Zeiss stage problem

[mcammer]

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We are having a problem with the stage on our Zeiss 710 with Zen 2009.

Our goal is to image a slide on one day and save positions and then to reimage the same positions a few days later.

This should be automated.  We are supposed to be able to record positions in the Positions window and reuse them later, but the positions are saved in a text file with unpredictable offsets and then when the file is reopened in Zen new unpredictable offsets are assigned so they can't be used.

If we zero the stage at a corner and write down each absolute position we need to return to, we can use the joystick to get back to those positions in later sessions, so at least there is a manual workaround.  Unfortunately, there is no way to type in the positions and the pre-zeroing does not solve the offsets problem either.

Has anybody else noticed this odd behavior or figured out a work around easier than using the joystick to manually return to positions?

Thank you.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

[Armstrong, Brian]

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Michael, we have the same problem. Once you exit the software the marked positions are gone.
I do not see a way around this other than what you already describe.
Zeiss does make a new stage to be used for Correlative Microscopy (correlates between light and electron microscopy applications) that has fiduciary markers so that the electron microscope can "find" the stage positions. However, this is probably an expensive solution to a simple problem.
Cheers,

Brian D Armstrong PhD
Assistant Research Professor
Director, Light Microscopy Core
Beckman Research Institute
City of Hope
Dept of Neuroscience
1450 E Duarte Rd
Duarte, CA 91010
626-256-4673 x62872

http://www.cityofhope.org/research/support/Light-Microscopy-Digital-Imaging/Pages/default.aspx


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, February 13, 2013 9:20 AM
To: [hidden email]
Subject: Zeiss stage problem

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*****

We are having a problem with the stage on our Zeiss 710 with Zen 2009.

Our goal is to image a slide on one day and save positions and then to reimage the same positions a few days later.

This should be automated.  We are supposed to be able to record positions in the Positions window and reuse them later, but the positions are saved in a text file with unpredictable offsets and then when the file is reopened in Zen new unpredictable offsets are assigned so they can't be used.

If we zero the stage at a corner and write down each absolute position we need to return to, we can use the joystick to get back to those positions in later sessions, so at least there is a manual workaround.  Unfortunately, there is no way to type in the positions and the pre-zeroing does not solve the offsets problem either.

Has anybody else noticed this odd behavior or figured out a work around easier than using the joystick to manually return to positions?

Thank you.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]


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[Julio Vazquez]

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Maybe just leave the system on. If you have a microscope control pad on your system, I guess you could also mark the locations using the control pad, leave the scope ON (you may shut down everything else, assuming this can be done with your set-up), and reload the locations from the control pad into ZEN when you need to reuse them.

--
Julio Vazquez
Fred Hutchinson Cancer Research Center
Seattle, WA 98109-1024


http://www.fhcrc.org



On Feb 13, 2013, at 9:19 AM, Cammer, Michael wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We are having a problem with the stage on our Zeiss 710 with Zen 2009.
>
> Our goal is to image a slide on one day and save positions and then to reimage the same positions a few days later.
>
> This should be automated.  We are supposed to be able to record positions in the Positions window and reuse them later, but the positions are saved in a text file with unpredictable offsets and then when the file is reopened in Zen new unpredictable offsets are assigned so they can't be used.
>
> If we zero the stage at a corner and write down each absolute position we need to return to, we can use the joystick to get back to those positions in later sessions, so at least there is a manual workaround.  Unfortunately, there is no way to type in the positions and the pre-zeroing does not solve the offsets problem either.
>
> Has anybody else noticed this odd behavior or figured out a work around easier than using the joystick to manually return to positions?
>
> Thank you.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]

[Angelov, Lyudmil]

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Hi Michael,

If you have Zeiss's license to use their Multi Time Series macro with Zen 2009 you can record the selected positions by updating the list of locations
in that macro before turning off the system. The macro keeps the last list of locations added even if you turn off the system. Later you can go to the selected positions through the macro and if you need you can add them again on Zen 2009 position window. All this works with Zeiss 510 and Zen 2009. I don't know if it's going to work with Zeiss 710.
Cheers,
Lyudmil

-----------
Lyudmil Angelov, M.S.
Head, Confocal Microscopy Core Facility
Lindsley F. Kimball Research Institute
New York Blood Center
310 East 67th Street, New York, NY 10065
Phone: [phone]
E-mail: [hidden email]


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, February 13, 2013 12:20 PM
To: [hidden email]
Subject: Zeiss stage problem

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

We are having a problem with the stage on our Zeiss 710 with Zen 2009.

Our goal is to image a slide on one day and save positions and then to reimage the same positions a few days later.

