hardware configuration wizard

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hardware configuration wizard

zhoulab2017
Dear micro-manager friends,

    I am new to the software and I would like to set up the software for our Zeiss LSM510 system as we want to do some customized upgrading of hardware (autofocus from ASI, sCMOS camera and a LED light source). As these new hardware will be mounted on the existing Observer Z1, so I was trying to establish the configuration for the current LSM hardware. However, when I try to add "ZeissScope| Zeiss AxioObserver controlled through serial interface" under the folder "ZeissCAN29", I keep get error msg "Error in device "COM1": Unknown eroor in the device (1)". Also I know there is no DefiniteFocus in our scope, but I cannot delete that property from the list. I tried different port, from COM1 to others, no luck. I tried to "Scan", but I was told that "This device does not support auto-detection. You have to manually choose port and settings". The microscope is running fine with the AIM software, so I know the system is fine. Can anyone provide input how to start? Thanks a lot!

Kai Zhou
Buck Institute for research on aging


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Re: hardware configuration wizard

Stuurman, Nico
Hi Kai,

>     I am new to the software and I would like to set up the software
> for our Zeiss LSM510 system as we want to do some customized upgrading
> of hardware (autofocus from ASI, sCMOS camera and a LED light source).
> As these new hardware will be mounted on the existing Observer Z1, so
> I was trying to establish the configuration for the current LSM
> hardware. However, when I try to add "ZeissScope| Zeiss AxioObserver
> controlled through serial interface" under the folder "ZeissCAN29", I
> keep get error msg "Error in device "COM1": Unknown eroor in the
> device (1)".

Do you have the microscope attached using a serial cable to COM1 of your
computer?  Also, if you operate the microscope normally through USB, you
may need to power cycle the microscope first.

Best,

Nico



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Re: hardware configuration wizard

zhoulab2017
Dear Nico,

  Thanks for your reply! I confirm that the scope is correctly connected to the COM1 through serial cable as that's also required for AIM to operate the system. Can you explain a little bit more about how to power cycle the microscope? I tried the configuration after people has used the AIM and microscope, but still the same error msg. 

Best,
Kai

On Wed, Apr 24, 2019 at 2:44 PM Stuurman, Nico <[hidden email]> wrote:
Hi Kai,

>     I am new to the software and I would like to set up the software
> for our Zeiss LSM510 system as we want to do some customized upgrading
> of hardware (autofocus from ASI, sCMOS camera and a LED light source).
> As these new hardware will be mounted on the existing Observer Z1, so
> I was trying to establish the configuration for the current LSM
> hardware. However, when I try to add "ZeissScope| Zeiss AxioObserver
> controlled through serial interface" under the folder "ZeissCAN29", I
> keep get error msg "Error in device "COM1": Unknown eroor in the
> device (1)".

Do you have the microscope attached using a serial cable to COM1 of your
computer?  Also, if you operate the microscope normally through USB, you
may need to power cycle the microscope first.

Best,

Nico



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Re: hardware configuration wizard

Stuurman, Nico
On 4/24/19 3:25 PM, Chuankai Zhou wrote:

> >     I am new to the software and I would like to set up the software
>
>     > for our Zeiss LSM510 system as we want to do some customized
>     upgrading
>     > of hardware (autofocus from ASI, sCMOS camera and a LED light
>     source).
>     > As these new hardware will be mounted on the existing Observer
>     Z1, so
>     > I was trying to establish the configuration for the current LSM
>     > hardware. However, when I try to add "ZeissScope| Zeiss
>     AxioObserver
>     > controlled through serial interface" under the folder
>     "ZeissCAN29", I
>     > keep get error msg "Error in device "COM1": Unknown eroor in the
>     > device (1)".
>
>     Do you have the microscope attached using a serial cable to COM1
>     of your
>     computer?  Also, if you operate the microscope normally through
>     USB, you
>     may need to power cycle the microscope first.
>

> Thanks for your reply! I confirm that the scope is correctly connected
> to the COM1 through serial cable as that's also required for AIM to
> operate the system. Can you explain a little bit more about how to
> power cycle the microscope? I tried the configuration after people has
> used the AIM and microscope, but still the same error msg.

Does the LSM510 come with an AxioObserver?  Aren't those the
Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
adapter.  I think that autodetection works for the Axiovert, otherwise
do make sure you have the correct serial port settings (see the MM website).

Best,

Nico



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Re: hardware configuration wizard

zhoulab2017
Yes, the LSM510 meta we have is with Observer. Z1, I just triple checked. Do you mean use the serialManager to resolve the problem? 

On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
On 4/24/19 3:25 PM, Chuankai Zhou wrote:
> >     I am new to the software and I would like to set up the software
>
>     > for our Zeiss LSM510 system as we want to do some customized
>     upgrading
>     > of hardware (autofocus from ASI, sCMOS camera and a LED light
>     source).
>     > As these new hardware will be mounted on the existing Observer
>     Z1, so
>     > I was trying to establish the configuration for the current LSM
>     > hardware. However, when I try to add "ZeissScope| Zeiss
>     AxioObserver
>     > controlled through serial interface" under the folder
>     "ZeissCAN29", I
>     > keep get error msg "Error in device "COM1": Unknown eroor in the
>     > device (1)".
>
>     Do you have the microscope attached using a serial cable to COM1
>     of your
>     computer?  Also, if you operate the microscope normally through
>     USB, you
>     may need to power cycle the microscope first.
>

> Thanks for your reply! I confirm that the scope is correctly connected
> to the COM1 through serial cable as that's also required for AIM to
> operate the system. Can you explain a little bit more about how to
> power cycle the microscope? I tried the configuration after people has
> used the AIM and microscope, but still the same error msg.

Does the LSM510 come with an AxioObserver?  Aren't those the
Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
adapter.  I think that autodetection works for the Axiovert, otherwise
do make sure you have the correct serial port settings (see the MM website).

Best,

Nico



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Re: hardware configuration wizard

zhoulab2017
In reply to this post by Stuurman, Nico
Hi Nico,

   Looks like the Observer Z1 is not connected through serial port, but through USB.......

On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
On 4/24/19 3:25 PM, Chuankai Zhou wrote:
> >     I am new to the software and I would like to set up the software
>
>     > for our Zeiss LSM510 system as we want to do some customized
>     upgrading
>     > of hardware (autofocus from ASI, sCMOS camera and a LED light
>     source).
>     > As these new hardware will be mounted on the existing Observer
>     Z1, so
>     > I was trying to establish the configuration for the current LSM
>     > hardware. However, when I try to add "ZeissScope| Zeiss
>     AxioObserver
>     > controlled through serial interface" under the folder
>     "ZeissCAN29", I
>     > keep get error msg "Error in device "COM1": Unknown eroor in the
>     > device (1)".
>
>     Do you have the microscope attached using a serial cable to COM1
>     of your
>     computer?  Also, if you operate the microscope normally through
>     USB, you
>     may need to power cycle the microscope first.
>

> Thanks for your reply! I confirm that the scope is correctly connected
> to the COM1 through serial cable as that's also required for AIM to
> operate the system. Can you explain a little bit more about how to
> power cycle the microscope? I tried the configuration after people has
> used the AIM and microscope, but still the same error msg.

