[OpenSPIM] A question about the Light Sheet software
Cristian Undurraga
undurragacristian at gmail.com
Mon Apr 7 20:15:45 CDT 2014
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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