identifying (and remedying) a problem we have not encountered before.
> One of our users reported that the laser intensity of the confocal was dropping off during each of her imaging sessions.   Today I put a mirror on the confocal and imaged for 4 1/2 hours in the reflectance mode with the slits to detect over than 20 nm open.  During that time the intensities at 488, 543, and 633 nm rose to a peak between 15 and 60 minutes and then fell off at a slower rate (graph posted at http://www.flickr.com/photos/mcammer/6512342071/ ).
> Has anyone seen this pattern before and could help us identify the cause?  Is it a laser issue (with three different lasers?), an AOTF issue, a detectors issue, a drifting out of alignment issue (although in this last case the resolution in fluorescent imaging continues to look fine)?
> Also, this is not a focus drift issue.
>
> The microscope is a Zeiss 710 with three spectral detectors.
>
> Any help identifying this greatly appreciated.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: (212) 263-3208  Cell: (914) 309-3270
>
> </PRE>
> <html>
> <body>
> ------------------------------------------------------------<br />
> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br />
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James Pawley James Pawley
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Re: odd inensity shift over time

In reply to this post by mmodel
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Or better yet, just monitor the light coming out of a (low NA)
objective with a simple photometer.

Motion of the laser-end of the fibre with respect to the "objective"
that focuses the laser light into it, might have times constants of
the length you mention.

JP

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Info: http://www.3dcourse.ubc.ca/                  Application
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>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>I would first check what's going on in the transmitted detector.
>Mike
>
>-----Original Message-----
>From: Confocal Microscopy List
>[mailto:[hidden email]] On Behalf Of Cammer,
>Michael
>Sent: Wednesday, December 14, 2011 3:44 PM
>To: [hidden email]
>Subject: odd inensity shift over time
>
>*****
>To join, leave or search the confocal microscopy listserv, go to:
>http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
>*****
>
>Dear confocalers,
>We would appreciate help identifying (and remedying) a problem we
>have not encountered before.
>One of our users reported that the laser intensity of the confocal
>was dropping off during each of her imaging sessions.   Today I put
>a mirror on the confocal and imaged for 4 1/2 hours in the
>reflectance mode with the slits to detect over than 20 nm open.
>During that time the intensities at 488, 543, and 633 nm rose to a
>peak between 15 and 60 minutes and then fell off at a slower rate
>(graph posted at http://www.flickr.com/photos/mcammer/6512342071/ ).
>Has anyone seen this pattern before and could help us identify the
>cause?  Is it a laser issue (with three different lasers?), an AOTF
>issue, a detectors issue, a drifting out of alignment issue
>(although in this last case the resolution in fluorescent imaging
>continues to look fine)?
>Also, this is not a focus drift issue.
>
>The microscope is a Zeiss 710 with three spectral detectors.
>
>Any help identifying this greatly appreciated.
>________________________________________________________
>Michael Cammer, Assistant Research Scientist
>Skirball Institute of Biomolecular Medicine
>Lab: (212) 263-3208  Cell: (914) 309-3270
>
></PRE>
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Zucker.Robert Zucker.Robert
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Re: odd intensity shift over time

In reply to this post by mcammer
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Dear Mike
This pattern probably has to do with the AOTF instability.
We have published a few papers on the instability of a confocal
microscope that are available on request.
The data is quite disturbing, but it is believed that this effect can
occur with AOTFs  that are not heat stabilized or are defective.
Please contact me directly for PDF copies of these publications
best wishes
bob

   1. Zucker RM  Confocal Slide Based System :Performance. Cytometry
      2006 69 A 659-676..

   2. Zucker  RM  Confocal Microscopy Slide Based Systems: Instability.
      Cytometry 2006 69A 677-690.

  3.    Zucker, R.M. Evaluation of Confocal Microscopy System
     Performance. Cell Imaging Techniques. Douglas Taajets editor Humana
     Press  Chapter 5 77-135 2005