Does the LSM510 come with an AxioObserver?  Aren't those the
Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
adapter.  I think that autodetection works for the Axiovert, otherwise
do make sure you have the correct serial port settings (see the MM website).

Best,

Nico



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Re: hardware configuration wizard

Chon U Chan
HI Chuankai:

If I understand correctly, your goal is to control an Observer Z1 with
Micromanager. If so, I have recently done so, and here are the steps:

1. Get a "Null Modem Cable, UL, DB9 Female to Female"

2. Turn off the Z1 base, and unplug the USB cable connected it to the PC

3. Connect the Null cable, one end to the PC serial port,  the other
to the CAN29 bus on the Z1 base.
the CAN29 bus is on the panel labeled "Main", DB9 male.

4. Turn on the Z1 base, wait for it to be completely on.

5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
Config. Wizard", add the applicable hardware under the "ZeissCAN29"
folder.
If the Status returns OK, you are all set.

Regards,

Chon




On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:

>
> Hi Nico,
>
>    Looks like the Observer Z1 is not connected through serial port, but through USB.......
>
> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
>>
>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
>> > >     I am new to the software and I would like to set up the software
>> >
>> >     > for our Zeiss LSM510 system as we want to do some customized
>> >     upgrading
>> >     > of hardware (autofocus from ASI, sCMOS camera and a LED light
>> >     source).
>> >     > As these new hardware will be mounted on the existing Observer
>> >     Z1, so
>> >     > I was trying to establish the configuration for the current LSM
>> >     > hardware. However, when I try to add "ZeissScope| Zeiss
>> >     AxioObserver
>> >     > controlled through serial interface" under the folder
>> >     "ZeissCAN29", I
>> >     > keep get error msg "Error in device "COM1": Unknown eroor in the
>> >     > device (1)".
>> >
>> >     Do you have the microscope attached using a serial cable to COM1
>> >     of your
>> >     computer?  Also, if you operate the microscope normally through
>> >     USB, you
>> >     may need to power cycle the microscope first.
>> >
>>
>> > Thanks for your reply! I confirm that the scope is correctly connected
>> > to the COM1 through serial cable as that's also required for AIM to
>> > operate the system. Can you explain a little bit more about how to
>> > power cycle the microscope? I tried the configuration after people has
>> > used the AIM and microscope, but still the same error msg.
>>
>> Does the LSM510 come with an AxioObserver?  Aren't those the
>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
>> adapter.  I think that autodetection works for the Axiovert, otherwise
>> do make sure you have the correct serial port settings (see the MM website).
>>
>> Best,
>>
>> Nico
>>
>>
>>
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: hardware configuration wizard

zhoulab2017
Hi Chon,

  Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!

Thanks!

Kai

Sent from my iPhone

> On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
>
> HI Chuankai:
>
> If I understand correctly, your goal is to control an Observer Z1 with
> Micromanager. If so, I have recently done so, and here are the steps:
>
> 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
>
> 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
>
> 3. Connect the Null cable, one end to the PC serial port,  the other
> to the CAN29 bus on the Z1 base.
> the CAN29 bus is on the panel labeled "Main", DB9 male.
>
> 4. Turn on the Z1 base, wait for it to be completely on.
>
> 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
> Config. Wizard", add the applicable hardware under the "ZeissCAN29"
> folder.
> If the Status returns OK, you are all set.
>
> Regards,
>
> Chon
>
>
>
>
>> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
>>
>> Hi Nico,
>>
>>   Looks like the Observer Z1 is not connected through serial port, but through USB.......
>>
>>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
>>>
>>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
>>>>>    I am new to the software and I would like to set up the software
>>>>
>>>>> for our Zeiss LSM510 system as we want to do some customized
>>>>    upgrading
>>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
>>>>    source).
>>>>> As these new hardware will be mounted on the existing Observer
>>>>    Z1, so
>>>>> I was trying to establish the configuration for the current LSM
>>>>> hardware. However, when I try to add "ZeissScope| Zeiss
>>>>    AxioObserver
>>>>> controlled through serial interface" under the folder
>>>>    "ZeissCAN29", I
>>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
>>>>> device (1)".
>>>>
>>>>    Do you have the microscope attached using a serial cable to COM1
>>>>    of your
>>>>    computer?  Also, if you operate the microscope normally through
>>>>    USB, you
>>>>    may need to power cycle the microscope first.
>>>>
>>>
>>>> Thanks for your reply! I confirm that the scope is correctly connected
>>>> to the COM1 through serial cable as that's also required for AIM to
>>>> operate the system. Can you explain a little bit more about how to
>>>> power cycle the microscope? I tried the configuration after people has
>>>> used the AIM and microscope, but still the same error msg.
>>>
>>> Does the LSM510 come with an AxioObserver?  Aren't those the
>>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
>>> adapter.  I think that autodetection works for the Axiovert, otherwise
>>> do make sure you have the correct serial port settings (see the MM website).
>>>
>>> Best,
>>>
>>> Nico
>>>
>>>
>>>
>>> _______________________________________________
>>> micro-manager-general mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: hardware configuration wizard

Chon U Chan
Could you elaborate more why do you want to use AIM/Zen to control the
motorized stage? It sounds to me you can do all with Micromanager
alone.

You can't connect the Z1 base to two separate protocol simultaneously.
Once the Z1 base finds the USB interface, it will ignore the CAN9,
vise verse.

