Arduino shutter error

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Arduino shutter error

Knecht, David
I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300.  We are stumped as to what could be causing the problem and have run out of things to try.  This is running on a Mac mini with the latest OS X version and we have tried both stable releases and nightly builds of MM with no difference.  Below is the core log of when the error occurs in case in means something to someone. It had successfully captured many images earlier, and this is the capture where the acquisition failed.  Thanks- Dave

2016-03-11T03:13:46.442932 tid0xba726000 [dbg,App] [AE] second attempt
2016-03-11T03:13:46.445449 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc waitForDevice "Arduino-Shutter")
2016-03-11T03:13:46.445491 tid0xba726000 [dbg,Core] Waiting for device Arduino-Shutter...
2016-03-11T03:13:46.445498 tid0xba726000 [dbg,Core] Finished waiting for device Arduino-Shutter
2016-03-11T03:13:46.445702 tid0xba726000 [dbg,App] [AE] --> nil
2016-03-11T03:13:46.447107 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc setShutterOpen false)
2016-03-11T03:13:46.447150 tid0xba726000 [dbg,dev:Arduino-Shutter] Request 0
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)
2016-03-11T03:13:46.697486 tid0xba726000 [IFO,App] 
                                         [       ] java.lang.RuntimeException: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107) in Thread[AcquisitionEngine2010 Thread (Clojure),6,main]
                                         [       ]   at clojure.lang.Util.runtimeException(Util.java:165)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:35)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
                                         [       ] Caused by: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107)
                                         [       ]   at mmcorej.MMCoreJJNI.CMMCore_setShutterOpen__SWIG_0(Native Method)
                                         [       ]   at mmcorej.CMMCore.setShutterOpen(CMMCore.java:890)
                                         [       ]   at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
                                         [       ]   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                                         [       ]   at java.lang.reflect.Method.invoke(Method.java:597)
                                         [       ]   at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:92)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:30)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
2016-03-11T03:13:46.699261 tid0xc7424000 [IFO,App] Acquisition failed.
                                         [       ] java.lang.Exception: Device failure: Arduino-Shutter in Thread[clojure-agent-send-off-pool-0,6,main]
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
                                         [       ]   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
                                         [       ]   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
                                         [       ]   at clojure.lang.Reflector.invokeConstructor(Reflector.java:183)
                                         [       ]   at org.micromanager.acq_engine$throw_exception.invoke(acq_engine.clj:71)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)


Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200


------------------------------------------------------------------------------
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Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
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Re: Arduino shutter error

Austin
I know this is basic stuff, but is the board a genuine arduino, and are you certain the USB cable is OK?
Also try a different USB port. 

Austin


On Mar 11, 2016, at 6:29 AM, Knecht, David <[hidden email]> wrote:

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300.  We are stumped as to what could be causing the problem and have run out of things to try.  This is running on a Mac mini with the latest OS X version and we have tried both stable releases and nightly builds of MM with no difference.  Below is the core log of when the error occurs in case in means something to someone. It had successfully captured many images earlier, and this is the capture where the acquisition failed.  Thanks- Dave

2016-03-11T03:13:46.442932 tid0xba726000 [dbg,App] [AE] second attempt
2016-03-11T03:13:46.445449 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc waitForDevice "Arduino-Shutter")
2016-03-11T03:13:46.445491 tid0xba726000 [dbg,Core] Waiting for device Arduino-Shutter...
2016-03-11T03:13:46.445498 tid0xba726000 [dbg,Core] Finished waiting for device Arduino-Shutter
2016-03-11T03:13:46.445702 tid0xba726000 [dbg,App] [AE] --> nil
2016-03-11T03:13:46.447107 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc setShutterOpen false)
2016-03-11T03:13:46.447150 tid0xba726000 [dbg,dev:Arduino-Shutter] Request 0
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)
2016-03-11T03:13:46.697486 tid0xba726000 [IFO,App] 
                                         [       ] java.lang.RuntimeException: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107) in Thread[AcquisitionEngine2010 Thread (Clojure),6,main]
                                         [       ]   at clojure.lang.Util.runtimeException(Util.java:165)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:35)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
                                         [       ] Caused by: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107)
                                         [       ]   at mmcorej.MMCoreJJNI.CMMCore_setShutterOpen__SWIG_0(Native Method)
                                         [       ]   at mmcorej.CMMCore.setShutterOpen(CMMCore.java:890)
                                         [       ]   at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
                                         [       ]   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                                         [       ]   at java.lang.reflect.Method.invoke(Method.java:597)
                                         [       ]   at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:92)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:30)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
2016-03-11T03:13:46.699261 tid0xc7424000 [IFO,App] Acquisition failed.
                                         [       ] java.lang.Exception: Device failure: Arduino-Shutter in Thread[clojure-agent-send-off-pool-0,6,main]
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
                                         [       ]   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
                                         [       ]   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
                                         [       ]   at clojure.lang.Reflector.invokeConstructor(Reflector.java:183)
                                         [       ]   at org.micromanager.acq_engine$throw_exception.invoke(acq_engine.clj:71)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)


Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general


------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785111&iu=/4140
_______________________________________________
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Re: Arduino shutter error

Knecht, David
Hi Austin-
Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 11, 2016, at 10:58 AM, Austin <[hidden email]> wrote:

I know this is basic stuff, but is the board a genuine arduino, and are you certain the USB cable is OK?
Also try a different USB port. 
Bought from Adafruit web site directly as I have with the other boards, so as far as I know it is.  Are there cheap knockoffs on the market?  
I will try swapping cable and port.  Good idea!  Dave


Austin


On Mar 11, 2016, at 6:29 AM, Knecht, David <[hidden email]> wrote:

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300.  We are stumped as to what could be causing the problem and have run out of things to try.  This is running on a Mac mini with the latest OS X version and we have tried both stable releases and nightly builds of MM with no difference.  Below is the core log of when the error occurs in case in means something to someone. It had successfully captured many images earlier, and this is the capture where the acquisition failed.  Thanks- Dave

2016-03-11T03:13:46.442932 tid0xba726000 [dbg,App] [AE] second attempt
2016-03-11T03:13:46.445449 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc waitForDevice "Arduino-Shutter")
2016-03-11T03:13:46.445491 tid0xba726000 [dbg,Core] Waiting for device Arduino-Shutter...
2016-03-11T03:13:46.445498 tid0xba726000 [dbg,Core] Finished waiting for device Arduino-Shutter
2016-03-11T03:13:46.445702 tid0xba726000 [dbg,App] [AE] --> nil
2016-03-11T03:13:46.447107 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc setShutterOpen false)
2016-03-11T03:13:46.447150 tid0xba726000 [dbg,dev:Arduino-Shutter] Request 0
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)
2016-03-11T03:13:46.697486 tid0xba726000 [IFO,App] 
                                         [       ] java.lang.RuntimeException: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107) in Thread[AcquisitionEngine2010 Thread (Clojure),6,main]
                                         [       ]   at clojure.lang.Util.runtimeException(Util.java:165)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:35)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
                                         [       ] Caused by: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107)
                                         [       ]   at mmcorej.MMCoreJJNI.CMMCore_setShutterOpen__SWIG_0(Native Method)
                                         [       ]   at mmcorej.CMMCore.setShutterOpen(CMMCore.java:890)
                                         [       ]   at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
                                         [       ]   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                                         [       ]   at java.lang.reflect.Method.invoke(Method.java:597)
                                         [       ]   at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:92)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:30)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
2016-03-11T03:13:46.699261 tid0xc7424000 [IFO,App] Acquisition failed.
                                         [       ] java.lang.Exception: Device failure: Arduino-Shutter in Thread[clojure-agent-send-off-pool-0,6,main]
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
                                         [       ]   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
                                         [       ]   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
                                         [       ]   at clojure.lang.Reflector.invokeConstructor(Reflector.java:183)
                                         [       ]   at org.micromanager.acq_engine$throw_exception.invoke(acq_engine.clj:71)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)


Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

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Re: Arduino shutter error

Nico Stuurman-2
In reply to this post by Knecht, David
Hi David,

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300. 
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)

Error code 107 in the Arduino adapter code stands for "ERR_COMMUNICATION", and occurs whenever reading or writing to the virtual serial port fails.  So, follow Austin's advice and swap cable/Arduino/USB port.  If that all fails (i.e. the problem stays with the Mac Mini, not the cable/Ardunio), then you could try to put the Arduino behind a powered USB hub.  And if it still fails, buy a PC;)

Best,

Nico



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Re: Arduino shutter error

David Biggs
Hi David,

I suggest you google 'osx serial port sniffer'.  That may show the disconnection issue.

