Configuring a Zeiss Axio Observer Z1

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Configuring a Zeiss Axio Observer Z1

Shaw A.N.

Hi all,

 

I am trying to use the hardware configuration wizard to setup this microscope with Micromanager and am having issues connecting. I have read that I need to use the ZeissCAN29 and have tried connected to some of the dropdown options in the wizard but get the following error. I realised it may have something to do with the “COM port” that the microscope is plugged into, and read that this particular microscope only uses serial interface (https://micro-manager.org/wiki/ZeissCAN29) and that USB is not supported. I originally had a USB to USB connection which I changed to a serial port to USB connection, but this still does not work. In device manager, I have checked to see which “COM port” the microscope is connected to – it is connected to ports 6 & 7 via a 2-way splitter. Unfortunately I cannot “see” these ports in the configuration wizard, I can only see ports 3,4,5 and TCP/IP serial port adapter, non of which are what I am trying to connect to. The “scan ports” button in the wizard is grey-out so I cannot perform that function at all. This is my first time trying to setup a microscope using micromanager so would appreciate any help in resolving this issue. Please can someone

 

Sent from Mail for Windows 10

 



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Re: Configuring a Zeiss Axio Observer Z1

Stuurman, Nico
Hi A.N.

> I am trying to use the hardware configuration wizard to setup this
> microscope with Micromanager and am having issues connecting.
>

> I originally had a USB to USB connection which I changed to a serial
> port to USB connection, but this still does not work.
>

What type of serial cable are you using?  It is essential that you use
the original Zeiss serial cable, or an equivalent (female to female null
modem, although I vaguely remember there may be more requirements to
that cable), otherwise things will not work.

> In device manager, I have checked to see which “COM port” the
> microscope is connected to – it is connected to ports 6 & 7 via a
> 2-way splitter.
>

Do you mean that you have a USB to serial converter that has two serial
end points?  In that case you may need to test both COM6 and COM7 (or
make your life easier and get a USB to serial converter with a single
COM port).

> Unfortunately I cannot “see” these ports in the configuration wizard,
> I can only see ports 3,4,5 and TCP/IP serial port adapter, non of
> which are what I am trying to connect to.
>

Restarting Micro-Manager should show all COM ports visible in the
Windows device manager.  If that is not the case, there is something
strange going on with your USB to serial converter.

Once you have all that worked out, make sure that you select the correct
COM port, and apply the correct settings.  Most important is the
baudrate, which should be 57600.  Also, if you used the microscope
before through the USB interface, make sure that you power-cycle the
microscope before connecting.

This is all based on information you can find here:
https://micro-manager.org/wiki/ZeissCAN29 (or click "Help" in the
Hardware conifguration wizard).


Best,


Nico





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Re: Configuring a Zeiss Axio Observer Z1

Shaw A.N.

Hi Nico,

 

Thanks for getting back to me.

 

I am using a female to female cable to connect the microscope to the PC. I am unsure whether it is the original as we have received a lot of our laboratory equipment in a shipment from an old lab so I do not know what is original and what may have been changed over the years.

 

Yes I have a USB to serial converter that has two serial end points as I had no other option immediately available in my lab. Yes I could test out a single connection converter. I’ll test out these things and see if I make any progress.

 

Thanks,

 

Alex Shaw MRes

 

Research Technician

Ward Ober Group

Centre for Cancer Immunology

University of Southampton (SGH)

 

02381205624

 


From: Stuurman, Nico <[hidden email]>
Sent: Thursday, February 13, 2020 6:16:01 PM
To: Micro-Manager General <[hidden email]>
Subject: Re: [micro-manager-general] Configuring a Zeiss Axio Observer Z1
 
Hi A.N.

> I am trying to use the hardware configuration wizard to setup this
> microscope with Micromanager and am having issues connecting.
>

> I originally had a USB to USB connection which I changed to a serial
> port to USB connection, but this still does not work.
>

What type of serial cable are you using?  It is essential that you use
the original Zeiss serial cable, or an equivalent (female to female null
modem, although I vaguely remember there may be more requirements to
that cable), otherwise things will not work.

> In device manager, I have checked to see which “COM port” the
> microscope is connected to – it is connected to ports 6 & 7 via a
> 2-way splitter.
>

Do you mean that you have a USB to serial converter that has two serial
end points?  In that case you may need to test both COM6 and COM7 (or
make your life easier and get a USB to serial converter with a single
COM port).

> Unfortunately I cannot “see” these ports in the configuration wizard,
> I can only see ports 3,4,5 and TCP/IP serial port adapter, non of
> which are what I am trying to connect to.
>

Restarting Micro-Manager should show all COM ports visible in the
Windows device manager.  If that is not the case, there is something
strange going on with your USB to serial converter.

Once you have all that worked out, make sure that you select the correct
COM port, and apply the correct settings.  Most important is the
baudrate, which should be 57600.  Also, if you used the microscope
before through the USB interface, make sure that you power-cycle the
microscope before connecting.

This is all based on information you can find here:
https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicro-manager.org%2Fwiki%2FZeissCAN29&amp;data=01%7C01%7CA.shaw%40soton.ac.uk%7C0c9ad3a650fe4c0e268808d7b0b12669%7C4a5378f929f44d3ebe89669d03ada9d8%7C0&amp;sdata=otlzaUnWJEq%2F5JT9uEz58rCeusCOYEeofEGEsvw4Rvw%3D&amp;reserved=0 (or click "Help" in the
Hardware conifguration wizard).


Best,


Nico





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