This should be automated.  We are supposed to be able to record positions in the Positions window and reuse them later, but the positions are saved in a text file with unpredictable offsets and then when the file is reopened in Zen new unpredictable offsets are assigned so they can't be used.

If we zero the stage at a corner and write down each absolute position we need to return to, we can use the joystick to get back to those positions in later sessions, so at least there is a manual workaround.  Unfortunately, there is no way to type in the positions and the pre-zeroing does not solve the offsets problem either.

Has anybody else noticed this odd behavior or figured out a work around easier than using the joystick to manually return to positions?

Thank you.
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]

[Kevin Ryan]

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It sounds like your stage is assigning "0,0" (or some other number) to the position it is in when the system is started, and offsets from that start.

I would suggest "parking" your stage in a particular corner _before_ shutting it down, or moving to that corner and restarting the stage controller, so that the same position is the starting point on each run. If the stage controller startup isn't assigning random numbers this should get you to repeatable offsets, as they will all be relative to the same starting point.

It's a bit ugly, and adds to the workflow, but it might be the least expensive solution for your system.

Kevin Ryan
Media Cybernetics, Inc.



---------------------------
On Feb 13, 2013, at 9:19 AM, Cammer, Michael wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We are having a problem with the stage on our Zeiss 710 with Zen 2009.
>
> Our goal is to image a slide on one day and save positions and then to reimage the same positions a few days later.
>
> This should be automated.  We are supposed to be able to record positions in the Positions window and reuse them later, but the positions are saved in a text file with unpredictable offsets and then when the file is reopened in Zen new unpredictable offsets are assigned so they can't be used.
>
> If we zero the stage at a corner and write down each absolute position we need to return to, we can use the joystick to get back to those positions in later sessions, so at least there is a manual workaround.  Unfortunately, there is no way to type in the positions and the pre-zeroing does not solve the offsets problem either.
>
> Has anybody else noticed this odd behavior or figured out a work around easier than using the joystick to manually return to positions?
>
> Thank you.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist Skirball Institute of
> Biomolecular Medicine
> Lab: [phone]  Cell: [phone]

[Marco Marcello]

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Hi Michael,

If you cannot implement any of the former suggestions, what about just using
a coverslip with a grid on it?
I know, it is not automated and certainly simplistic, but it can also be of help to double check the validity of other methods.

Cheers

Marco

Dr. Marco Marcello
Imaging Manager
Institute of Integrative Biology
University of Liverpool
L69 7ZB
Liverpool
UK
tel [phone]
http://pcwww.liv.ac.uk/~cci/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Kevin Ryan
Sent: 13 February 2013 20:32
To: [hidden email]
Subject: Re: Zeiss stage problem

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

It sounds like your stage is assigning "0,0" (or some other number) to the position it is in when the system is started, and offsets from that start.

I would suggest "parking" your stage in a particular corner _before_ shutting it down, or moving to that corner and restarting the stage controller, so that the same position is the starting point on each run. If the stage controller startup isn't assigning random numbers this should get you to repeatable offsets, as they will all be relative to the same starting point.

It's a bit ugly, and adds to the workflow, but it might be the least expensive solution for your system.

Kevin Ryan
Media Cybernetics, Inc.



---------------------------
On Feb 13, 2013, at 9:19 AM, Cammer, Michael wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We are having a problem with the stage on our Zeiss 710 with Zen 2009.
>
> Our goal is to image a slide on one day and save positions and then to reimage the same positions a few days later.
>
> This should be automated.  We are supposed to be able to record positions in the Positions window and reuse them later, but the positions are saved in a text file with unpredictable offsets and then when the file is reopened in Zen new unpredictable offsets are assigned so they can't be used.
>
> If we zero the stage at a corner and write down each absolute position we need to return to, we can use the joystick to get back to those positions in later sessions, so at least there is a manual workaround.  Unfortunately, there is no way to type in the positions and the pre-zeroing does not solve the offsets problem either.
>
> Has anybody else noticed this odd behavior or figured out a work around easier than using the joystick to manually return to positions?
>
> Thank you.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist Skirball Institute of
> Biomolecular Medicine
> Lab: [phone]  Cell: [phone]

[mcammer]

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Dear all,

Yesterday we wrote a draft protocol for solving the problem of imaging multiple positions on the same sample repeatedly in serial imaging sessions where other users have access to the instrument in between.  I have used this successfully and now other users need to test it.
https://dl.dropbox.com/u/20760630/stage%20protocol%20as%20of%20feb%2021.pdf
The key, we figured out, is moving the stage to an absolute position and cycling the power (as many of you suggested).  Only the microscope stand, stage, and Zen software need to be restarted; all other components may remain powered up.
We are going to try recovering the old positions by manually finding one field that matches and the calculating the dx dy translation for all the other positions.