Regards,

Chon

On Thu, 25 Apr 2019 at 00:39, <[hidden email]> wrote:

>
> Hi Chon,
>
>   Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!
>
> Thanks!
>
> Kai
>
> Sent from my iPhone
>
> > On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
> >
> > HI Chuankai:
> >
> > If I understand correctly, your goal is to control an Observer Z1 with
> > Micromanager. If so, I have recently done so, and here are the steps:
> >
> > 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
> >
> > 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
> >
> > 3. Connect the Null cable, one end to the PC serial port,  the other
> > to the CAN29 bus on the Z1 base.
> > the CAN29 bus is on the panel labeled "Main", DB9 male.
> >
> > 4. Turn on the Z1 base, wait for it to be completely on.
> >
> > 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
> > Config. Wizard", add the applicable hardware under the "ZeissCAN29"
> > folder.
> > If the Status returns OK, you are all set.
> >
> > Regards,
> >
> > Chon
> >
> >
> >
> >
> >> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
> >>
> >> Hi Nico,
> >>
> >>   Looks like the Observer Z1 is not connected through serial port, but through USB.......
> >>
> >>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
> >>>
> >>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
> >>>>>    I am new to the software and I would like to set up the software
> >>>>
> >>>>> for our Zeiss LSM510 system as we want to do some customized
> >>>>    upgrading
> >>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
> >>>>    source).
> >>>>> As these new hardware will be mounted on the existing Observer
> >>>>    Z1, so
> >>>>> I was trying to establish the configuration for the current LSM
> >>>>> hardware. However, when I try to add "ZeissScope| Zeiss
> >>>>    AxioObserver
> >>>>> controlled through serial interface" under the folder
> >>>>    "ZeissCAN29", I
> >>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
> >>>>> device (1)".
> >>>>
> >>>>    Do you have the microscope attached using a serial cable to COM1
> >>>>    of your
> >>>>    computer?  Also, if you operate the microscope normally through
> >>>>    USB, you
> >>>>    may need to power cycle the microscope first.
> >>>>
> >>>
> >>>> Thanks for your reply! I confirm that the scope is correctly connected
> >>>> to the COM1 through serial cable as that's also required for AIM to
> >>>> operate the system. Can you explain a little bit more about how to
> >>>> power cycle the microscope? I tried the configuration after people has
> >>>> used the AIM and microscope, but still the same error msg.
> >>>
> >>> Does the LSM510 come with an AxioObserver?  Aren't those the
> >>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
> >>> adapter.  I think that autodetection works for the Axiovert, otherwise
> >>> do make sure you have the correct serial port settings (see the MM website).
> >>>
> >>> Best,
> >>>
> >>> Nico
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> micro-manager-general mailing list
> >>> [hidden email]
> >>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>
> >> _______________________________________________
> >> micro-manager-general mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >
> >
> > _______________________________________________
> > micro-manager-general mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: hardware configuration wizard

zhoulab2017
Hi Chon,

 It is just for convenience as the system (LSM+confocor3) are running well with Aim at this moment and completely overwrite AIM with micromanager will be a lot for us to take. Also this LSM510 meta was built for facility in the beginning, so there are 7 laser lines and the LSM part has too many filters and light paths, I feel it will be a huge project to configure them and completely switch to micromanager. Also we need to do FCS sometimes and the protocol in AIM is the one we are familiar with. It probably fine when we get more familiar with micromanager down the road.

So probably every time I need to switch the cable when switch the protocol/software? Will micromanager overwrite some setting in the hardware(probably only the z1 base which is shared between micromanager and AIM/Zen) and make AIM/Zen not compatible with it?


Thanks!
Kai

Sent from my iPhone

> On Apr 24, 2019, at 10:22 PM, Chon U Chan <[hidden email]> wrote:
>
> Could you elaborate more why do you want to use AIM/Zen to control the
> motorized stage? It sounds to me you can do all with Micromanager
> alone.
>
> You can't connect the Z1 base to two separate protocol simultaneously.
> Once the Z1 base finds the USB interface, it will ignore the CAN9,
> vise verse.
>
> Regards,
>
> Chon
>
>> On Thu, 25 Apr 2019 at 00:39, <[hidden email]> wrote:
>>
>> Hi Chon,
>>
>> Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!
>>
>> Thanks!
>>
>> Kai
>>
>> Sent from my iPhone
>>
>>> On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
>>>
>>> HI Chuankai:
>>>
>>> If I understand correctly, your goal is to control an Observer Z1 with
>>> Micromanager. If so, I have recently done so, and here are the steps:
>>>
>>> 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
>>>
>>> 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
>>>
>>> 3. Connect the Null cable, one end to the PC serial port,  the other
>>> to the CAN29 bus on the Z1 base.
>>> the CAN29 bus is on the panel labeled "Main", DB9 male.
>>>
>>> 4. Turn on the Z1 base, wait for it to be completely on.
>>>
>>> 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
>>> Config. Wizard", add the applicable hardware under the "ZeissCAN29"
>>> folder.
>>> If the Status returns OK, you are all set.
>>>
>>> Regards,
>>>
>>> Chon
>>>
>>>
>>>
>>>
>>>> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
>>>>
>>>> Hi Nico,
>>>>
>>>> Looks like the Observer Z1 is not connected through serial port, but through USB.......
>>>>
>>>>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
>>>>>
>>>>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
>>>>>>>  I am new to the software and I would like to set up the software
>>>>>>
>>>>>>> for our Zeiss LSM510 system as we want to do some customized
>>>>>>  upgrading
>>>>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
>>>>>>  source).
>>>>>>> As these new hardware will be mounted on the existing Observer
>>>>>>  Z1, so
>>>>>>> I was trying to establish the configuration for the current LSM
>>>>>>> hardware. However, when I try to add "ZeissScope| Zeiss
>>>>>>  AxioObserver
>>>>>>> controlled through serial interface" under the folder
>>>>>>  "ZeissCAN29", I
>>>>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
>>>>>>> device (1)".
>>>>>>
>>>>>>  Do you have the microscope attached using a serial cable to COM1
>>>>>>  of your
>>>>>>  computer?  Also, if you operate the microscope normally through
>>>>>>  USB, you
>>>>>>  may need to power cycle the microscope first.
>>>>>
>>>>>> Thanks for your reply! I confirm that the scope is correctly connected
>>>>>> to the COM1 through serial cable as that's also required for AIM to
>>>>>> operate the system. Can you explain a little bit more about how to
>>>>>> power cycle the microscope? I tried the configuration after people has
>>>>>> used the AIM and microscope, but still the same error msg.
>>>>>
>>>>> Does the LSM510 come with an AxioObserver?  Aren't those the
>>>>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
>>>>> adapter.  I think that autodetection works for the Axiovert, otherwise
>>>>> do make sure you have the correct serial port settings (see the MM website).
>>>>>
>>>>> Best,
>>>>>
>>>>> Nico
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> micro-manager-general mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>
>>>> _______________________________________________
>>>> micro-manager-general mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>
>>>
>>> _______________________________________________
>>> micro-manager-general mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> _______________________________________________
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> [hidden email]
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Re: hardware configuration wizard

Chon U Chan
So long as every hardware is added to MMG, you can group them into a
single configuration, so having more components shouldn't be a
problem.

We do switch between Zen and MMG frequently due to user preference -
no problem at all.

I would suggest you start off by configuring your LSM with MMG - if
you can't do it within a reasonable time, just use AIM/Zen. In that
case, their engineer will do everything for you - for a price.

