[OpenSPIM] OpenSPIM in 64bit system?

Wed Jul 9 09:18:03 CDT 2014

Thanks Luke.

The older version I have "just works" out if the box so I wont update.
Fiji updates often bugger up local stuff like this *sigh*. We use a Jython
script for something else and a recent fiji update did something that now
gives us Jython script errors. Nothing major but still a bit annoying.
Sometimes I wish the updates were better tested before rollout but I guess
that's the price of speedy updates.

Cheers Kieran
On 09/07/2014 10:45 PM, "Luke Stuyvenberg" <stuyvenberg at wisc.edu> wrote:

> Hi Kieran and Ke,
>
> I just tested a fresh, completely up-to-date installation of OpenSPIM
> (*only* OpenSPIM-20140207.zip) on a 64-bit computer. On my machine, the
> software had the error Ke refers to: "Failed to load the MMCoreJ_wrap
> native library." The problem seems to happen when OpenSPIM uses a 64-bit
> JRE to load a 32-bit DLL. Please make sure you install a 32-bit JRE from
> http://www.java.com .
>
>
> If you already have a 32-bit JRE installed on your computer, either of
> these additional steps should help:
>
>
> This solution may change how other Java applications run:
> - Click Start -> Right click "My Computer" -> Properties.
> - On the left, click "Advanced System Settings".
> - Click "Environment Variables...".
> - Under System Variables, click "New..."
> - In Variable name, enter "JAVA_HOME". In Variable value, put the full
> path to the 32-bit JRE (for example, "C:\Program Files (x86)\Java\jre7").
>
>
> This solution may use some extra hard-drive space, but will only affect
> OpenSPIM:
> - Download and Extract OpenSPIM-20140207.zip. In OpenSPIM.app, make a new
> folder called "java".
> - Copy all files from the Java JRE directory (i.e. "C:\Program Files
> (x86)\Java\jre7") into this new folder.
>
>
> Now OpenSPIM will use the 32-bit JRE to run, which should resolve the
> problem.
>
>
> Please let me know if this helps!
> Luke
>
>
> On 07/08/14, Kieran Short  wrote:
> >
> > This is not what I did. Just use the openspim.org(http://openspim.org)
> distribution. It comes with *everything pre installed*. Dont do anything
> else, you shouldn't need to download the fiji installer. Just open the
> OpenSpim distribution in compatibility mode. Micromanager will be in the
> plugins waiting for you.
> >
> > Fwiw I haven't updated either. But if you download from the
> openspim.org(http://openspim.org) website it should be relatively fresh
> and up to date.
> >
> > Cheers Kieran
> > On 09/07/2014 8:04 AM, "Ke Li" <tianlankeke at gmail.com <
> tianlankeke at gmail.com>> wrote:
> >
> > > For base installation, you mean install the OpenSPIM/Fiji package here:
> http://openspim.org/Downloads again?
> > >
> > > I followed the troubleshooting instructions in the compatibility tab
> and the result is "its an incompatible application".
> > >
> > >
> > > I did the following steps to open the uManager studio:
> > >
> > >
> > > 1. Download the Fiji package of the continuous release version for
> Windows 7(64bit) from : http://fiji.sc/Fiji
> > >
> > >
> > > 2. Download the OpenSPIM package (OpenSPIM-20140207.zip) from :
> http://openspim.org/Downloads
> > >
> > >
> > > 3. Launch Fiji: in the Fiji.app/folder, open ImageJ-win64.exe
> > >
> > >
> > > 4. Update Fiji (and OpenSPIM and uManager): Help->Update Fiji
> > >
> > >
> > > 5. Run Micromanager Studio: In the OpenSPIM.app folder, open
> ImageJ-win32.exe, then plugins->Micro-manager->Micro-manager studio (Before
> this step, I have followed your steps and set the compatibility mode of the
> ImageJ-win32.exe as Windows XP (Service Pack 3))
> > >
> > >
> > > After Step 5, an error shows as follows:
> > > Error:Failed to load the MMCoreJ_wrap native library
> mmcorej.MMCoreJJNI.swig_module_init()V
> > >
> > >
> > > To solve this error, I copied the file MMCoreJ_wrap.dll in the mm
> folder of the OpenSPIM.app folder into the same directory of the
> ImageJ-win32.exe. Then when I reloaded the uManager studio from the ImageJ
> (32bit), the error was as follows:
> > > Error:Failed to load the MMcoreJ_wrap native library
> > >
> C:\Users\Kuolab\Downloads\SPIM\OpenSPIM-20140207\OpenSPIM.app\MMCoreJ_wrap.dll:
> Can't load IA 32-bit. dll on a AMD 64-bit platform.
> > >
> > >
> > > I tried to open the uManager studio from ImageJ-win32.exe and
> ImageJ-win64.exe, while the second error above happened all the time in the
> two cases.
> > >
> > > The camera driver has been installed correctly before based on the
> test image results.
> > >
> > >
> > > Is there any step I misconducted? (Maybe copying the MMCoreJ_warp.dll
