<div dir="ltr"><div><div>Hello, <br><br></div>Thanks! I'm glad you are enjoying my constant questions. <br><br></div>I have added the Volvox picture to the gallery on the wiki, and also added my lab to the "who has an OpenSPIM" page. <br>
<div><br>There is in fact an exception, here is the debug console output: <br><br><br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.lang.R<br>unnable<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.progac<br>
q.AcqOutputHandler<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.lang.T<br>hread$UncaughtExceptionHandler<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.progac<br>
q.AcqOutputHandler<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.progac<br>q.AcqOutputHandler<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.progac<br>q.AcqOutputHandler<br>
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.progac<br>q.AntiDrift$Callback<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.lang.R<br>unnable<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.lang.R<br>
unnable<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.progac<br>q.AntiDrift$Callback<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.awt.ev<br>ent.KeyListener<br>
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: javax.swing<br>.event.ChangeListener<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.awt.ev<br>ent.KeyListener<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.lang.I<br>
terable<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.awt.ev<br>ent.ItemListener<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: java.util.E<br>
ventListener<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>
Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>
LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.793132, 7896, 60C856A8:): > interface found: spim.setup.<br>Device$Factory<br>LOG(2013-10-09T18:35:30.794132, 7896, 60C856A8:): > Attempting to install plugin<br>
spim.SPIMAcquisition<br>LOG(2013-10-09T18:35:31.725185, 7896, 633ED618:): All devices unloaded.<br>LOG(2013-10-09T18:35:31.725185, 7896, 633ED618:): > Notification for Device: Cor<br>e Property: Initialize changed to value: 0<br>
LOG(2013-10-09T18:35:31.780188, 7896, 633ED618:): Device COM3 loaded from Serial<br>Manager and labeled as COM3<br>LOG(2013-10-09T18:35:31.817191, 7896, 633ED618:): Device Camera-1 loaded from PV<br>CAM and labeled as CoolsnapMyo<br>
LOG(2013-10-09T18:35:31.817191, 7896, 633ED618:): Device CoolsnapMyo set as defa<br>ult camera.<br>Pinging motors...<br>Found 3 motors and 1 twisters.<br>LOG(2013-10-09T18:35:32.917254, 7896, 633ED618:): Device Picard Twister loaded f<br>
rom PicardStage and labeled as Picard Twister<br>LOG(2013-10-09T18:35:32.917254, 7896, 633ED618:): Device Picard Z Stage loaded f<br>rom PicardStage and labeled as Picard Z Stage<br>LOG(2013-10-09T18:35:32.918254, 7896, 633ED618:): Device Picard XY Stage loaded<br>
from PicardStage and labeled as Picard XY Stage<br>LOG(2013-10-09T18:35:32.918254, 7896, 633ED618:): Device Picard XY Stage set as<br>default xyStage.<br>LOG(2013-10-09T18:35:32.967256, 7896, 633ED618:): Device SC10 loaded from Thorla<br>
bsSC10 and labeled as SC10<br>LOG(2013-10-09T18:35:32.967256, 7896, 633ED618:): Device SC10 set as default shu<br>tter.<br>LOG(2013-10-09T18:35:33.020259, 7896, 633ED618:): Starting initialization sequen<br>ce for 6 devices...<br>
LOG(2013-10-09T18:35:33.114265, 7896, 633ED618:): Device COM3 initialized.<br>LOG(2013-10-09T18:35:33.121265, 7896, 633ED618:): Device CoolsnapMyo message: PV<br>CAM VERSION: 2.9.5. Number of cameras detected: 1<br>LOG(2013-10-09T18:35:33.174268, 7896, 633ED618:): Device CoolsnapMyo message: Bu<br>
ilding Speed Table<br>LOG(2013-10-09T18:35:33.291275, 7896, 633ED618:): Device CoolsnapMyo message: In<br>itializing Static Camera Properties<br>LOG(2013-10-09T18:35:33.303276, 7896, 633ED618:): Device CoolsnapMyo message: In<br>
itializing Dynamic Camera Properties<br>LOG(2013-10-09T18:35:33.484286, 7896, 633ED618:): Device CoolsnapMyo message: Th<br>is Camera does not have EM Gain<br>LOG(2013-10-09T18:35:33.484286, 7896, 633ED618:): Device CoolsnapMyo message: Fr<br>
ame Transfer mode not available<br>LOG(2013-10-09T18:35:33.528288, 7896, 633ED618:): Device CoolsnapMyo message: Us<br>ing PVCAM callbacks for frame acquisition<br>LOG(2013-10-09T18:35:33.528288, 7896, 633ED618:): Device CoolsnapMyo initialized<br>
.<br>LOG(2013-10-09T18:35:33.536289, 7896, 633ED618:): Device Picard Twister initiali<br>zed.<br>LOG(2013-10-09T18:35:33.540289, 7896, 633ED618:): Device Picard Z Stage initiali<br>zed.<br>LOG(2013-10-09T18:35:33.564291, 7896, 633ED618:): Device Picard XY Stage initial<br>
ized.<br>LOG(2013-10-09T18:35:33.612293, 7896, 633ED618:): Device SC10 message: THORLABS<br>SC10 VERSION 1.07<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Device SC10 initialized.<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for Device: Cor<br>
e Property: Initialize changed to value: 1<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Camera device set to CoolsnapM<br>yo<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for Device: Cor<br>
e Property: Camera changed to value: CoolsnapMyo<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for Device: Cor<br>e Property: Shutter changed to value: SC10<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Focus device set to Picard Z S<br>