Regards,

Chon

On Thu, 25 Apr 2019 at 02:23, <[hidden email]> wrote:

>
> Hi Chon,
>
>  It is just for convenience as the system (LSM+confocor3) are running well with Aim at this moment and completely overwrite AIM with micromanager will be a lot for us to take. Also this LSM510 meta was built for facility in the beginning, so there are 7 laser lines and the LSM part has too many filters and light paths, I feel it will be a huge project to configure them and completely switch to micromanager. Also we need to do FCS sometimes and the protocol in AIM is the one we are familiar with. It probably fine when we get more familiar with micromanager down the road.
>
> So probably every time I need to switch the cable when switch the protocol/software? Will micromanager overwrite some setting in the hardware(probably only the z1 base which is shared between micromanager and AIM/Zen) and make AIM/Zen not compatible with it?
>
>
> Thanks!
> Kai
>
> Sent from my iPhone
>
> > On Apr 24, 2019, at 10:22 PM, Chon U Chan <[hidden email]> wrote:
> >
> > Could you elaborate more why do you want to use AIM/Zen to control the
> > motorized stage? It sounds to me you can do all with Micromanager
> > alone.
> >
> > You can't connect the Z1 base to two separate protocol simultaneously.
> > Once the Z1 base finds the USB interface, it will ignore the CAN9,
> > vise verse.
> >
> > Regards,
> >
> > Chon
> >
> >> On Thu, 25 Apr 2019 at 00:39, <[hidden email]> wrote:
> >>
> >> Hi Chon,
> >>
> >> Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!
> >>
> >> Thanks!
> >>
> >> Kai
> >>
> >> Sent from my iPhone
> >>
> >>> On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
> >>>
> >>> HI Chuankai:
> >>>
> >>> If I understand correctly, your goal is to control an Observer Z1 with
> >>> Micromanager. If so, I have recently done so, and here are the steps:
> >>>
> >>> 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
> >>>
> >>> 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
> >>>
> >>> 3. Connect the Null cable, one end to the PC serial port,  the other
> >>> to the CAN29 bus on the Z1 base.
> >>> the CAN29 bus is on the panel labeled "Main", DB9 male.
> >>>
> >>> 4. Turn on the Z1 base, wait for it to be completely on.
> >>>
> >>> 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
> >>> Config. Wizard", add the applicable hardware under the "ZeissCAN29"
> >>> folder.
> >>> If the Status returns OK, you are all set.
> >>>
> >>> Regards,
> >>>
> >>> Chon
> >>>
> >>>
> >>>
> >>>
> >>>> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
> >>>>
> >>>> Hi Nico,
> >>>>
> >>>> Looks like the Observer Z1 is not connected through serial port, but through USB.......
> >>>>
> >>>>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
> >>>>>
> >>>>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
> >>>>>>>  I am new to the software and I would like to set up the software
> >>>>>>
> >>>>>>> for our Zeiss LSM510 system as we want to do some customized
> >>>>>>  upgrading
> >>>>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
> >>>>>>  source).
> >>>>>>> As these new hardware will be mounted on the existing Observer
> >>>>>>  Z1, so
> >>>>>>> I was trying to establish the configuration for the current LSM
> >>>>>>> hardware. However, when I try to add "ZeissScope| Zeiss
> >>>>>>  AxioObserver
> >>>>>>> controlled through serial interface" under the folder
> >>>>>>  "ZeissCAN29", I
> >>>>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
> >>>>>>> device (1)".
> >>>>>>
> >>>>>>  Do you have the microscope attached using a serial cable to COM1
> >>>>>>  of your
> >>>>>>  computer?  Also, if you operate the microscope normally through
> >>>>>>  USB, you
> >>>>>>  may need to power cycle the microscope first.
> >>>>>
> >>>>>> Thanks for your reply! I confirm that the scope is correctly connected
> >>>>>> to the COM1 through serial cable as that's also required for AIM to
> >>>>>> operate the system. Can you explain a little bit more about how to
> >>>>>> power cycle the microscope? I tried the configuration after people has
> >>>>>> used the AIM and microscope, but still the same error msg.
> >>>>>
> >>>>> Does the LSM510 come with an AxioObserver?  Aren't those the
> >>>>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
> >>>>> adapter.  I think that autodetection works for the Axiovert, otherwise
> >>>>> do make sure you have the correct serial port settings (see the MM website).
> >>>>>
> >>>>> Best,
> >>>>>
> >>>>> Nico
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> micro-manager-general mailing list
> >>>>> [hidden email]
> >>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>>
> >>>> _______________________________________________
> >>>> micro-manager-general mailing list
> >>>> [hidden email]
> >>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>
> >>>
> >>> _______________________________________________
> >>> micro-manager-general mailing list
> >>> [hidden email]
> >>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>
> >>
> >> _______________________________________________
> >> micro-manager-general mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >
> >
> > _______________________________________________
> > micro-manager-general mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general


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Re: hardware configuration wizard

zhoulab2017
Thanks so much for your suggestions! Do you know any engineer who can help with configuration of MM? I was thinking about change the USB to Modem cable and have AIM/Zen adapt to the Modem cable as well so I don’t need to switch in between. I really like MM as I like to have more control on the software side and allow users to customize the program a little bit, or even add new function that not exist in commercial software. I would like to switch to MM as much as possible. Thanks again!

