[OpenSPIM] Micro-Manager Issue

[Johannes Schindelin]

Hi Dylan,

I Cc:ed the mailing list again so that the OpenSPIM community knows 
about your kind offer. For future record, I would also like to ask 
keeping communication with me on public record (unless there are good 
reasons to take the conversation private, of course).

On 2015-01-27 12:26, Windell, Dylan wrote:
> Dear Johannes,
> 
> Thank you very much for the email and information.
> 
> I followed all the steps once again and installed mfiji in a different
> directory and now the plugin works, I have attached all the log files
> I could find anyway, the first one is of the failed version this
> morning and the second two are the successful ones. I had tried to
> update ImageJ in one version but there were a list of duplicate
> plugins.
> 
> However, if I try and acquire any images I just get black or blank
> pictures, this error comes up when I try and calibrate the pixel size:
> 
> (Fiji Is Just) ImageJ 2.0.0-rc-13/1.49e; Java 1.6.0_31 [64-bit];
> Windows 7 6.1; 128MB of 2000MB (6%)
> 
> java.lang.Exception: Internal inconsistency: unknown system exception
> encountered
> 	at mmcorej.MMCoreJJNI.CMMCore_snapImage(Native Method)
> 	at mmcorej.CMMCore.snapImage(CMMCore.java:813)
> 	at 
> spim.PixelSizeCalibrator.fetchFreshImage(PixelSizeCalibrator.java:308)
> 	at spim.PixelSizeCalibrator.<init>(PixelSizeCalibrator.java:160)
> 	at spim.SPIMAcquisition$2.actionPerformed(SPIMAcquisition.java:395)
> 	at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
> 	at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
> 	at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
> 	at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
> 	at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown 
> Source)
> 	at java.awt.Component.processMouseEvent(Unknown Source)
> 	at javax.swing.JComponent.processMouseEvent(Unknown Source)
> 	at java.awt.Component.processEvent(Unknown Source)
> 	at java.awt.Container.processEvent(Unknown Source)
> 	at java.awt.Component.dispatchEventImpl(Unknown Source)
> 	at java.awt.Container.dispatchEventImpl(Unknown Source)
> 	at java.awt.Component.dispatchEvent(Unknown Source)
> 	at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
> 	at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
> 	at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
> 	at java.awt.Container.dispatchEventImpl(Unknown Source)
> 	at java.awt.Window.dispatchEventImpl(Unknown Source)
> 	at java.awt.Component.dispatchEvent(Unknown Source)
> 	at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
> 	at java.awt.EventQueue.access$000(Unknown Source)
> 	at java.awt.EventQueue$1.run(Unknown Source)
> 	at java.awt.EventQueue$1.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at 
> java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown 
> Source)
> 	at 
> java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown 
> Source)
> 	at java.awt.EventQueue$2.run(Unknown Source)
> 	at java.awt.EventQueue$2.run(Unknown Source)
> 	at java.security.AccessController.doPrivileged(Native Method)
> 	at 
> java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown 
> Source)
> 	at java.awt.EventQueue.dispatchEvent(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> 	at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
> 	at java.awt.EventDispatchThread.run(Unknown Source)
> 
> I have contacted Andor to find out if there is something I am missing
> regarding the camera setup.
> 
> Thank you very much for taking the time to look into this, I do hope
> one day I will be able to help others with related issues.
> 
> Kind regards,
> 
> Dylan
> 
> Dylan Windell
> Postgraduate Researcher
> College of Life and Environmental Sciences
> University of Exeter, Geoffrey Pope
> Stocker Road, Exeter EX4 4QD, UK
> phone: +44 (0) 7596725056
> email: dw388 at exeter.ac.uk
> 
> 
> 
> -----Original Message-----
> From: Johannes Schindelin [mailto:johannes.schindelin at gmx.de]
> Sent: 26 January 2015 23:50
> To: Windell, Dylan
> Cc: openspim-owner at openspim.org; openspim at openspim.org
> Subject: Re: Micro-Manager Issue
> 
> Hi Dylan,
> 
> On 2015-01-26 18:55, Windell, Dylan wrote:
> 
>> I am having trouble sending an email which I have attached below to
>> the normal mailing address, I have registered on the site under this
>> email account so I am not sure what is the problem.
> 
> Unfortunately I cannot see the mail. And I could not see any previous
> attempts to subscribe, either, so I allowed myself to subscribe you
> directly.
> 
>> After reading the recent post regarding SPIM at x64, I am trying to
>> get MM to work on my Windows 7 OS working at 64-bit but thus far I
>> have not been able to.
> 
> Please provide the full information, including all relevant log files
> that you can find. Even if they do not make sense to you, they might
> help others to help you.
> 
>> I have installed my Andor drivers and followed the steps to install
>> all the software but despite the new SPIM plugin, it does not run at
>> all.
> 
> Again, a detailed error report is required to help you. If
> Micro-Manager crashes, or if it shows you an error message, or if
> another message pops up; all of that is crucial information that is
> required to help you make sense of the problem and resolve it.
> 
>> In addition, when trying to load my
>> configuration the program continues to freeze and crash.
> 
> That description is unfortunately not precise enough to identify the
> problem. You probably have a CoreLog in your OpenSPIM.app/CoreLogs/
> directory that should shed light into the issues.
> 
>> I know it is still not yet finished being fixed but I was just
>> wandering if there is a temporary fix for this?
> 
> Unfortunately, it is not possible with specific information (such as
> the information provided by the CoreLog) to know enough about the
> problem in order to assess any possible fix. Please copy & paste
> precise error messages whenever possible, otherwise write them into a
> mail as faithfully as possible, and attach the relevant (parts of the)
> CoreLog.
> 
> Once you do that, I am confident that you will find the OpenSPIM
> community to be helpful in getting your system to work, hopefully so
> much that you also help others to get their systems to work, too.
> 
> Ciao,
> Johannes