tage<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for Device: Cor<br>e Property: Focus changed to value: Picard Z Stage<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Auto shutter ON.<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): > Notification for Device: Cor<br>
e Property: AutoShutter changed to value: 1<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard Z Stage defined as StepSize=1.5000<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard Z Stage defined as Velocity=10<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard XY Stage defined as TransposeMirrorX=0<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard XY Stage defined as TransposeMirrorY=0<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard XY Stage defined as X-StepSize=1.5000<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard XY Stage defined as X-Velocity=10<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard XY Stage defined as Y-StepSize=1.5000<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.627294, 7896, 633ED618:): Resolution ID 20X: for device<br>Picard XY Stage defined as Y-Velocity=10<br>LOG(2013-10-09T18:35:33.628294, 7896, 633ED618:): Pixel size 0.500000 um set for<br>
resolution ID: 20X<br>LOG(2013-10-09T18:35:33.656296, 7896, 633ED618:): System state cache updated.<br>LOG(2013-10-09T18:35:33.740301, 7896, 633ED618:): Device SC10 message: 1<br>LOG(2013-10-09T18:35:33.752301, 7896, 633ED618:): System state cache updated.<br>
LOG(2013-10-09T18:35:33.820305, 7896, 633ED618:): > Startup script file (C:\User<br>s\ah659\Desktop\OpenSPIM-20130131\OpenSPIM.app/MMStartup.bsh) not present.<br>LOG(2013-10-09T18:40:18.799605, 7896, 633ED618:): > Plugin command: Acquire SPIM<br>
image<br>LOG(2013-10-09T18:40:19.135624, 7896, 633ED618:): Device SC10 message: 1<br>LOG(2013-10-09T18:40:19.220629, 7896, 633ED618:): Device CoolsnapMyo message: St<br>arted sequence on CoolsnapMyo, at 434659219 220629, with 2147483647 and 0 ms<br>
<br>LOG(2013-10-09T18:40:19.902668, 7896, 633ED618:): Device SC10 message: 1<br>LOG(2013-10-09T18:40:20.040676, 7896, 633ED618:): Device CoolsnapMyo message: St<br>arted sequence on CoolsnapMyo, at 434659220 40676, with 2147483647 and 0 ms<br>
<br>java.lang.NoClassDefFoundError: loci/common/services/ServiceFactory<br> at spim.progacq.OMETIFFHandler.<init>(OMETIFFHandler.java:55)<br> at spim.SPIMAcquisition.actionPerformed(SPIMAcquisition.java:1721)<br>
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:19<br>95)<br> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav<br>a:2318)<br> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel<br>
.java:387)<br> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242<br>)<br> at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL<br>istener.java:236)<br> at java.awt.Component.processMouseEvent(Component.java:6289)<br>
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br> at java.awt.Component.processEvent(Component.java:6054)<br> at java.awt.Container.processEvent(Container.java:2041)<br> at java.awt.Component.dispatchEventImpl(Component.java:4652)<br>
at java.awt.Container.dispatchEventImpl(Container.java:2099)<br> at java.awt.Component.dispatchEvent(Component.java:4482)<br> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577<br>
)<br> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br><br> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br> at java.awt.Container.dispatchEventImpl(Container.java:2085)<br>
at java.awt.Window.dispatchEventImpl(Window.java:2478)<br> at java.awt.Component.dispatchEvent(Component.java:4482)<br> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)<br> at java.awt.EventQueue.access$000(EventQueue.java:85)<br>
at java.awt.EventQueue$1.run(EventQueue.java:603)<br> at java.awt.EventQueue$1.run(EventQueue.java:601)<br> at java.security.AccessController.doPrivileged(Native Method)<br> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo<br>
ntrolContext.java:87)<br> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo<br>ntrolContext.java:98)<br> at java.awt.EventQueue$2.run(EventQueue.java:617)<br> at java.awt.EventQueue$2.run(EventQueue.java:615)<br>
at java.security.AccessController.doPrivileged(Native Method)<br> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo<br>ntrolContext.java:87)<br> at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)<br>
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre<br>ad.java:269)<br> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.<br>java:184)<br> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre<br>
ad.java:174)<br> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br><br> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br><br> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br>
Caused by: java.lang.ClassNotFoundException: loci.common.services.ServiceFactory<br><br> at java.net.URLClassLoader$1.run(URLClassLoader.java:202)<br> at java.security.AccessController.doPrivileged(Native Method)<br>
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)<br> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)<br> at java.lang.ClassLoader.loadClass(ClassLoader.java:248)<br> ... 38 more<br>