For the PC I recommend a Serial Port Monitor as described by Austin:

Just start the monitor before starting MM.

Cheers,
David

On Fri, Mar 11, 2016 at 8:36 AM, Nico Stuurman <[hidden email]> wrote:
Hi David,

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300. 
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)

Error code 107 in the Arduino adapter code stands for "ERR_COMMUNICATION", and occurs whenever reading or writing to the virtual serial port fails.  So, follow Austin's advice and swap cable/Arduino/USB port.  If that all fails (i.e. the problem stays with the Mac Mini, not the cable/Ardunio), then you could try to put the Arduino behind a powered USB hub.  And if it still fails, buy a PC;)

Best,

Nico



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Re: Arduino shutter error

Austin
In reply to this post by Knecht, David
Macs should be able to run any arduino available on the market. I do all my development on a macbook pro and I’ve only seen issues with knockoff brand nano boards, and even then rarely. Never had an issue with 100+ boards genuine 

Here’s an example of a knockoff board - they are nice for generic prototyping as if you hook something up wrong or cook the board, the loss isn’t so great. 
Generally they are OK, i’ve seen some issues with lower quality oscillators used on them, and with the knockoff FTDI serial interfaces used with them. 

Austin


On Mar 11, 2016, at 8:04 AM, Knecht, David <[hidden email]> wrote:

On Mar 11, 2016, at 10:58 AM, Austin <[hidden email]> wrote:

I know this is basic stuff, but is the board a genuine arduino, and are you certain the USB cable is OK?
Also try a different USB port. 
Bought from Adafruit web site directly as I have with the other boards, so as far as I know it is.  Are there cheap knockoffs on the market?  
I will try swapping cable and port.  Good idea!  Dave


Austin


On Mar 11, 2016, at 6:29 AM, Knecht, David <[hidden email]> wrote:

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300.  We are stumped as to what could be causing the problem and have run out of things to try.  This is running on a Mac mini with the latest OS X version and we have tried both stable releases and nightly builds of MM with no difference.  Below is the core log of when the error occurs in case in means something to someone. It had successfully captured many images earlier, and this is the capture where the acquisition failed.  Thanks- Dave

2016-03-11T03:13:46.442932 tid0xba726000 [dbg,App] [AE] second attempt
2016-03-11T03:13:46.445449 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc waitForDevice "Arduino-Shutter")
2016-03-11T03:13:46.445491 tid0xba726000 [dbg,Core] Waiting for device Arduino-Shutter...
2016-03-11T03:13:46.445498 tid0xba726000 [dbg,Core] Finished waiting for device Arduino-Shutter
2016-03-11T03:13:46.445702 tid0xba726000 [dbg,App] [AE] --> nil
2016-03-11T03:13:46.447107 tid0xba726000 [dbg,App] [AE] <-- (. org.micromanager.mm/mmc setShutterOpen false)
2016-03-11T03:13:46.447150 tid0xba726000 [dbg,dev:Arduino-Shutter] Request 0
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)
2016-03-11T03:13:46.697486 tid0xba726000 [IFO,App] 
                                         [       ] java.lang.RuntimeException: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107) in Thread[AcquisitionEngine2010 Thread (Clojure),6,main]
                                         [       ]   at clojure.lang.Util.runtimeException(Util.java:165)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:35)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
                                         [       ] Caused by: java.lang.Exception: Error in device "Arduino-Shutter": (Error message unavailable) (107)
                                         [       ]   at mmcorej.MMCoreJJNI.CMMCore_setShutterOpen__SWIG_0(Native Method)
                                         [       ]   at mmcorej.CMMCore.setShutterOpen(CMMCore.java:890)
                                         [       ]   at sun.reflect.GeneratedMethodAccessor47.invoke(Unknown Source)
                                         [       ]   at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
                                         [       ]   at java.lang.reflect.Method.invoke(Method.java:597)
                                         [       ]   at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:92)
                                         [       ]   at clojure.lang.Reflector.invokeInstanceMethod(Reflector.java:30)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$attempt__813__auto____849.invoke(acq_engine.clj:225)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open$fn__855.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)
2016-03-11T03:13:46.699261 tid0xc7424000 [IFO,App] Acquisition failed.
                                         [       ] java.lang.Exception: Device failure: Arduino-Shutter in Thread[clojure-agent-send-off-pool-0,6,main]
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
                                         [       ]   at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
                                         [       ]   at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
                                         [       ]   at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
                                         [       ]   at clojure.lang.Reflector.invokeConstructor(Reflector.java:183)
                                         [       ]   at org.micromanager.acq_engine$throw_exception.invoke(acq_engine.clj:71)
                                         [       ]   at org.micromanager.acq_engine$set_shutter_open.invoke(acq_engine.clj:223)
                                         [       ]   at org.micromanager.acq_engine$snap_image.invoke(acq_engine.clj:279)
                                         [       ]   at clojure.lang.AFn.applyToHelper(AFn.java:163)
                                         [       ]   at clojure.lang.AFn.applyTo(AFn.java:151)
                                         [       ]   at clojure.core$apply.invoke(core.clj:600)
                                         [       ]   at org.micromanager.acq_engine$expose.invoke(acq_engine.clj:578)
                                         [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1294.invoke(acq_engine.clj:756)
                                         [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:764)
                                         [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:779)
                                         [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:946)
                                         [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                         [       ]   at java.lang.Thread.run(Thread.java:695)


Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

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Re: Arduino shutter error

Knecht, David
In reply to this post by Nico Stuurman-2
I swapped the Arduino board and cable and the problem stayed with the computer and not the board.  So it seems to be something about that particular Mac.  It is the most recent Mac and the only one running 10.11 (El Capitan).  I am tempted to downgrade it to 10.10 and see what happens, but will try the hub idea first.

I also have to say that I do not appreciate the “buy a PC” comment.  I am not sure if it was tongue in cheek or serious, but either way it is annoying. The major reason I got on the MM bandwagon at its earliest phase was because I supported both open source and cross platform.  Are you saying you have given up on supporting Macs?  

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 11, 2016, at 11:36 AM, Nico Stuurman <[hidden email]> wrote:

Hi David,

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300. 
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)

Error code 107 in the Arduino adapter code stands for "ERR_COMMUNICATION", and occurs whenever reading or writing to the virtual serial port fails.  So, follow Austin's advice and swap cable/Arduino/USB port.  If that all fails (i.e. the problem stays with the Mac Mini, not the cable/Ardunio), then you could try to put the Arduino behind a powered USB hub.  And if it still fails, buy a PC;)

Best,

Nico


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Re: Arduino shutter error

Austin
I’d look @ the driver files, or try swapping USB ports. Very weird as I mentioned I’ve used them w/ several macs without trouble. 
Maybe this guide will help?



- Austin


On Mar 15, 2016, at 12:05 PM, Knecht, David <[hidden email]> wrote:

I swapped the Arduino board and cable and the problem stayed with the computer and not the board.  So it seems to be something about that particular Mac.  It is the most recent Mac and the only one running 10.11 (El Capitan).  I am tempted to downgrade it to 10.10 and see what happens, but will try the hub idea first.

I also have to say that I do not appreciate the “buy a PC” comment.  I am not sure if it was tongue in cheek or serious, but either way it is annoying. The major reason I got on the MM bandwagon at its earliest phase was because I supported both open source and cross platform.  Are you saying you have given up on supporting Macs?  

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 11, 2016, at 11:36 AM, Nico Stuurman <[hidden email]> wrote:

Hi David,

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300. 
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)

Error code 107 in the Arduino adapter code stands for "ERR_COMMUNICATION", and occurs whenever reading or writing to the virtual serial port fails.  So, follow Austin's advice and swap cable/Arduino/USB port.  If that all fails (i.e. the problem stays with the Mac Mini, not the cable/Ardunio), then you could try to put the Arduino behind a powered USB hub.  And if it still fails, buy a PC;)

Best,

Nico


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Re: Arduino shutter error

Mark Tsuchida-3
In reply to this post by Knecht, David
Hi Dave,

On Tue, Mar 15, 2016 at 12:05 PM, Knecht, David <[hidden email]> wrote:
> Are you saying you have given up on supporting Macs?

