[OpenSPIM] Lightsheet characterization
LIM Soon Yew John (IMB)
john.lim at imb.a-star.edu.sg
Tue Apr 8 21:21:35 CDT 2014
Dear All,
I had measured the light sheet using 45 degree mirror last week and I had also did a Gaussian fit for it. I will happily share the data with everyone here. Attached are the max intensity projection along x-axis and the FWHM measurement. The max intensity projection shows the light sheet along different x-position as I move the mirror.
Best Regards,
John
IMB, Singapore
________________________________________
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Subject: OpenSPIM Digest, Vol 12, Issue 7
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Today's Topics:
1. Re: A question about the Light Sheet software (Alexis Maizel)
2. Re: Lightsheet characterization (Michael Weber)
3. X-SPIM (R?diger Rudolf)
----------------------------------------------------------------------
Message: 1
Date: Tue, 8 Apr 2014 08:19:12 +0200
From: Alexis Maizel <Alexis.Maizel at cos.uni-heidelberg.de>
To: Cristian Undurraga <undurragacristian at gmail.com>
Cc: Jan Felix Evers <jan-felix.evers at cos.uni-heidelberg.de>,
"openspim at openspim.org" <openspim at openspim.org>
Subject: Re: [OpenSPIM] A question about the Light Sheet software
Message-ID:
<E821E006-1374-49A1-975E-56FBA86194C2 at cos.uni-heidelberg.de>
Content-Type: text/plain; charset=utf-8
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 escribi?:
>
>> 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 escribi?:
>>>
>>>
>>>> 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 escribi?:
>>>>
>>>>
>>>>>
>>>>>> 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
>
------------------------------
Message: 2
Date: Tue, 8 Apr 2014 14:18:20 +0200
From: Michael Weber <weber at mpi-cbg.de>
To: "openspim at openspim.org" <openspim at openspim.org>
Subject: Re: [OpenSPIM] Lightsheet characterization
Message-ID: <C61ACEB8-2201-4087-9444-4A5B9353A18A at mpi-cbg.de>
Content-Type: text/plain; charset="iso-8859-1"
Hey Jan,
I started a page about light sheet characterization in the wiki, maybe you want to contribute to it?
http://openspim.org/Light_sheet_characterization
Best,
Michael
On Apr 6, 2014, at 3:34 PM, "Krieger, Jan" <j.krieger at Dkfz-Heidelberg.de> wrote:
> Dear Julien!
>
> you should use a mirror mounted under 45?. This is described in detail in http://www.freidok.uni-freiburg.de/volltexte/1533/pdf/huisken_phd.pdf, or e.g. in http://staff.science.nus.edu.sg/~chmwt/publications/Singh%20AP%202013%202D%20array_supplementary.pdf and http://www.dkfz.de/Macromol/publications/files/spimfccs2013_supplement.pdf
>
> Then you can do a Gaussian fit to cuts through the light sheet.
>
> Best,
> JAN
>
>
> Dipl.-Phys. Jan Krieger
> German Cancer Research Center (dkfz)
> Department B040 - Biophysics of Macromolecules (Prof. J. Langowski)
> Im Neuenheimer Feld 580
> 69120 Heidelberg
>
> fon: +49 / 6221 / 42-3395
> fax: +49 / 6221 / 42-3391
> e-mail: j.krieger at dkfz.de
> www: http://www.dkfz.de/Macromol/
> ________________________________________
> Von: openspim-bounces at openspim.org [openspim-bounces at openspim.org] im Auftrag von Julien DUMONT [julien.dumont at inaf.cnrs-gif.fr]
> Gesendet: Sonntag, 6. April 2014 14:59
> An: openspim at openspim.org
> Betreff: [OpenSPIM] Lightsheet characterization
>
> Hi,
>
> On our setup, we would like to measure precisely the width of the lightsheet at the focal point, but I'm running out of ideas to do that, as the resolution of our beam profiler is not able to go down to the size of it. Is anyone of you have a trick to do that ?
>
> Cheers
>
> Julien Dumont
> --
> Ing?nieur d'?tude microscopie
> 1 Avenue de la Terrasse
> CNRS, NeD, B?timent 32
> 91190 Gif-sur-Yvette
> 01.69.82.34.19
>
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_____________
Michael Weber
PhD Student, Huisken lab
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108, 01307 Dresden
Tel. 0049 351/2102837
http://www.mpi-cbg.de/huisken
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Message: 3
Date: Tue, 8 Apr 2014 14:36:26 +0200
From: R?diger Rudolf <r.rudolf at hs-mannheim.de>
To: openspim at openspim.org
Subject: [OpenSPIM] X-SPIM
Message-ID: <4D9DA952-25CA-4EEF-9EDC-9A0D920D3521 at hs-mannheim.de>
Content-Type: text/plain; charset="windows-1252"
Dear OPEN-SPIM team,
your website is terrific!
Since a while we are now getting more and more interested in setting up our own SPIM for a multitude of potential applications.
My impression is, that for many purposes a dual color-X-SPIM would be needed.
You show nice pictures on your page of such a system (X-SPIM), but in the parts list the corresponding chamber is not listed.
Do you, in general, sell the parts listed under ?OPEN SPIM? at the prices indicated on your page and do you also distribute the chambers for X-SPIM?
Thanks a lot in advance, looking forward to hearing from you!
Best regards, R?diger
******************************************************
Dr. R?diger Rudolf, Professor of Biosensorics
University of Applied Sciences Mannheim
Faculty of Biotechnology
Institute of Molecular and Cell Biology
Paul-Wittsack-Strasse 10
68163 Mannheim
Tel: +49 (0)621 2926804
Email: r.rudolf at hs-mannheim.de
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