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: java.<br>lang.NoClassDefFoundError: loci/common/services/ServiceFactory<br> at spim.progacq.OMETIFFHandler.<init>(OMETIFFHandler.java:110)<br>
at spim.SPIMAcquisition.actionPerformed(SPIMAcquisition.java:1721)<br> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:19<br>95)<br> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav<br>
a:2318)<br> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel<br>.java:387)<br> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242<br>)<br> at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL<br>
istener.java:236)<br> at java.awt.Component.processMouseEvent(Component.java:6289)<br> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br> at java.awt.Component.processEvent(Component.java:6054)<br>
at java.awt.Container.processEvent(Container.java:2041)<br> at java.awt.Component.dispatchEventImpl(Component.java:4652)<br> at java.awt.Container.dispatchEventImpl(Container.java:2099)<br> at java.awt.Component.dispatchEvent(Component.java:4482)<br>
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577<br>)<br> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br><br> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br>
at java.awt.Container.dispatchEventImpl(Container.java:2085)<br> at java.awt.Window.dispatchEventImpl(Window.java:2478)<br> at java.awt.Component.dispatchEvent(Component.java:4482)<br> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:644)<br>
at java.awt.EventQueue.access$000(EventQueue.java:85)<br> at java.awt.EventQueue$1.run(EventQueue.java:603)<br> at java.awt.EventQueue$1.run(EventQueue.java:601)<br> at java.security.AccessController.doPrivileged(Native Method)<br>
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo<br>ntrolContext.java:87)<br> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo<br>ntrolContext.java:98)<br> at java.awt.EventQueue$2.run(EventQueue.java:617)<br>
at java.awt.EventQueue$2.run(EventQueue.java:615)<br> at java.security.AccessController.doPrivileged(Native Method)<br> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessCo<br>ntrolContext.java:87)<br>
at java.awt.EventQueue.dispatchEvent(EventQueue.java:614)<br> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThre<br>ad.java:269)<br> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.<br>
java:184)<br> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre<br>ad.java:174)<br> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br><br> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br>
<br> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br>Caused by: java.lang.NoClassDefFoundError: loci/common/services/ServiceFactory<br> at spim.progacq.OMETIFFHandler.<init>(OMETIFFHandler.java:55)<br>
... 37 more<br>Caused by: java.lang.ClassNotFoundException: loci.common.services.ServiceFactory<br><br> at java.net.URLClassLoader$1.run(URLClassLoader.java:202)<br> at java.security.AccessController.doPrivileged(Native Method)<br>
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)<br> at java.lang.ClassLoader.loadClass(ClassLoader.java:307)<br> at java.lang.ClassLoader.loadClass(ClassLoader.java:248)<br> ... 38 more<br>
<br></div><div>Hopefully that is useful.<br></div><div><br>Thanks again,<br></div><div>Aurelia<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Oct 9, 2013 at 1:37 AM, Johannes Schindelin <span dir="ltr"><<a href="mailto:Johannes.Schindelin@gmx.de" target="_blank">Johannes.Schindelin@gmx.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Aurelia,<br>
<div class="im"><br>
On Tue, 8 Oct 2013, Aurelia Honerkamp-Smith wrote:<br>
<br>
> Sorry, I have been asking a lot of questions lately,<br>
<br>
</div>There is really no reason to be sorry about that. Scientists have a track<br>
record of lacking the desire to communicate effectively, so I enjoy very<br>
much that you are an exception!<br>
<div class="im"><br>
> but I have at least one more today. I can now acquire a stack, but only<br>
> if I leave the Output directory field blank (I attach a projection of my<br>
> first SPIM image, which I'm very happy about).<br>
<br>
</div>This is a really awesome picture! Would you mind uploading it to the wiki<br>
and adding it to the gallery? I can help you with that should there be any<br>
problems.<br>
<div class="im"><br>
> If I put in a directory, then when I push Snap nothing happens. It<br>
> doesn't seem to matter which folder I use, and there's no entry in the<br>
> core log.<br>
<br>
</div>Could you copy the ImageJ-win32.exe in OpenSPIM.app/ and rename the copied<br>
file to debug.exe and run that? This should give you a console output (I<br>
strongly suspect an exception to occur, which I would be really eager to<br>
see, maybe you could copy/paste it into a reply?).<br>
<div class="im"><br>
> If it's a non-empty directory, I do get a message warning me that any<br>
> OME-tiff files will be deleted, but after I dismiss the message nothing<br>
> happens once more.<br>
<br>
</div>It is probably the same issue in that case.<br>
<div class="im"><br>
> Has anyone had a problem like this before? Could it be Windows 7 related?<br>
<br>
</div>Quite possibly. But I can only guess without having a glimpse at the<br>
console output.<br>
<br>
Ciao,<br>
Johannes<br>
</blockquote></div><br></div></div>