Kai

Sent from my iPhone

> On Apr 25, 2019, at 6:00 AM, Chon U Chan <[hidden email]> wrote:
>
> So long as every hardware is added to MMG, you can group them into a
> single configuration, so having more components shouldn't be a
> problem.
>
> We do switch between Zen and MMG frequently due to user preference -
> no problem at all.
>
> I would suggest you start off by configuring your LSM with MMG - if
> you can't do it within a reasonable time, just use AIM/Zen. In that
> case, their engineer will do everything for you - for a price.
>
> Regards,
>
> Chon
>
>> On Thu, 25 Apr 2019 at 02:23, <[hidden email]> wrote:
>>
>> Hi Chon,
>>
>> It is just for convenience as the system (LSM+confocor3) are running well with Aim at this moment and completely overwrite AIM with micromanager will be a lot for us to take. Also this LSM510 meta was built for facility in the beginning, so there are 7 laser lines and the LSM part has too many filters and light paths, I feel it will be a huge project to configure them and completely switch to micromanager. Also we need to do FCS sometimes and the protocol in AIM is the one we are familiar with. It probably fine when we get more familiar with micromanager down the road.
>>
>> So probably every time I need to switch the cable when switch the protocol/software? Will micromanager overwrite some setting in the hardware(probably only the z1 base which is shared between micromanager and AIM/Zen) and make AIM/Zen not compatible with it?
>>
>>
>> Thanks!
>> Kai
>>
>> Sent from my iPhone
>>
>>> On Apr 24, 2019, at 10:22 PM, Chon U Chan <[hidden email]> wrote:
>>>
>>> Could you elaborate more why do you want to use AIM/Zen to control the
>>> motorized stage? It sounds to me you can do all with Micromanager
>>> alone.
>>>
>>> You can't connect the Z1 base to two separate protocol simultaneously.
>>> Once the Z1 base finds the USB interface, it will ignore the CAN9,
>>> vise verse.
>>>
>>> Regards,
>>>
>>> Chon
>>>
>>>> On Thu, 25 Apr 2019 at 00:39, <[hidden email]> wrote:
>>>>
>>>> Hi Chon,
>>>>
>>>> Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!
>>>>
>>>> Thanks!
>>>>
>>>> Kai
>>>>
>>>> Sent from my iPhone
>>>>
>>>>> On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
>>>>>
>>>>> HI Chuankai:
>>>>>
>>>>> If I understand correctly, your goal is to control an Observer Z1 with
>>>>> Micromanager. If so, I have recently done so, and here are the steps:
>>>>>
>>>>> 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
>>>>>
>>>>> 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
>>>>>
>>>>> 3. Connect the Null cable, one end to the PC serial port,  the other
>>>>> to the CAN29 bus on the Z1 base.
>>>>> the CAN29 bus is on the panel labeled "Main", DB9 male.
>>>>>
>>>>> 4. Turn on the Z1 base, wait for it to be completely on.
>>>>>
>>>>> 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
>>>>> Config. Wizard", add the applicable hardware under the "ZeissCAN29"
>>>>> folder.
>>>>> If the Status returns OK, you are all set.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Chon
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Nico,
>>>>>>
>>>>>> Looks like the Observer Z1 is not connected through serial port, but through USB.......
>>>>>>
>>>>>>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
>>>>>>>
>>>>>>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
>>>>>>>>> I am new to the software and I would like to set up the software
>>>>>>>>
>>>>>>>>> for our Zeiss LSM510 system as we want to do some customized
>>>>>>>> upgrading
>>>>>>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
>>>>>>>> source).
>>>>>>>>> As these new hardware will be mounted on the existing Observer
>>>>>>>> Z1, so
>>>>>>>>> I was trying to establish the configuration for the current LSM
>>>>>>>>> hardware. However, when I try to add "ZeissScope| Zeiss
>>>>>>>> AxioObserver
>>>>>>>>> controlled through serial interface" under the folder
>>>>>>>> "ZeissCAN29", I
>>>>>>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
>>>>>>>>> device (1)".
>>>>>>>>
>>>>>>>> Do you have the microscope attached using a serial cable to COM1
>>>>>>>> of your
>>>>>>>> computer?  Also, if you operate the microscope normally through
>>>>>>>> USB, you
>>>>>>>> may need to power cycle the microscope first.
>>>>>>>
>>>>>>>> Thanks for your reply! I confirm that the scope is correctly connected
>>>>>>>> to the COM1 through serial cable as that's also required for AIM to
>>>>>>>> operate the system. Can you explain a little bit more about how to
>>>>>>>> power cycle the microscope? I tried the configuration after people has
>>>>>>>> used the AIM and microscope, but still the same error msg.
>>>>>>>
>>>>>>> Does the LSM510 come with an AxioObserver?  Aren't those the
>>>>>>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
>>>>>>> adapter.  I think that autodetection works for the Axiovert, otherwise
>>>>>>> do make sure you have the correct serial port settings (see the MM website).
>>>>>>>
>>>>>>> Best,
>>>>>>>
>>>>>>> Nico
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> micro-manager-general mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>>>
>>>>>> _______________________________________________
>>>>>> micro-manager-general mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> micro-manager-general mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>
>>>>
>>>> _______________________________________________
>>>> micro-manager-general mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>
>>>
>>> _______________________________________________
>>> micro-manager-general mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> _______________________________________________
> micro-manager-general mailing list
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Re: hardware configuration wizard

Chon U Chan
I asked half yr ago, Zeiss engineers are not allowed to work/advice on
MM at all.

As far as I know, "change the USB to Modem cable and have AIM/Zen
adapt to the Modem cable " won't work. But that is something you can
consult Zeiss engineer... keep us posted on the result please.

Regards,

Chon

On Thu, 25 Apr 2019 at 10:27, <[hidden email]> wrote:

