[OpenSPIM] A question about the Light Sheet software
Alexis Maizel
Alexis.Maizel at cos.uni-heidelberg.de
Tue Apr 8 01:19:12 CDT 2014
Hi cristian,
I am happy to read that you were fearless and updated.
Basically by simply swapping the cobolt device adapter currently shipping with MM in place of the one bundled with OpenSpIm solves your issue and showed that it works out-of-the-box.
This is great news as it means no modification of the driver required.
Thanks again for your leap of faith.
You are more adventurous than me.
@luke: this basically answers many of the questions you had, no?
Best,
Alexis
--
This message was composed on and sent from a mobile device.
On 8 avr. 2014, at 03:15, Cristian Undurraga <undurragacristian at gmail.com> wrote:
> Hi Luke!
>
> The force is with us!! :D
> After the update via "Advanced Mode", appeared two updates, one for the "Hamamatsu camera" and one for the "SPIMAcquisition", I apply the changes, restart the app and after that, the software is working wonderful!. I can save the experiment in another directory (always delete the data inside the selected file!, but now displays a warning), and hence, we can use the computer storage (300Gb).
> I started a time-lapse and everything wasl ok, saved in the correct directory etc.
> Thanks a lot for the help to everybody!, Jan-Felix, Alexis and Luke!, when I go to Germany, I`ll take a good chilean wine for each.
> :-)
> Best regards to all,
>
> Cristian
>
> El 07-04-2014, a las 647, Luke Stuyvenberg escribió:
>
>> Hi Christian,
>>
>> On 04/07/14, Cristian Undurraga wrote:
>>>> 2. Send a new CoreLog (from a day when this error was encountered) to me.
>>> Sending the corelog: CoreLog20140402.txt
>> Odd. This core log, and the next one, suggest that the OpenSPIM plugin isn't up-to-date. Please check the following:
>>
>> 1. Run the software and click "Help -> Update Fiji"
>> 2. If the software says, "Your ImageJ is up to date!", please let me know (but click "OK" and continue with these instructions).
>> 3. Click "Advanced Mode" in the lower-right corner.
>> 4. At the top of the window, change "View Options" to "View files of the 'OpenSPIM' site".
>> 5. If anything in the list is not "Up-to-date", click on the status/action and set it to "Update it" or "Install it".
>> 6. Click "Apply changes" to update all of OpenSPIM's files.
>> 7. Restart the software, and see if the plugin shows up now.
>>
>>
>> If you're still having trouble after this, I'll want to explore the problem more directly. If the software still isn't working, please:
>> 1. Click "Plugins -> Utilities -> Make Fiji Package".
>> 2. For type, select "ZIP" and click "OK".
>> 3. Save the package somewhere you'll remember. (The Desktop works.)
>> 4. Let the plugin run until it tells you, "Wrote <file name>", then click "OK".
>> 5. Click "Help -> Upload Sample Image".
>> 6. Browse to where you saved the file, select it, and click "Open".
>> 7. Wait for the upload to finish.
>>
>>
>>>> 4. Copy the file "C:\Program Files\Micro-Manager 1.4\mmgr_dal_Cobolt.dll" [2] to "C:\Users\User\Desktop\OpenSPIM.app\mm\win32\" (and overwrite the file that exists there).
>>> I didn`t find the file in "Program Files x86" (althought we are using "Windows 7_64bit"), I copied the file "C:\Program Files\Micro-Manager 1.4\mmgr_dal_Cobolt.dll" to "C:\Users\User\Desktop\OpenSPIM.app\mm\win32\"
>>
>>
>>> Other data: 1) A message appeared to update Java for Windows, would be necessary?.
>> It should not be, but I've just noticed that OpenSPIM may not have been packaged with Java. If you downloaded the software very recently (OpenSPIM-20140207.zip), it may be using your system Java instead of its own.
>>
>>
>>> 2) when I specified a new directory for ex. a "file 1" in the desktop, the pic was no taken or the time-lapse don`t start, but also, if I had some file inside the "file 1", these were deleted without any notice!.
>> This behavior was certainly removed from recent versions of OpenSPIM. (To be precise, it was removed on 26 August 2013 -- the latest version of OpenSPIM is from 7 February 2014.) For some reason, it seems your update updated everything except OpenSPIM itself.