Open Imaging plans to continue Mac (OS X) support where practical. OS
X 32-bit version support will be dropped when we move to Java 8, and
of course it continues to be the case that many non-serial devices can
only (realistically) be supported on the platforms for which the
manufacturer provides a driver, which, for cameras and microscopy
equipment, often (though not always) happens to be Windows only. (This
situation has been explained on this mailing list in the recent past,
if I recall correctly.)

Usually, serial devices should not be a problem on OS X, provided that
the driver for the serial port itself does not have compatibility
issues.

However, it is my general impression that Microsoft (at least up to
Windows 7, I'm not so sure about Windows 10) has always prioritized
backward compatibility a little more than Apple has (if only as a
side-effect of the less-frequent major updates), at least for things
like device drivers. You will find that the FTDI USB-serial driver's
latest version (2.3) is "Updated for 10.9 and 10.10", which means you
might be right that it's not yet compatible with 10.11. Because of
cases like this, if you want a computer that has the least chance of
causing incompatibility issues, I would also be forced to recommend a
PC (specifically, a Windows 7 box for the foreseeable future). I wish
things were equally easy on Mac and Linux, but it's not something we
have any control over.

Best,
Mark

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Re: Arduino shutter error

Nico Stuurman-2
In reply to this post by Knecht, David


On 3/15/16 12:05 PM, Knecht, David wrote:
I also have to say that I do not appreciate the “buy a PC” comment. 
You must have missed the " ;) "

Come to think about it, you don't even have to buy a PC, just install Windows on your current machine ;) ;) ;(

Best,

Nico


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Re: Arduino shutter error

Knecht, David
In reply to this post by Austin
Hi Austin- Are any of the Macs you have working running El Capitan?  My problem seems isolated to that OS X.  I have tried swapping USB ports, a powered hub and swapping Aruduino boards and the problem stays with the computer.  I read the Sparkfun site.  It appears that most people have problems getting the board recognized by the computer as a serial port device.  I did not have that problem.  As a test, I went through and removed the Apple Usbserial driver and installed the FTDI drivers.  The same error happens, but the problem is even worse with those drivers.  If I did anything on the computer at all while it was acquiring, the Arduino failed.  If I did nothing, it went for a few hours and then failed.  I am going to try putting Virtualbox on the computer and see if that works.  Any other suggestions welcome.  Dave

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 15, 2016, at 4:33 PM, Austin <[hidden email]> wrote:

I’d look @ the driver files, or try swapping USB ports. Very weird as I mentioned I’ve used them w/ several macs without trouble. 
Maybe this guide will help?



- Austin


On Mar 15, 2016, at 12:05 PM, Knecht, David <[hidden email]> wrote:

I swapped the Arduino board and cable and the problem stayed with the computer and not the board.  So it seems to be something about that particular Mac.  It is the most recent Mac and the only one running 10.11 (El Capitan).  I am tempted to downgrade it to 10.10 and see what happens, but will try the hub idea first.

I also have to say that I do not appreciate the “buy a PC” comment.  I am not sure if it was tongue in cheek or serious, but either way it is annoying. The major reason I got on the MM bandwagon at its earliest phase was because I supported both open source and cross platform.  Are you saying you have given up on supporting Macs?  

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 11, 2016, at 11:36 AM, Nico Stuurman <[hidden email]> wrote:

Hi David,

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300. 
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)

Error code 107 in the Arduino adapter code stands for "ERR_COMMUNICATION", and occurs whenever reading or writing to the virtual serial port fails.  So, follow Austin's advice and swap cable/Arduino/USB port.  If that all fails (i.e. the problem stays with the Mac Mini, not the cable/Ardunio), then you could try to put the Arduino behind a powered USB hub.  And if it still fails, buy a PC;)

Best,

Nico


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Re: Arduino shutter error

Mark Tsuchida-3
Hi Dave,

On Fri, Mar 18, 2016 at 7:05 AM, Knecht, David <[hidden email]> wrote:
> Hi Austin- Are any of the Macs you have working running El Capitan?  My

One more thing which I should have mentioned earlier:
Java 6 (from Apple), which Micro-Manager currently uses, is not
supported on El Capitan.
We will work on migrating to Java 8 (from Oracle) (as ImageJ has done
recently) over the next months, but until then, we recommend sticking
to Yosemite or Mavericks.