>
> Thanks so much for your suggestions! Do you know any engineer who can help with configuration of MM? I was thinking about change the USB to Modem cable and have AIM/Zen adapt to the Modem cable as well so I don’t need to switch in between. I really like MM as I like to have more control on the software side and allow users to customize the program a little bit, or even add new function that not exist in commercial software. I would like to switch to MM as much as possible. Thanks again!
>
> Kai
>
> Sent from my iPhone
>
> > On Apr 25, 2019, at 6:00 AM, Chon U Chan <[hidden email]> wrote:
> >
> > So long as every hardware is added to MMG, you can group them into a
> > single configuration, so having more components shouldn't be a
> > problem.
> >
> > We do switch between Zen and MMG frequently due to user preference -
> > no problem at all.
> >
> > I would suggest you start off by configuring your LSM with MMG - if
> > you can't do it within a reasonable time, just use AIM/Zen. In that
> > case, their engineer will do everything for you - for a price.
> >
> > Regards,
> >
> > Chon
> >
> >> On Thu, 25 Apr 2019 at 02:23, <[hidden email]> wrote:
> >>
> >> Hi Chon,
> >>
> >> It is just for convenience as the system (LSM+confocor3) are running well with Aim at this moment and completely overwrite AIM with micromanager will be a lot for us to take. Also this LSM510 meta was built for facility in the beginning, so there are 7 laser lines and the LSM part has too many filters and light paths, I feel it will be a huge project to configure them and completely switch to micromanager. Also we need to do FCS sometimes and the protocol in AIM is the one we are familiar with. It probably fine when we get more familiar with micromanager down the road.
> >>
> >> So probably every time I need to switch the cable when switch the protocol/software? Will micromanager overwrite some setting in the hardware(probably only the z1 base which is shared between micromanager and AIM/Zen) and make AIM/Zen not compatible with it?
> >>
> >>
> >> Thanks!
> >> Kai
> >>
> >> Sent from my iPhone
> >>
> >>> On Apr 24, 2019, at 10:22 PM, Chon U Chan <[hidden email]> wrote:
> >>>
> >>> Could you elaborate more why do you want to use AIM/Zen to control the
> >>> motorized stage? It sounds to me you can do all with Micromanager
> >>> alone.
> >>>
> >>> You can't connect the Z1 base to two separate protocol simultaneously.
> >>> Once the Z1 base finds the USB interface, it will ignore the CAN9,
> >>> vise verse.
> >>>
> >>> Regards,
> >>>
> >>> Chon
> >>>
> >>>> On Thu, 25 Apr 2019 at 00:39, <[hidden email]> wrote:
> >>>>
> >>>> Hi Chon,
> >>>>
> >>>> Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!
> >>>>
> >>>> Thanks!
> >>>>
> >>>> Kai
> >>>>
> >>>> Sent from my iPhone
> >>>>
> >>>>> On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
> >>>>>
> >>>>> HI Chuankai:
> >>>>>
> >>>>> If I understand correctly, your goal is to control an Observer Z1 with
> >>>>> Micromanager. If so, I have recently done so, and here are the steps:
> >>>>>
> >>>>> 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
> >>>>>
> >>>>> 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
> >>>>>
> >>>>> 3. Connect the Null cable, one end to the PC serial port,  the other
> >>>>> to the CAN29 bus on the Z1 base.
> >>>>> the CAN29 bus is on the panel labeled "Main", DB9 male.
> >>>>>
> >>>>> 4. Turn on the Z1 base, wait for it to be completely on.
> >>>>>
> >>>>> 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
> >>>>> Config. Wizard", add the applicable hardware under the "ZeissCAN29"
> >>>>> folder.
> >>>>> If the Status returns OK, you are all set.
> >>>>>
> >>>>> Regards,
> >>>>>
> >>>>> Chon
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
> >>>>>>
> >>>>>> Hi Nico,
> >>>>>>
> >>>>>> Looks like the Observer Z1 is not connected through serial port, but through USB.......
> >>>>>>
> >>>>>>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
> >>>>>>>
> >>>>>>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
> >>>>>>>>> I am new to the software and I would like to set up the software
> >>>>>>>>
> >>>>>>>>> for our Zeiss LSM510 system as we want to do some customized
> >>>>>>>> upgrading
> >>>>>>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
> >>>>>>>> source).
> >>>>>>>>> As these new hardware will be mounted on the existing Observer
> >>>>>>>> Z1, so
> >>>>>>>>> I was trying to establish the configuration for the current LSM
> >>>>>>>>> hardware. However, when I try to add "ZeissScope| Zeiss
> >>>>>>>> AxioObserver
> >>>>>>>>> controlled through serial interface" under the folder
> >>>>>>>> "ZeissCAN29", I
> >>>>>>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
> >>>>>>>>> device (1)".
> >>>>>>>>
> >>>>>>>> Do you have the microscope attached using a serial cable to COM1
> >>>>>>>> of your
> >>>>>>>> computer?  Also, if you operate the microscope normally through
> >>>>>>>> USB, you
> >>>>>>>> may need to power cycle the microscope first.
> >>>>>>>
> >>>>>>>> Thanks for your reply! I confirm that the scope is correctly connected
> >>>>>>>> to the COM1 through serial cable as that's also required for AIM to
> >>>>>>>> operate the system. Can you explain a little bit more about how to
> >>>>>>>> power cycle the microscope? I tried the configuration after people has
> >>>>>>>> used the AIM and microscope, but still the same error msg.
> >>>>>>>
> >>>>>>> Does the LSM510 come with an AxioObserver?  Aren't those the
> >>>>>>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
> >>>>>>> adapter.  I think that autodetection works for the Axiovert, otherwise
> >>>>>>> do make sure you have the correct serial port settings (see the MM website).
> >>>>>>>
> >>>>>>> Best,
> >>>>>>>
> >>>>>>> Nico
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> micro-manager-general mailing list
> >>>>>>> [hidden email]
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> micro-manager-general mailing list
> >>>>>> [hidden email]
> >>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> micro-manager-general mailing list
> >>>>> [hidden email]
> >>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> micro-manager-general mailing list
> >>>> [hidden email]
> >>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>
> >>>
> >>> _______________________________________________
> >>> micro-manager-general mailing list
> >>> [hidden email]
> >>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>
> >>
> >> _______________________________________________
> >> micro-manager-general mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >
> >
> > _______________________________________________
> > micro-manager-general mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> _______________________________________________
> micro-manager-general mailing list
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Re: hardware configuration wizard

zhoulab2017
I have a friend who is a previous Zeiss engineer, he is the one help maintain this quite old LSM510 meta for us. I will talk to him and sort this out. Thanks for the suggestions! I will keep you updated.

On Thu, Apr 25, 2019 at 9:03 AM Chon U Chan <[hidden email]> wrote:
I asked half yr ago, Zeiss engineers are not allowed to work/advice on
MM at all.

As far as I know, "change the USB to Modem cable and have AIM/Zen
adapt to the Modem cable " won't work. But that is something you can
consult Zeiss engineer... keep us posted on the result please.