This morning we received from Zeiss their suggested protocol which looks similar.  One thing that won't work with their protocol on our system is that if we extend the stage to the maximum position at the back (or top), then the controller hangs and the system has to be restarted, so their choice of which corner doesn't work.  Otherwise, it looks essentially the same.
https://dl.dropbox.com/u/20760630/Repeat%20positions%20in%20ZEN%20black.docx

Thank you for the helpful discussion.  And maybe now Zeiss will include this as part of their standard protocols so other customers may benefit.

Regards,

Michael
________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of CCI
Sent: Friday, February 15, 2013 6:18 AM
To: [hidden email]
Subject: Re: Zeiss stage problem

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

Hi Michael,

If you cannot implement any of the former suggestions, what about just using a coverslip with a grid on it?
I know, it is not automated and certainly simplistic, but it can also be of help to double check the validity of other methods.

Cheers

Marco

Dr. Marco Marcello
Imaging Manager
Institute of Integrative Biology
University of Liverpool
L69 7ZB
Liverpool
UK
tel [phone]
http://pcwww.liv.ac.uk/~cci/

-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Kevin Ryan
Sent: 13 February 2013 20:32
To: [hidden email]
Subject: Re: Zeiss stage problem

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

It sounds like your stage is assigning "0,0" (or some other number) to the position it is in when the system is started, and offsets from that start.

I would suggest "parking" your stage in a particular corner _before_ shutting it down, or moving to that corner and restarting the stage controller, so that the same position is the starting point on each run. If the stage controller startup isn't assigning random numbers this should get you to repeatable offsets, as they will all be relative to the same starting point.

It's a bit ugly, and adds to the workflow, but it might be the least expensive solution for your system.

Kevin Ryan
Media Cybernetics, Inc.



---------------------------
On Feb 13, 2013, at 9:19 AM, Cammer, Michael wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> We are having a problem with the stage on our Zeiss 710 with Zen 2009.
>
> Our goal is to image a slide on one day and save positions and then to reimage the same positions a few days later.
>
> This should be automated.  We are supposed to be able to record positions in the Positions window and reuse them later, but the positions are saved in a text file with unpredictable offsets and then when the file is reopened in Zen new unpredictable offsets are assigned so they can't be used.
>
> If we zero the stage at a corner and write down each absolute position we need to return to, we can use the joystick to get back to those positions in later sessions, so at least there is a manual workaround.  Unfortunately, there is no way to type in the positions and the pre-zeroing does not solve the offsets problem either.
>
> Has anybody else noticed this odd behavior or figured out a work around easier than using the joystick to manually return to positions?
>
> Thank you.
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist Skirball Institute of
> Biomolecular Medicine
> Lab: [phone]  Cell: [phone]

[Chris Tully]

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Michael,

I do not currently have access to the necessary equipment to test your
protocol but after skimming it I do have some suggestions.

I worked for Media Cybernetics from 2001-2007 and did most of the QA work
on their Scope-Pro microscope automation drivers in that time period. One
common problems with mechanical stages is back lash - meaning that when I
reverse directions of movement the gearing needs some portion of a
revolution to make contact in the reverse direction. If you have many users
on the system in between your runs this can accumulate.  Methods of
combating this include:
1. Drive the stage to Max X, Max Y then to 0,0.
2. When approaching 0,0 reduce the speed of the stage.
3. Once you have hit 0,0, back off from it a little bit and then return to
0,0 VERY slowly.

In all honesty, this problem you are seeing should not be an issue, because
it can be almost completely corrected in software - all of the major
independent microscope automation vendors (Media Cybernetics, Meta Morph
and Intelligent Imaging Innovations have all solved this in my personal
experience).  I would strongly suggest that you put as much pressure as you
can on Zeiss to fix the software.

However, you have not addressed one problem that I have seen and solved on
automated stages in the past - reproducibility of the slide's position on
the stage.  It is entirely possible for the slide to be shifted by a full
frame or more in any direction if it is not placed carefully each time.
This means having a hard stop (think machined AL holder) at one corner and
one or more springs forcing the slide into that corner.  It also means
regularly cleaning dust out of the slide holder.

I would offer to come by your lab and help out in person but I live in
North Carolina so it's a bit of a hike for me to make it to NYC.