>>
>>
>>> Thanks to you for the help!, I guess the idea is that all we go to cooperate with the project.
>> Every little bit helps! You may not be the only person having trouble with our software, but only the first to contact us -- and so if we can fix this issue, it will benefit the project as a whole. :)
>>
>>
>>
>> Once again, thanks for your cooperation.
>> Luke
>>
>>
>>>
>>> El 04-04-2014, a las 906, Luke Stuyvenberg escribió:
>>>
>>>
>>>> Hi Cristian,
>>>>
>>>>
>>>>> I Updated the Fiji (just Help->Update Fiji) and had many files to update, I accepted all.
>>>>
>>>>> Now is running ImageJ 1.48t and Java 1.6.0_24, and the MicroManager 1.4.x dev (Picture 1), but when I start the OpenSpim.app, appeared the message of "Picture2", and doesn`t recognize the Cobolt device.
>>>> Well, somewhere, Alexis is shaking his head. ;-) He did, after all, warn us about this...
>>>>
>>>>
>>>> Please try the following:
>>>> 1. Check that the file "C:\Users\User\Desktop\OpenSPIM.app\mm\win32\mmgr_dal_Cobolt.dll" exists (it probably does).
>>>> 2. Send a new CoreLog (from a day when this error was encountered) to me.
>>>> 3. Download a new, 32-bit version of Micro-Manager from the website[1] and install it.
>>>> 4. Copy the file "C:\Program Files\Micro-Manager 1.4\mmgr_dal_Cobolt.dll" [2] to "C:\Users\User\Desktop\OpenSPIM.app\mm\win32\" (and overwrite the file that exists there).
>>>> 5. Try launching the software again. If it still fails, send me yet another CoreLog.
>>>>
>>>>
>>>> Thanks again, and I'm sorry for the trouble!
>>>> Luke
>>>>
>>>>
>>>> P.S. Please use reply-all, to keep the mailing list CC'd. :-)
>>>>
>>>>
>>>> [1] https://micro-manager.org/wiki/Download_Micro-Manager_Latest_Release
>>>> [2] If your computer is 64-bit Windows 7, it will be under "Program Files (x86)" instead.
>>>>
>>>> On 04/01/14, Cristian Undurraga wrote:
>>>>
>>>>> Hi Luke,
>>>>
>>>>
>>>>> What`s could gone wrong?
>>>>
>>>>> Best,
>>>>
>>>>
>>>>> Cristian
>>>>
>>>>
>>>>
>>>>> ----- Picture1.jpg -----
>>>>
>>>>
>>>>
>>>>> ----- Picture2.jpg -----
>>>>
>>>>
>>>>
>>>>
>>>>> El 31-03-2014, a las 547, Luke Stuyvenberg escribió:
>>>>
>>>>
>>>>>
>>>>>> Hi Christian,
>>>>
>>>>>
>>>>
>>>>>
>>>>>> On 03/31/14, Cristian Undurraga wrote:
>>>>
>>>>>
>>>>>>
>>>>>>> Hi Luke,
>>>>
>>>>>
>>>>>>
>>>>
>>>>>
>>>>>>
>>>>>>> I`m sending the file that you asked after to try to start a time lapse, specified a new directory in the desktop (new folder named "1" in the desktop).Thank you very much. The file seems to indicate that a necessary JAR file is missing for OME-TIFF output -- the most likely candidate is OpenSPIM.app/jars/bio-formats/formats-api-5.0.0.jar (the latest version available through the Fiji Updater).
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>>
>>>>>> Did you download the OpenSPIM package from our website? If you run the Fiji Updater (Help -> Update Fiji), it should give you a list of files that need to be updated. Most likely, you can accept the Updater's proposal by clicking "Accept changes" at the bottom; this should fix your issue.
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>>
>>>>>> I should be clear that this is different from updating Micro-Manager. Our plugin does not currently come with Micro-Manager, so if you download Micro-Manager's latest version from their website, you won't be able to control an OpenSPIM. The Fiji updater, on the other hand, downloads newer versions of the files OpenSPIM relies on.
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>>
>>>>>> If you have any questions, or if this doesn't resolve your issue, please don't hesitate to mail me and/or the list (openspim at openspim.org <openspim at openspim.org>) again!
>>>>
>>>>>
>>>>>> Thanks,
>>>>
>>>>>
>>>>>> Luke
>
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