Trouble switching filter cubes Zeiss Observer.Z1

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Trouble switching filter cubes Zeiss Observer.Z1

arashid
Hello,

I am using micromanager to control my Obersever.Z1. We have a motorized
turret on the microscope. When I change channels on micromanger by selecting
the different channels on the drop down bar, the turret responds half the
time, but does not respond the other half. In response to the micromanager
command, the touch screen on the microscope always shows a change in turning
the light source on and off even when the channel does not change. When
using the touch screen on the microscope, the turret always moves correctly.

I am able to load my old hardware configuration file containing this
microscope into micromanager. However, I tried to create a new hardware
configuration on micromanager for the microscope in case that would make any
difference (using ZeissCAN29), and I receive an error message "Error in
device 'ZeissScope': The Zeiss microscope does not answer. Is it switched on
and connected to this computer? (10015)"

Any thoughts on what the issue could be?

Thanks for the help,
Alina



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Re: Trouble switching filter cubes Zeiss Observer.Z1

Stuurman, Nico
Hi Alina,
> I am using micromanager to control my Obersever.Z1. We have a motorized
> turret on the microscope. When I change channels on micromanger by selecting
> the different channels on the drop down bar, the turret responds half the
> time, but does not respond the other half. In response to the micromanager
> command, the touch screen on the microscope always shows a change in turning
> the light source on and off even when the channel does not change. When
> using the touch screen on the microscope, the turret always moves correctly.

That reminds me of the "LightManager".  I thought that the code tried to
disable the light manager (since it thinks it knows the right thing to
do, but it really doesn't;).  I think that you can check the status of
the LightManager through the touch screen, and switch it off there (if
it indeed is on).

> I am able to load my old hardware configuration file containing this
> microscope into micromanager. However, I tried to create a new hardware
> configuration on micromanager for the microscope in case that would make any
> difference (using ZeissCAN29), and I receive an error message "Error in
> device 'ZeissScope': The Zeiss microscope does not answer. Is it switched on
> and connected to this computer? (10015)"

Interesting.  Did you select the correct serial port and serial port
settings (see the micro-manager ZeissCAN29 page:
https://micro-manager.org/wiki/ZeissCAN29). If you generate a Trouble
Report (through the help menu), I'll have a look to see if anything
stands out.


Best,


Nico



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Re: Trouble switching filter cubes Zeiss Observer.Z1

Alina Rashid

Hi Nico,


>That reminds me of the "LightManager".  I thought that the code tried to 
>disable the light manager (since it thinks it knows the right thing to 
>do, but it really doesn't;).  I think that you can check the status of 
>the LightManager through the touch screen, and switch it off there (if 
>it indeed is on).


I saw that LightManager was enabled on the microscope. I disabled it, but the issue is persisting where the reflector turret only changes about half the time. Our microscope was just serviced and the service engineer just informed me that the firmware on the main board/main controller was updated from version 02.662 to version 02.703. Would this be associated with the issue?


>Interesting.  Did you select the correct serial port and serial port 
>settings


Turns out one of the settings for the port were wrong so I am able to build a new hardware configuration file with the microscope now. This new file is still having the same issue of switching between channels. 


Thanks for the help,

Alina 




From: Stuurman, Nico <[hidden email]>
Sent: Friday, August 2, 2019 1:52:14 PM
To: Micro-Manager General <[hidden email]>; arashid <[hidden email]>
Subject: Re: [micro-manager-general] Trouble switching filter cubes Zeiss Observer.Z1
 
Hi Alina,
> I am using micromanager to control my Obersever.Z1. We have a motorized
> turret on the microscope. When I change channels on micromanger by selecting
> the different channels on the drop down bar, the turret responds half the
> time, but does not respond the other half. In response to the micromanager
> command, the touch screen on the microscope always shows a change in turning
> the light source on and off even when the channel does not change. When
> using the touch screen on the microscope, the turret always moves correctly.

That reminds me of the "LightManager".  I thought that the code tried to
disable the light manager (since it thinks it knows the right thing to
do, but it really doesn't;).  I think that you can check the status of
the LightManager through the touch screen, and switch it off there (if
it indeed is on).

> I am able to load my old hardware configuration file containing this
> microscope into micromanager. However, I tried to create a new hardware
> configuration on micromanager for the microscope in case that would make any
> difference (using ZeissCAN29), and I receive an error message "Error in
> device 'ZeissScope': The Zeiss microscope does not answer. Is it switched on
> and connected to this computer? (10015)"

Interesting.  Did you select the correct serial port and serial port
settings (see the micro-manager ZeissCAN29 page:
https://urldefense.proofpoint.com/v2/url?u=https-3A__micro-2Dmanager.org_wiki_ZeissCAN29&d=DwIGaQ&c=JeTkUgVztGMmhKYjxsy2rfoWYibK1YmxXez1G3oNStg&r=Uh6_278As_Q3cSdV3iTFDyYrkHxJMYUdwEH6vwZPltw&m=I4g1y6yVy_K_WusaQSf4YyetPzYb6d9XPlKtpEZMKEs&s=S5SzemUPKXfdh__mWsc5KrPzKH5zozgNueGp0RmgwBQ&e= ). If you generate a Trouble
Report (through the help menu), I'll have a look to see if anything
stands out.