Regards,

Chon

On Thu, 25 Apr 2019 at 10:27, <[hidden email]> wrote:
>
> Thanks so much for your suggestions! Do you know any engineer who can help with configuration of MM? I was thinking about change the USB to Modem cable and have AIM/Zen adapt to the Modem cable as well so I don’t need to switch in between. I really like MM as I like to have more control on the software side and allow users to customize the program a little bit, or even add new function that not exist in commercial software. I would like to switch to MM as much as possible. Thanks again!
>
> Kai
>
> Sent from my iPhone
>
> > On Apr 25, 2019, at 6:00 AM, Chon U Chan <[hidden email]> wrote:
> >
> > So long as every hardware is added to MMG, you can group them into a
> > single configuration, so having more components shouldn't be a
> > problem.
> >
> > We do switch between Zen and MMG frequently due to user preference -
> > no problem at all.
> >
> > I would suggest you start off by configuring your LSM with MMG - if
> > you can't do it within a reasonable time, just use AIM/Zen. In that
> > case, their engineer will do everything for you - for a price.
> >
> > Regards,
> >
> > Chon
> >
> >> On Thu, 25 Apr 2019 at 02:23, <[hidden email]> wrote:
> >>
> >> Hi Chon,
> >>
> >> It is just for convenience as the system (LSM+confocor3) are running well with Aim at this moment and completely overwrite AIM with micromanager will be a lot for us to take. Also this LSM510 meta was built for facility in the beginning, so there are 7 laser lines and the LSM part has too many filters and light paths, I feel it will be a huge project to configure them and completely switch to micromanager. Also we need to do FCS sometimes and the protocol in AIM is the one we are familiar with. It probably fine when we get more familiar with micromanager down the road.
> >>
> >> So probably every time I need to switch the cable when switch the protocol/software? Will micromanager overwrite some setting in the hardware(probably only the z1 base which is shared between micromanager and AIM/Zen) and make AIM/Zen not compatible with it?
> >>
> >>
> >> Thanks!
> >> Kai
> >>
> >> Sent from my iPhone
> >>
> >>> On Apr 24, 2019, at 10:22 PM, Chon U Chan <[hidden email]> wrote:
> >>>
> >>> Could you elaborate more why do you want to use AIM/Zen to control the
> >>> motorized stage? It sounds to me you can do all with Micromanager
> >>> alone.
> >>>
> >>> You can't connect the Z1 base to two separate protocol simultaneously.
> >>> Once the Z1 base finds the USB interface, it will ignore the CAN9,
> >>> vise verse.
> >>>
> >>> Regards,
> >>>
> >>> Chon
> >>>
> >>>> On Thu, 25 Apr 2019 at 00:39, <[hidden email]> wrote:
> >>>>
> >>>> Hi Chon,
> >>>>
> >>>> Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!
> >>>>
> >>>> Thanks!
> >>>>
> >>>> Kai
> >>>>
> >>>> Sent from my iPhone
> >>>>
> >>>>> On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
> >>>>>
> >>>>> HI Chuankai:
> >>>>>
> >>>>> If I understand correctly, your goal is to control an Observer Z1 with
> >>>>> Micromanager. If so, I have recently done so, and here are the steps:
> >>>>>
> >>>>> 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
> >>>>>
> >>>>> 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
> >>>>>
> >>>>> 3. Connect the Null cable, one end to the PC serial port,  the other
> >>>>> to the CAN29 bus on the Z1 base.
> >>>>> the CAN29 bus is on the panel labeled "Main", DB9 male.
> >>>>>
> >>>>> 4. Turn on the Z1 base, wait for it to be completely on.
> >>>>>
> >>>>> 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
> >>>>> Config. Wizard", add the applicable hardware under the "ZeissCAN29"
> >>>>> folder.
> >>>>> If the Status returns OK, you are all set.
> >>>>>
> >>>>> Regards,
> >>>>>
> >>>>> Chon
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
> >>>>>>
> >>>>>> Hi Nico,
> >>>>>>
> >>>>>> Looks like the Observer Z1 is not connected through serial port, but through USB.......
> >>>>>>
> >>>>>>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
> >>>>>>>
> >>>>>>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
> >>>>>>>>> I am new to the software and I would like to set up the software
> >>>>>>>>
> >>>>>>>>> for our Zeiss LSM510 system as we want to do some customized
> >>>>>>>> upgrading
> >>>>>>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
> >>>>>>>> source).
> >>>>>>>>> As these new hardware will be mounted on the existing Observer
> >>>>>>>> Z1, so
> >>>>>>>>> I was trying to establish the configuration for the current LSM
> >>>>>>>>> hardware. However, when I try to add "ZeissScope| Zeiss
> >>>>>>>> AxioObserver
> >>>>>>>>> controlled through serial interface" under the folder
> >>>>>>>> "ZeissCAN29", I
> >>>>>>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
> >>>>>>>>> device (1)".
> >>>>>>>>
> >>>>>>>> Do you have the microscope attached using a serial cable to COM1
> >>>>>>>> of your
> >>>>>>>> computer?  Also, if you operate the microscope normally through
> >>>>>>>> USB, you
> >>>>>>>> may need to power cycle the microscope first.
> >>>>>>>
> >>>>>>>> Thanks for your reply! I confirm that the scope is correctly connected
> >>>>>>>> to the COM1 through serial cable as that's also required for AIM to
> >>>>>>>> operate the system. Can you explain a little bit more about how to
> >>>>>>>> power cycle the microscope? I tried the configuration after people has
> >>>>>>>> used the AIM and microscope, but still the same error msg.
> >>>>>>>
> >>>>>>> Does the LSM510 come with an AxioObserver?  Aren't those the
> >>>>>>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
> >>>>>>> adapter.  I think that autodetection works for the Axiovert, otherwise
> >>>>>>> do make sure you have the correct serial port settings (see the MM website).
> >>>>>>>
> >>>>>>> Best,
> >>>>>>>
> >>>>>>> Nico
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> _______________________________________________
> >>>>>>> micro-manager-general mailing list
> >>>>>>> [hidden email]
> >>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> micro-manager-general mailing list
> >>>>>> [hidden email]
> >>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> micro-manager-general mailing list
> >>>>> [hidden email]
> >>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> micro-manager-general mailing list
> >>>> [hidden email]
> >>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>>
> >>>
> >>> _______________________________________________
> >>> micro-manager-general mailing list
> >>> [hidden email]
> >>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >>
> >>
> >> _______________________________________________
> >> micro-manager-general mailing list
> >> [hidden email]
> >> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
> >
> >
> > _______________________________________________
> > micro-manager-general mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
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Re: hardware configuration wizard

zhoulab2017
In reply to this post by Chon U Chan
Hi Chon,

  I read some old post for MM and seems the Nikon system database file (.dll) is able to be read after copy to MM. Do you know if there is something similar I should do with zeiss database file, which is the one used in AIM/ZEN now?