Cheers!
Chris

Chris Tully
Microscopy and Image Analysis Expert
[hidden email]
240-475-9753 (c)

[image: View my profile on LinkedIn]<http://www.linkedin.com/in/christully/>


On Fri, Feb 22, 2013 at 12:43 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 all,
>
> Yesterday we wrote a draft protocol for solving the problem of imaging
> multiple positions on the same sample repeatedly in serial imaging sessions
> where other users have access to the instrument in between.  I have used
> this successfully and now other users need to test it.
> https://dl.dropbox.com/u/20760630/stage%20protocol%20as%20of%20feb%2021.pdf
> The key, we figured out, is moving the stage to an absolute position and
> cycling the power (as many of you suggested).  Only the microscope stand,
> stage, and Zen software need to be restarted; all other components may
> remain powered up.
> We are going to try recovering the old positions by manually finding one
> field that matches and the calculating the dx dy translation for all the
> other positions.
>
> This morning we received from Zeiss their suggested protocol which looks
> similar.  One thing that won't work with their protocol on our system is
> that if we extend the stage to the maximum position at the back (or top),
> then the controller hangs and the system has to be restarted, so their
> choice of which corner doesn't work.  Otherwise, it looks essentially the
> same.
>
> https://dl.dropbox.com/u/20760630/Repeat%20positions%20in%20ZEN%20black.docx
>
> Thank you for the helpful discussion.  And maybe now Zeiss will include
> this as part of their standard protocols so other customers may benefit.
>
> Regards,
>
> Michael
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of CCI
> Sent: Friday, February 15, 2013 6:18 AM
> To: [hidden email]
> Subject: Re: Zeiss stage problem
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> Hi Michael,
>
> If you cannot implement any of the former suggestions, what about just
> using a coverslip with a grid on it?
> I know, it is not automated and certainly simplistic, but it can also be
> of help to double check the validity of other methods.
>
> Cheers
>
> Marco
>
> Dr. Marco Marcello
> Imaging Manager
> Institute of Integrative Biology
> University of Liverpool
> L69 7ZB
> Liverpool
> UK
> tel [phone]
> http://pcwww.liv.ac.uk/~cci/
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[hidden email]]
> On Behalf Of Kevin Ryan
> Sent: 13 February 2013 20:32
> To: [hidden email]
> Subject: Re: Zeiss stage problem
>
> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> *****
>
> It sounds like your stage is assigning "0,0" (or some other number) to the
> position it is in when the system is started, and offsets from that start.
>
> I would suggest "parking" your stage in a particular corner _before_
> shutting it down, or moving to that corner and restarting the stage
> controller, so that the same position is the starting point on each run. If
> the stage controller startup isn't assigning random numbers this should get
> you to repeatable offsets, as they will all be relative to the same
> starting point.
>
> It's a bit ugly, and adds to the workflow, but it might be the least
> expensive solution for your system.
>
> Kevin Ryan
> Media Cybernetics, Inc.
>
>
>
> ---------------------------
> On Feb 13, 2013, at 9:19 AM, Cammer, Michael wrote:
>
> > *****
> > To join, leave or search the confocal microscopy listserv, go to:
> > http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> > *****
> >
> > We are having a problem with the stage on our Zeiss 710 with Zen 2009.
> >
> > Our goal is to image a slide on one day and save positions and then to
> reimage the same positions a few days later.
> >
> > This should be automated.  We are supposed to be able to record
> positions in the Positions window and reuse them later, but the positions
> are saved in a text file with unpredictable offsets and then when the file
> is reopened in Zen new unpredictable offsets are assigned so they can't be
> used.
> >
> > If we zero the stage at a corner and write down each absolute position
> we need to return to, we can use the joystick to get back to those
> positions in later sessions, so at least there is a manual workaround.
>  Unfortunately, there is no way to type in the positions and the
> pre-zeroing does not solve the offsets problem either.
> >
> > Has anybody else noticed this odd behavior or figured out a work around
> easier than using the joystick to manually return to positions?
> >
> > Thank you.
> > ________________________________________________________
> > Michael Cammer, Assistant Research Scientist Skirball Institute of
> > Biomolecular Medicine
> > Lab: [phone]  Cell: [phone]
>

[mcammer]

*****
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http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
*****

More on the stage issue...

While it appears that the protocol we posted last week to return to the same field after restarting the microscope works, if we load an image and click the "Reuse" button to set up channels, lasers, etc. it also messes up the stage offsets in Zen.

Regards,
Michael

> > ________________________________________________________
> > Michael Cammer, Assistant Research Scientist Skirball Institute of
> > Biomolecular Medicine
> > Lab: [phone]  Cell: [phone]
>