Best,


Nico




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Re: Trouble switching filter cubes Zeiss Observer.Z1

arashid
In reply to this post by Stuurman, Nico
Hi Nico,

>That reminds me of the "LightManager".  I thought that the code tried to
>disable the light manager (since it thinks it knows the right thing to
>do, but it really doesn't;).  I think that you can check the status of
>the LightManager through the touch screen, and switch it off there (if
>it indeed is on).

I saw that LightManager was enabled on the microscope. I disabled it, but
the issue is persisting where the reflector turret only changes about half
the time. Our microscope was just serviced and the service engineer just
informed me that the firmware on the main board/main controller was updated
from version 02.662 to version 02.703. Would this be associated with the
issue?


>Interesting.  Did you select the correct serial port and serial port
>settings

Turns out one of the settings for the port were wrong so I am able to build
a new hardware configuration file with the microscope now. This new file is
still having the same issue of switching between channels.


Thanks for the help,
Alina



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Re: Trouble switching filter cubes Zeiss Observer.Z1

Stuurman, Nico
Hi Alina,

On 8/2/2019 12:31 PM, arashid wrote:

>
>> That reminds me of the "LightManager".  I thought that the code tried to
>> disable the light manager (since it thinks it knows the right thing to
>> do, but it really doesn't;).  I think that you can check the status of
>> the LightManager through the touch screen, and switch it off there (if
>> it indeed is on).
> I saw that LightManager was enabled on the microscope. I disabled it, but
> the issue is persisting where the reflector turret only changes about half
> the time. Our microscope was just serviced and the service engineer just
> informed me that the firmware on the main board/main controller was updated
> from version 02.662 to version 02.703. Would this be associated with the
> issue?

Did you not have this issue before the firmware update?  If so, that
most likely is the problem.  It could be that the newer firmware
communicates differently, or has a time out or something.  Try
generating a trouble report from one of these sessions (you can indicate
in the report when the switching did not happen correctly).

Best,

Nico



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Re: Trouble switching filter cubes Zeiss Observer.Z1

arashid
Hi Nico,

The issue did not occur before the firmware update. I'm not very
experienced, so I can't tell exactly where to annotate the commands in the
trouble report. I attached the log file to the e-mail and kept a list of the
filters I switched to. The fluorescent light source is a lumencor spectra
LED light source.

Thanks so much for your help,
Alina

switch to gfp - unsuccessful
switch to gfp - unsuccessful
switch to gfp - success
switch to yfp - unsuccessful
switch to yfp - success
switch to mcherry - unsuccessful
switch to mcherry - success
switch to dic - unsuccessful
switch to dic - success
switch to gfp_dual - unsuccessful
switch to gfp_dual - unsuccessful
switch to gfp_dual - success
switch to gfp - unsuccessful
switch to mcherry_dual - unsuccessful
switch to yfp - unsuccessful
switch to yfp - success
  CoreLog20190805T104529_pid3980.txt
<http://micro-manager.3463995.n2.nabble.com/file/t397390/CoreLog20190805T104529_pid3980.txt>  



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Re: Trouble switching filter cubes Zeiss Observer.Z1

Stuurman, Nico
Hi Alina,

> The issue did not occur before the firmware update. I'm not very
> experienced, so I can't tell exactly where to annotate the commands in the
> trouble report. I attached the log file to the e-mail and kept a list of the
> filters I switched to. The fluorescent light source is a lumencor spectra
> LED light source.

Instead of posting here, please use the "send" button.  That will give
me information missing in this file, and useful for understanding what
is going on.

Also, please do not switch the channel, but go into the device/property
browser and move only the reflector turret.  This will isolate the issue
from other things going on.  It is - for instance - possible that in
isolation the turret moves fine (which would already give insight in
what the actual problem may be).

Best,


Nico



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Re: Trouble switching filter cubes Zeiss Observer.Z1

Stuurman, Nico
Summarizing this thread:

Alina reported that - after a firmware update - the Zeiss AxioObserver
Z1 had problems switching between channel configurations in
Micro-Manager.  Although evidence is a bit scarce (since I have been
helping remotely), it seems that the new Zeiss firmware no longer allows
for fluorescence turret movements while the reflected light shutter is
open (a pull request on github for an upright Zeiss scope suggested the
same problem.

This change was doubtlessly made to improve safety, but is quite
annoying when using an LED light source that has its own "shutter" (as
Alina had).  Alina solved the problem by using the "multi-shutter"
device in the "Utility" device adapter to combine both the LED shutter
and Zeiss reflected light shutter in one "virtual" shutter.  Downside of
that approach is that the Zeiss reflected light shutter is much slower
than the LED.

If anyone runs into this same issue again, it would be good to ask Zeiss
if there is any way to go around this limitation.

Best,

Nico




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