[OpenSPIM] Micro-Manager Issue

Wed Jan 28 06:15:09 CST 2015

  Hello Dylan,

just to confirm - have you followed the instructions at http://openspim.org/64bit_OpenSPIM
 or which ones?
It’s quite important that you install the latest Andor Driver Pack and turn off Link State Power Management as indicated on the wiki page.

cheers,

ulrik

—
Ulrik Günther, Dipl.-Phys.
PhD Student
MOSAIC Group & Tomancak Lab, Center of Systems Biology Dresden
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108, D-01307 Dresden, Germany

E-Mail: guenther at mpi-cbg.de

> On Jan 28, 2015, at 1:00 PM, Johannes Schindelin <johannes.schindelin at gmx.de> wrote:
> 
> 
> 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
>> 
>> 
>> 
> 
> 
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