(This is independent of any Arduino or FTDI issues.)

Best,
Mark

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Re: Arduino shutter error

Austin
In reply to this post by Knecht, David
Hi David,

All of my systems are on Yosemite. One thing which would be easy to test, would be to run a simple loop script in the arudino, which repeatedly calls the serial port, to test if it’s something going on with communication stability in the mac. 

Something like the example below (just a gross example, please excuse syntax errors or omissions). 
Basically, have the ‘duino send ver a chunk of serial data every so often. Then open the serial port monitor in the arduino software, and see if it stays working. IF things are set up correctly, the below code should run for infinity. 


void setup()
{
Serial.begin(9600); //open the com port
}

void loop()
{
Serial.println(“Test of comms”); //test message
delay(10000); //10 second delay
}

Austin


On Mar 18, 2016, at 7:05 AM, Knecht, David <[hidden email]> wrote:

Hi Austin- Are any of the Macs you have working running El Capitan?  My problem seems isolated to that OS X.  I have tried swapping USB ports, a powered hub and swapping Aruduino boards and the problem stays with the computer.  I read the Sparkfun site.  It appears that most people have problems getting the board recognized by the computer as a serial port device.  I did not have that problem.  As a test, I went through and removed the Apple Usbserial driver and installed the FTDI drivers.  The same error happens, but the problem is even worse with those drivers.  If I did anything on the computer at all while it was acquiring, the Arduino failed.  If I did nothing, it went for a few hours and then failed.  I am going to try putting Virtualbox on the computer and see if that works.  Any other suggestions welcome.  Dave

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 15, 2016, at 4:33 PM, Austin <[hidden email]> wrote:

I’d look @ the driver files, or try swapping USB ports. Very weird as I mentioned I’ve used them w/ several macs without trouble. 
Maybe this guide will help?



- Austin


On Mar 15, 2016, at 12:05 PM, Knecht, David <[hidden email]> wrote:

I swapped the Arduino board and cable and the problem stayed with the computer and not the board.  So it seems to be something about that particular Mac.  It is the most recent Mac and the only one running 10.11 (El Capitan).  I am tempted to downgrade it to 10.10 and see what happens, but will try the hub idea first.

I also have to say that I do not appreciate the “buy a PC” comment.  I am not sure if it was tongue in cheek or serious, but either way it is annoying. The major reason I got on the MM bandwagon at its earliest phase was because I supported both open source and cross platform.  Are you saying you have given up on supporting Macs?  

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 11, 2016, at 11:36 AM, Nico Stuurman <[hidden email]> wrote:

Hi David,

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300. 
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)

Error code 107 in the Arduino adapter code stands for "ERR_COMMUNICATION", and occurs whenever reading or writing to the virtual serial port fails.  So, follow Austin's advice and swap cable/Arduino/USB port.  If that all fails (i.e. the problem stays with the Mac Mini, not the cable/Ardunio), then you could try to put the Arduino behind a powered USB hub.  And if it still fails, buy a PC;)

Best,

Nico


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Re: Arduino shutter error

Knecht, David
I think I fixed it.  I was rechecking everything and found that when I had downloaded the latest nightly build, I had neglected to go into the Get Info window and check the Prevent App Nap box.  I came up against that problem previously.  I have run two tests with that box checked and both worked perfectly.  Hopefully this i solved.  Is this something that can be preset in the downloaded app to prevent others from having this problem?  Dave

On Mar 18, 2016, at 3:29 PM, Austin <[hidden email]> wrote:

Hi David,

All of my systems are on Yosemite. One thing which would be easy to test, would be to run a simple loop script in the arudino, which repeatedly calls the serial port, to test if it’s something going on with communication stability in the mac. 