Kai

Sent from my iPhone

> On Apr 25, 2019, at 9:02 AM, Chon U Chan <[hidden email]> wrote:
>
> I asked half yr ago, Zeiss engineers are not allowed to work/advice on
> MM at all.
>
> As far as I know, "change the USB to Modem cable and have AIM/Zen
> adapt to the Modem cable " won't work. But that is something you can
> consult Zeiss engineer... keep us posted on the result please.
>
> Regards,
>
> Chon
>
>> On Thu, 25 Apr 2019 at 10:27, <[hidden email]> wrote:
>>
>> Thanks so much for your suggestions! Do you know any engineer who can help with configuration of MM? I was thinking about change the USB to Modem cable and have AIM/Zen adapt to the Modem cable as well so I don’t need to switch in between. I really like MM as I like to have more control on the software side and allow users to customize the program a little bit, or even add new function that not exist in commercial software. I would like to switch to MM as much as possible. Thanks again!
>>
>> Kai
>>
>> Sent from my iPhone
>>
>>> On Apr 25, 2019, at 6:00 AM, Chon U Chan <[hidden email]> wrote:
>>>
>>> So long as every hardware is added to MMG, you can group them into a
>>> single configuration, so having more components shouldn't be a
>>> problem.
>>>
>>> We do switch between Zen and MMG frequently due to user preference -
>>> no problem at all.
>>>
>>> I would suggest you start off by configuring your LSM with MMG - if
>>> you can't do it within a reasonable time, just use AIM/Zen. In that
>>> case, their engineer will do everything for you - for a price.
>>>
>>> Regards,
>>>
>>> Chon
>>>
>>>> On Thu, 25 Apr 2019 at 02:23, <[hidden email]> wrote:
>>>>
>>>> Hi Chon,
>>>>
>>>> It is just for convenience as the system (LSM+confocor3) are running well with Aim at this moment and completely overwrite AIM with micromanager will be a lot for us to take. Also this LSM510 meta was built for facility in the beginning, so there are 7 laser lines and the LSM part has too many filters and light paths, I feel it will be a huge project to configure them and completely switch to micromanager. Also we need to do FCS sometimes and the protocol in AIM is the one we are familiar with. It probably fine when we get more familiar with micromanager down the road.
>>>>
>>>> So probably every time I need to switch the cable when switch the protocol/software? Will micromanager overwrite some setting in the hardware(probably only the z1 base which is shared between micromanager and AIM/Zen) and make AIM/Zen not compatible with it?
>>>>
>>>>
>>>> Thanks!
>>>> Kai
>>>>
>>>> Sent from my iPhone
>>>>
>>>>> On Apr 24, 2019, at 10:22 PM, Chon U Chan <[hidden email]> wrote:
>>>>>
>>>>> Could you elaborate more why do you want to use AIM/Zen to control the
>>>>> motorized stage? It sounds to me you can do all with Micromanager
>>>>> alone.
>>>>>
>>>>> You can't connect the Z1 base to two separate protocol simultaneously.
>>>>> Once the Z1 base finds the USB interface, it will ignore the CAN9,
>>>>> vise verse.
>>>>>
>>>>> Regards,
>>>>>
>>>>> Chon
>>>>>
>>>>>> On Thu, 25 Apr 2019 at 00:39, <[hidden email]> wrote:
>>>>>>
>>>>>> Hi Chon,
>>>>>>
>>>>>> Thanks so much for your guideline! That’s fantastic! Do you happen to have the catalog # of the “Null modem cable”? Is that possible to have both Aim/Zen and micromanager to talk to the scope, but not simultaneously? I am doing some upgrading for the scope, so I need some basic information regarding how the system will run in the future in order to plan the resource well accordingly. I plan to add a autofocus (either DF1 or CRISP from ASI), a highly sensitive sCMOS/EMCCD, and associated illumination setups(either LED or laser for epifluorescent). I am thinking about having AIM/Zen running the motorized stage&LSM part and micromanager running the stage, autofocus, LED/laser, and sCMOS/EMCCD), this is because the camera and autofocus is for long term time lapse imaging, a function distinct from LSM. Any suggestion will be appreciated!
>>>>>>
>>>>>> Thanks!
>>>>>>
>>>>>> Kai
>>>>>>
>>>>>> Sent from my iPhone
>>>>>>
>>>>>>> On Apr 24, 2019, at 8:52 PM, Chon U Chan <[hidden email]> wrote:
>>>>>>>
>>>>>>> HI Chuankai:
>>>>>>>
>>>>>>> If I understand correctly, your goal is to control an Observer Z1 with
>>>>>>> Micromanager. If so, I have recently done so, and here are the steps:
>>>>>>>
>>>>>>> 1. Get a "Null Modem Cable, UL, DB9 Female to Female"
>>>>>>>
>>>>>>> 2. Turn off the Z1 base, and unplug the USB cable connected it to the PC
>>>>>>>
>>>>>>> 3. Connect the Null cable, one end to the PC serial port,  the other
>>>>>>> to the CAN29 bus on the Z1 base.
>>>>>>> the CAN29 bus is on the panel labeled "Main", DB9 male.
>>>>>>>
>>>>>>> 4. Turn on the Z1 base, wait for it to be completely on.
>>>>>>>
>>>>>>> 5.  Open Micromanager (I only tested 1.4.23), and under the "Hardware
>>>>>>> Config. Wizard", add the applicable hardware under the "ZeissCAN29"
>>>>>>> folder.
>>>>>>> If the Status returns OK, you are all set.
>>>>>>>
>>>>>>> Regards,
>>>>>>>
>>>>>>> Chon
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> On Wed, 24 Apr 2019 at 22:04, Chuankai Zhou <[hidden email]> wrote:
>>>>>>>>
>>>>>>>> Hi Nico,
>>>>>>>>
>>>>>>>> Looks like the Observer Z1 is not connected through serial port, but through USB.......
>>>>>>>>
>>>>>>>>> On Wed, Apr 24, 2019 at 4:04 PM Stuurman, Nico <[hidden email]> wrote:
>>>>>>>>>
>>>>>>>>> On 4/24/19 3:25 PM, Chuankai Zhou wrote:
>>>>>>>>>>> I am new to the software and I would like to set up the software
>>>>>>>>>>
>>>>>>>>>>> for our Zeiss LSM510 system as we want to do some customized
>>>>>>>>>> upgrading
>>>>>>>>>>> of hardware (autofocus from ASI, sCMOS camera and a LED light
>>>>>>>>>> source).
>>>>>>>>>>> As these new hardware will be mounted on the existing Observer
>>>>>>>>>> Z1, so
>>>>>>>>>>> I was trying to establish the configuration for the current LSM
>>>>>>>>>>> hardware. However, when I try to add "ZeissScope| Zeiss
>>>>>>>>>> AxioObserver
>>>>>>>>>>> controlled through serial interface" under the folder
>>>>>>>>>> "ZeissCAN29", I
>>>>>>>>>>> keep get error msg "Error in device "COM1": Unknown eroor in the
>>>>>>>>>>> device (1)".
>>>>>>>>>>
>>>>>>>>>> Do you have the microscope attached using a serial cable to COM1
>>>>>>>>>> of your
>>>>>>>>>> computer?  Also, if you operate the microscope normally through
>>>>>>>>>> USB, you
>>>>>>>>>> may need to power cycle the microscope first.
>>>>>>>>>
>>>>>>>>>> Thanks for your reply! I confirm that the scope is correctly connected
>>>>>>>>>> to the COM1 through serial cable as that's also required for AIM to
>>>>>>>>>> operate the system. Can you explain a little bit more about how to
>>>>>>>>>> power cycle the microscope? I tried the configuration after people has
>>>>>>>>>> used the AIM and microscope, but still the same error msg.
>>>>>>>>>
>>>>>>>>> Does the LSM510 come with an AxioObserver?  Aren't those the
>>>>>>>>> Axiovert's?  If so, you need to use the ZeissCAN (not the ZeissCAN29)
>>>>>>>>> adapter.  I think that autodetection works for the Axiovert, otherwise
>>>>>>>>> do make sure you have the correct serial port settings (see the MM website).
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>>
>>>>>>>>> Nico
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> micro-manager-general mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> micro-manager-general mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> micro-manager-general mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> micro-manager-general mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> micro-manager-general mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>>
>>>>
>>>> _______________________________________________
>>>> micro-manager-general mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>>
>>>
>>> _______________________________________________
>>> micro-manager-general mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>
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Re: hardware configuration wizard

Stuurman, Nico
On 4/25/19 9:46 PM, [hidden email] wrote:
>   I read some old post for MM and seems the Nikon system database file (.dll) is able to be read after copy to MM. Do you know if there is something similar I should do with zeiss database file, which is the one used in AIM/ZEN now?
>

No.  The Zeiss device adapters do not use apis from Zeiss, but
communicate directly with the equipment (through the serial port). That
is also the reason why you can run Zeiss microscopes equally well from a
Mac or using Linux.


Best,


Nico

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