> into the same directory of the ImageJ-win32.exe is not correct?)
> > >
> > >
> > > Thanks,
> > > Ke
> > >
> > >
> > > Ke LiResearch Assistant
> > > Biomedical Engineering
> > > Johns Hopkins University
> > > Phone: 410-934-9802(tel:410-934-9802)
> > > Email: kli26 at jhu.edu(javascript:main.compose()
> > >
> > >
> > >
> > >
> > > On Tue, Jul 8, 2014 at 5:16 PM, Kieran Short <kieran.short at gmail.com(javascript:main.compose()>
> wrote:
> > >
> > > >
> > > > This is strange. I'm not sure what OpenSPIM fiji build we are
> running but it works here.
> > > >
> > > > Have you tried going back to a base installation?
> > > >
> > > > It sounds odd that uManager can even detect your pc as a "amd64"
> system as compatibility mode should mask that as 32bit.
> > > >
> > > > What says "its an incompatible application"?
> > > >
> > > > Of course, mm *should* be able to load a 32bit dll on 64bit
> architecture. I don't understand why that should be a problem for mm in
> the first place. The whole x86 instruction set is encapsulated within the
> x64 set. To Johannes/Mark is this directly related to the available jre?
> > > > On 09/07/2014 5:18 AM, "Ke Li" <tianlankeke at gmail.com(javascript:main.compose()>
> wrote:
> > > >
> > > > > Hi Kieran,
> > > > >
> > > > > I followed your suggestion. While the problem still existed. When
> I tried to launch the uManager studio from the ImageJ(ImageJ-win32.exe) in
> the OpenSPIM.app folder, an error: Failed to load the MMCoreJ_wrap native
> library (Can't load IA 32-bit.dll on a AMD 64-bit platform) showed
> every time. I did the troubleshooting and the result showed that it's a
> incompatible application.
> > > > >
> > > > >
> > > > > Is there any other way to solve this problem?
> > > > >
> > > > >
> > > > > Thanks,
> > > > > Ke
> > > > >
> > > > >
> > > > > Ke LiResearch Assistant
> > > > > Biomedical Engineering
> > > > > Johns Hopkins University
> > > > > Phone: 410-934-9802(tel:410-934-9802)
> > > > > Email: kli26 at jhu.edu(javascript:main.compose()
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > On Mon, Jul 7, 2014 at 9:03 PM, Ke Li <tianlankeke at gmail.com(javascript:main.compose()>
> wrote:
> > > > >
> > > > > > Hi Kieran,
> > > > > >
> > > > > > Thanks so much for your solution. I'll try it tomorrow.
> > > > > >
> > > > > >
> > > > > > Best,
> > > > > > Ke
> > > > > >
> > > > > > Kieran Short <kieran.short at gmail.com
> (javascript:main.compose()>于2014年7月7日星期一写道：
> > > > > >
> > > > > > >
> > > > > > > Run it in compatibility mode.
> > > > > > >
> > > > > > > To do this, do the following.
> > > > > > >
> > > > > > > Right click imagej/fiji.
> > > > > > > Select properties.
> > > > > > > Go to the Compatibility tab.
> > > > > > > Check the "run this program in compatibility mode for:" box.
> > > > > > > Select Windows XP (Service Pack 3).
> > > > > > > Click Apply.
> > > > > > > Click OK.
> > > > > > >
> > > > > > > Then try and run it.
> > > > > > >
> > > > > > > When I can work out how to include plugins during compilation
> I will try to compile.a win64 version. At such q time i'd happily
> provide binaries. Im only a part time python progammer though and therefore
> have little experience with debugging compilation issues. Since
> Compatibility Mode 'just works' for us, it isn't a high
> priority for me.
> > > > > > >
> > > > > > > Cheers Kieran
> > > > > > > On 08/07/2014 10:32 AM, "Ke Li" <tianlankeke at gmail.com> wrote:
> > > > > > >
> > > > > > > > Hi Mark & Luke,
> > > > > > > >
> > > > > > > > I'm writing to ask whether there is a solution for
> running the openSPIM software in the 64bit system? (The uManager studio
> can't be loaded normally in my 64 bit system) Can I get access to the
> source code for modification?
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > Thanks,
> > > > > > > > Ke
> > > > > > > >
> > > > > > > > Ke LiResearch Assistant
> > > > > > > > Biomedical Engineering
> > > > > > > > Johns Hopkins University
> > > > > > > > Phone: 410-934-9802(tel:410-934-9802)
> > > > > > > > Email: kli26 at jhu.edu
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > _______________________________________________
> > > > > > > > OpenSPIM mailing list
> > > > > > > > OpenSPIM at openspim.org
> > > > > > > > http://openspim.org/mailman/listinfo/openspim
> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > > Ke LiResearch Assistant
> > > > > > Biomedical Engineering
> > > > > > Johns Hopkins University
> > > > > > Phone: 410-934-9802(tel:410-934-9802)
> > > > > > Email: kli26 at jhu.edu(javascript:main.compose()
> > > > > >
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