Something like the example below (just a gross example, please excuse syntax errors or omissions). 
Basically, have the ‘duino send ver a chunk of serial data every so often. Then open the serial port monitor in the arduino software, and see if it stays working. IF things are set up correctly, the below code should run for infinity. 


void setup()
{
Serial.begin(9600); //open the com port
}

void loop()
{
Serial.println(“Test of comms”); //test message
delay(10000); //10 second delay
}

Austin


On Mar 18, 2016, at 7:05 AM, Knecht, David <[hidden email]> wrote:

Hi Austin- Are any of the Macs you have working running El Capitan?  My problem seems isolated to that OS X.  I have tried swapping USB ports, a powered hub and swapping Aruduino boards and the problem stays with the computer.  I read the Sparkfun site.  It appears that most people have problems getting the board recognized by the computer as a serial port device.  I did not have that problem.  As a test, I went through and removed the Apple Usbserial driver and installed the FTDI drivers.  The same error happens, but the problem is even worse with those drivers.  If I did anything on the computer at all while it was acquiring, the Arduino failed.  If I did nothing, it went for a few hours and then failed.  I am going to try putting Virtualbox on the computer and see if that works.  Any other suggestions welcome.  Dave

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 15, 2016, at 4:33 PM, Austin <[hidden email]> wrote:

I’d look @ the driver files, or try swapping USB ports. Very weird as I mentioned I’ve used them w/ several macs without trouble. 
Maybe this guide will help?



- Austin


On Mar 15, 2016, at 12:05 PM, Knecht, David <[hidden email]> wrote:

I swapped the Arduino board and cable and the problem stayed with the computer and not the board.  So it seems to be something about that particular Mac.  It is the most recent Mac and the only one running 10.11 (El Capitan).  I am tempted to downgrade it to 10.10 and see what happens, but will try the hub idea first.

I also have to say that I do not appreciate the “buy a PC” comment.  I am not sure if it was tongue in cheek or serious, but either way it is annoying. The major reason I got on the MM bandwagon at its earliest phase was because I supported both open source and cross platform.  Are you saying you have given up on supporting Macs?  

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200

On Mar 11, 2016, at 11:36 AM, Nico Stuurman <[hidden email]> wrote:

Hi David,

I have 9 microscope systems where I have an Arduino board controlling LED illuminators off/on during time lapse acquisition with Micro-manager Multi-D.  The only things being controlled are the Arduino and the camera.  On the latest unit I built, I am getting an Arduino shutter error that stops acquisition.  The error occurs randomly in time, as early as frame 3 and as late as frame 300. 
2016-03-11T03:13:46.697182 tid0xba726000 [ERR,Core] Error occurred in device CMMCore::setShutterOpen(): Error in device "Arduino-Shutter": (Error message unavailable) (107)

Error code 107 in the Arduino adapter code stands for "ERR_COMMUNICATION", and occurs whenever reading or writing to the virtual serial port fails.  So, follow Austin's advice and swap cable/Arduino/USB port.  If that all fails (i.e. the problem stays with the Mac Mini, not the cable/Ardunio), then you could try to put the Arduino behind a powered USB hub.  And if it still fails, buy a PC;)

Best,

Nico


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Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
91 N. Eagleville Rd.
Storrs, CT 06269
860-486-2200


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USB joystick for Prior stage

PEARSON Matthew
In reply to this post by Mark Tsuchida-3
Hi all,

I have recently inherited what was an applied imaging Ariol slide scanning microscope.  As part of this is a USB joystick which operated a Prior H101A XY stage.  The joystick appears to have controlled the stage via the PC perhaps through whatever the ariol used for acquisition software.  Does anyone know how/if i could still use this joystick to control the stage through Micro-Manager?  There is a Prior proscan II with the system which the stage is attached too, so it seems an odd arrangement for the joystick to not be linked to the Proscan but Prior have confirmed it couldn't be used with this controller directly.  It might be easier to buy a new prior joystick instead..

Thanks for any advice,

Matt

 
--
Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
IGMM
University of Edinburgh
Crewe Road
EH4 2XU



On 18 Mar 2016, at 19:08, Mark Tsuchida <[hidden email]> wrote:

> Hi Dave,
>
> On Fri, Mar 18, 2016 at 7:05 AM, Knecht, David <[hidden email]> wrote:
>> Hi Austin- Are any of the Macs you have working running El Capitan?  My
>
> One more thing which I should have mentioned earlier:
> Java 6 (from Apple), which Micro-Manager currently uses, is not
> supported on El Capitan.
> We will work on migrating to Java 8 (from Oracle) (as ImageJ has done
> recently) over the next months, but until then, we recommend sticking
> to Yosemite or Mavericks.
>
> (This is independent of any Arduino or FTDI issues.)
>
> Best,
> Mark
>
> ------------------------------------------------------------------------------
> Transform Data into Opportunity.
> Accelerate data analysis in your applications with
> Intel Data Analytics Acceleration Library.
> Click to learn more.
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--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.


