[OpenSPIM] problems with adding CUBE to Fiji-SPIM

[Luke Stuyvenberg]

Hi Martin,

(I hope you don't mind that I've taken the liberty of also addressing 
these e-mails to the OpenSPIM mailing list: openspim at openspim.org -- 
that way anyone who works with OpenSPIM can have a chance to address 
your question.)

On 9/24/2014 7:46 AM, Martin Capek wrote:
> we communicated some time ago about Andor camera. May I ask you for 
> help with adding Coherent CUBE to Fiji-SPIM sw? I use a pc with win xp 
> and a usb-to-rs232 converter. When using this with Coherent Connection 
> sw, cube works fine - please see the first attachment.
>
> However, when trying to add cube to fiji-spim, autoscan does not work 
> and I am getting a message that I should choose settings and a port 
> manually, see the second attach. If it is the solution, could you 
> please help me how to do it?
>
> ...
>
> PS: I also updated the baudrate to 19200 bps for COM, as recommended. 
My immediate guess would have been trouble with the USB-RS232 converter; 
however, since the Coherent software is connecting without trouble, that 
seems unlikely.

As you've probably realized, the Coherent CUBE device adapter can't 
auto-detect the laser's presence, so it really will come down to a 
matter of settings. In my experience, the only setting that has actually 
required changing was the baud rate, which should be reduced to no more 
than the recommended 19200 bps.

If having all-default settings except the baud rate won't connect to the 
laser, I'd speculate it to be related to the error seen in your device 
manager -- perhaps MM is conflicted over the two assignments to COM1 
where the CUBE software is having no such difficulty?

> I spent this whole day by changing COM port numbers, using various 
> usb-rs232 converters, updating drivers, trying various versions of MM 
> to get the connection to cube using MM, but with no success till now.
If it wasn't among the versions you've tried already, it may also be of 
merit to try adding the CUBE to a completely vanilla Micro-Manager 
installation. The device adapter in the OpenSPIM software can lag behind 
the 'official' distribution, so it may be that a newer device adapter 
will solve the problem.

I'm afraid I just don't know enough to provide a definitive answer. If 
trying the above suggestions doesn't work, please do the following:
- Run (preferably vanilla) Micro-Manager, select no hardware configuration.
- Start the hardware configuration wizard, and advance it to the devices 
screen.
- Attempt to add the CUBE with all default settings except a reduced 
baud rate, trying all available COM ports.
- Close Micro-Manager, then locate the most recent core log and e-mail 
it to the list/me.
Hopefully this will include some information on the problem.

Thanks,
Luke Stuyvenberg

On 9/24/2014 7:46 AM, Martin Capek wrote:
> Hi Luke,
> we communicated some time ago about Andor camera. May I ask you for 
> help with adding Coherent CUBE to Fiji-SPIM sw? I use a pc with win xp 
> and a usb-to-rs232 converter. When using this with Coherent Connection 
> sw, cube works fine - please see the first attachment.
>
> However, when trying to add cube to fiji-spim, autoscan does not work 
> and I am getting a message that I should choose settings and a port 
> manually, see the second attach. If it is the solution, could you 
> please help me how to do it?
>
> I spent this whole day by changing COM port numbers, using various 
> usb-rs232 converters, updating drivers, trying various versions of MM 
> to get the connection to cube using MM, but with no success till now.
>
> Thank you very much in advance!
> Best regards,
> Martin
>
> PS: I also updated the baudrate to 19200 bps for COM, as recommended.
>
>
> Dne 17.4.2014 v 2:15 Luke Stuyvenberg napsal(a):
>> Hi Martin,
>>
>> Sorry about the delay.
>>
>> On 04/11/14, Martin Capek  wrote:
>>> I need to use an Andor iXon3 camera in the OpenSPIM setup. This 
>>> camera works well in standalone installations of the micromanager 
>>> (MM), I tried them more. However, when I copy, according to 
>>> instructions in the web, the corresponding dll to MM included in 
>>> OpenSPIM sw, it does not work. I also used Dependency Walker as 
>>> there described.
>>
>> Could you please clarify how it does not work? When in Hardware 
>> Configuration, is the 'Andor' device not listed? Is it listed, but 
>> with a gray dot next to it? Is it available, but gives an error when 
>> you try to add it?
>>
>>
>> Which instructions did you follow, exactly? And did the Dependency 
>> Walker show any errors?
>>
>>
>>> Could anybody help me, please? What is the number of MM version used 
>>> in the OpenSPIM from February 7 2014 ? I see only 1.4.x dev, which 
>>> is probably not enough to choose the proper one.
>>
>> As near as I can determine, OpenSPIM from 7 Feb 2014 is based on[1] 
>> Micro-Manager v1.4.16 (which was released 31 January, 2014). This 
>> means that copying DLLs from that version of Micro-Manager to 
>> OpenSPIM's mm/win32 directory should work. If it does not, please try 
>> downloading the nightly build from 5 February 2014[2]:
>>
>>
>> - From the Micro-Manager website, click 'Downloads'.
>> - On the left, click 'Download Nightly Builds'.
>> - Click 'Version 1.4 (Windows)'.
>> - Scroll through the list looking for 
>> 'MMSetup_64bit_1.4.17_20140205.exe'.
>>
>>
>> That version of Micro-Manager should be completely compatible with 
>> OpenSPIM.
>>
>>
>> I hope this is helpful! Please let me know if you continue to run 
>> into problems.
>>
>>
>> Thanks,
>> Luke
>>
>>
>> [1] To be completely precise, it is based on SVN revision r12726, 
>> dated 5 February 2014. This was shortly after the release of 1.4.16 
>> as I mention above.
>> [2] The direct link is: 
>> http://valelab.ucsf.edu/~MM/nightlyBuilds/1.4/Windows/MMSetup_64bit_1.4.17_20140205.exe 
>> -- however, please always beware of direct links in e-mails! It is 
>> safer to find the file yourself, from a trusted website.
>>
>>
>> On 04/11/14, Martin Capek wrote:
>>>       Dear all,
>>>   I need to use an Andor iXon3 camera in the OpenSPIM setup. This 
>>> camera works well in standalone installations of the micromanager 
>>> (MM), I tried them more. However, when I copy, according to 
>>> instructions in the web, the corresponding dll to MM included in 
>>> OpenSPIM sw, it does not work. I also used Dependency Walker as 
>>> there described.
>>>   Could anybody help me, please? What is the number of MM version 
>>> used in the OpenSPIM from February 7 2014 ? I see only 1.4.x dev, 
>>> which is probably not enough to choose the proper one.
>>>   Any comment will be welcome.
>>>   Thank you very much in advance!
>>> Martin
>>>   --
>>>     Ing. Martin Čapek, Ph.D.
>>> oddělení biomatematiky
>>>       Fyziologický ústav AV ČR, v.v.i.
>>> Vídeňská 1083
>>> 142 20 Praha 4
>>>   Tel. +420 241 062 334
>>> http://www.biomed.cas.cz/fgu/
>>>
>