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From: "Cammer, Michael" <[hidden email]>
To: [hidden email]
Date: 12/14/2011 03:44 PM
Subject: odd inensity shift over time
Sent by: Confocal Microscopy List <[hidden email]>



*****
To join, leave or search the confocal microscopy listserv, go to:
http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Dear confocalers,
We would appreciate help identifying (and remedying) a problem we have
not encountered before.
One of our users reported that the laser intensity of the confocal was
dropping off during each of her imaging sessions.   Today I put a mirror
on the confocal and imaged for 4 1/2 hours in the reflectance mode with
the slits to detect over than 20 nm open.  During that time the
intensities at 488, 543, and 633 nm rose to a peak between 15 and 60
minutes and then fell off at a slower rate (graph posted at
http://www.flickr.com/photos/mcammer/6512342071/ ).
Has anyone seen this pattern before and could help us identify the
cause?  Is it a laser issue (with three different lasers?), an AOTF
issue, a detectors issue, a drifting out of alignment issue (although in
this last case the resolution in fluorescent imaging continues to look
fine)?
Also, this is not a focus drift issue.

The microscope is a Zeiss 710 with three spectral detectors.

Any help identifying this greatly appreciated.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270

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mcammer mcammer
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Re: odd intensity shift over time

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Thank you everybody for the suggestions.

We ran a test overnight while recording room temperature.  There were independent drifts in each wavelength's power and no correlation with room temperature.  We're repeating the readings right now using the transmission detector.

Based on your comments, I'm thinking the problem is the AOTF or its controller.  Regardless, we filed a service request with Zeiss.

I'll let you know the what happens.

Regards,

Michael



________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: (212) 263-3208  Cell: (914) 309-3270


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Ekaterina PAPUSHEVA-2 Ekaterina PAPUSHEVA-2
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molecular beacons for RNA expression analysis

In reply to this post by Vladimir Ghukasyan-2
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Hi all,

My question is not strictly confocal, but maybe you would have an idea....

we are considering using molecular beacons tp follow promoter activity in isolated cells from zebrafish embryos. We have problem cloning a GFP reporter for the gene expression (the recombinant promoter is not functional), therefore considering using molecular beacons for following mRNA concentration (mRNA sequence is known).

I am a novice with molecular beacons, and have a beginners question: how does binding of a molecular beacon affect RNA lifecycle? Would not we fall in a trap, that the area of RNA that is bound to the beacon is not degraded=false positive signal persists? What are the controls for this?

I would be very grateful  if you could give a tip or recommend a literature!  (while surfing myself)

good weekend to everyone!
Ekaterina

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-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Vladimir Ghukasyan
Sent: Mittwoch, 14. Dezember 2011 22:16
To: [hidden email]
Subject: Re: odd inensity shift over time

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Michael,

Does this happen when you run imaging with a single laser at a time?

Vladimir


On Wed, Dec 14, 2011 at 3:44 PM, Cammer, Michael <[hidden email]> wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
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>
> Dear confocalers,
> We would appreciate help identifying (and remedying) a problem we have not encountered before.
> One of our users reported that the laser intensity of the confocal was dropping off during each of her imaging sessions.   Today I put a mirror on the confocal and imaged for 4 1/2 hours in the reflectance mode with the slits to detect over than 20 nm open.  During that time the intensities at 488, 543, and 633 nm rose to a peak between 15 and 60 minutes and then fell off at a slower rate (graph posted at http://www.flickr.com/photos/mcammer/6512342071/ ).
> Has anyone seen this pattern before and could help us identify the cause?  Is it a laser issue (with three different lasers?), an AOTF issue, a detectors issue, a drifting out of alignment issue (although in this last case the resolution in fluorescent imaging continues to look fine)?
> Also, this is not a focus drift issue.
>
> The microscope is a Zeiss 710 with three spectral detectors.
>
> Any help identifying this greatly appreciated.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist Skirball Institute of
> Biomolecular Medicine
> Lab: (212) 263-3208  Cell: (914) 309-3270
>
> </PRE>
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