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Strange inability to launch MM on Mac laptop with Oracle JVM and Apple JVM installed

jdhardin
In reply to this post by Mark Tsuchida-3
Hi all,
I have a weird problem that I believe involves how Java is installed/setup on one of my Mac laptops running MacOS 10.12 (Sierra). I installed JRE 8 from Oracle for running Fiji. Fiji runs fine. I can also run ImageJ, and it tells me I’m running JVM 1.6.0_65 (the legacy Apple JVM). When I try to launch Micr-Manager 1.4 or 2.0beta, I get a brief flash and then neither launches. If I use Apple Jar Launcher to launch the ij.jar file then both MM 1.4 and 2.0beta launch, and they show I”m running JVM 1.8. I tried redownloading fresh apps from the Micro-Manager web site, with no effect.

I have another laptop on which Micro-Manager 1.4 and 2.0 beta are installed in which (I think) I did the same Java install involving JVM 1.8. They launch flawlessly and are running JVM 1.6.0_35. This all suggests some environment variable or something is weird on the other laptop. However, the fact that ImageJ runs fine has me baffled.

Can anyone provide some advice? I mainly want to open Micro-Manager datasets on the laptops; we use Windows machines to control hardware.

Thanks in advance for your help!
Cheers,
Jeff
__________________________
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Zoology
Faculty Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]
web page: http://worms.zoology.wisc.edu

On Mar 18, 2016, at 2:08 PM, Mark Tsuchida <[hidden email]> wrote:

Hi Dave,

On Fri, Mar 18, 2016 at 7:05 AM, Knecht, David <[hidden email]> wrote:
Hi Austin- Are any of the Macs you have working running El Capitan?  My

One more thing which I should have mentioned earlier:
Java 6 (from Apple), which Micro-Manager currently uses, is not
supported on El Capitan.
We will work on migrating to Java 8 (from Oracle) (as ImageJ has done
recently) over the next months, but until then, we recommend sticking
to Yosemite or Mavericks.

(This is independent of any Arduino or FTDI issues.)

Best,
Mark

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Re: Strange inability to launch MM on Mac laptop with Oracle JVM and Apple JVM installed

jdhardin
Hi all,
Hoping someone might recognize something here, here’s an update on my failure to launch issues…

I deleted Apples Java 1.6 JDK, and Oracle 1.8 JRE and reinstalled everything. I still got the same error. The console, predictably, gives little info:
"Jun 11 08:55:35 Jeffs-MacBook-Pro com.apple.xpc.launchd[1] (org.micro-manager.MMImageJ.22608[1274]): Service exited with abnormal code: 1”

I’m guessing I have a corrupted file someplace, since ImageJ32 runs under Java 1.6 just fine using the Apple JDK, and Fiji runs under JRE 1.8, and this same setup runs great on another machine. I’m afraid I don’t know what might be amiss, however. 

Thanks in advance for any help!
Cheers,
Jeff
__________________________
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Zoology
Faculty Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]
web page: http://worms.zoology.wisc.edu

On Jun 7, 2017, at 10:49 PM, Jeff Hardin <[hidden email]> wrote:

Hi all,
I have a weird problem that I believe involves how Java is installed/setup on one of my Mac laptops running MacOS 10.12 (Sierra). I installed JRE 8 from Oracle for running Fiji. Fiji runs fine. I can also run ImageJ, and it tells me I’m running JVM 1.6.0_65 (the legacy Apple JVM). When I try to launch Micr-Manager 1.4 or 2.0beta, I get a brief flash and then neither launches. If I use Apple Jar Launcher to launch the ij.jar file then both MM 1.4 and 2.0beta launch, and they show I”m running JVM 1.8. I tried redownloading fresh apps from the Micro-Manager web site, with no effect.

I have another laptop on which Micro-Manager 1.4 and 2.0 beta are installed in which (I think) I did the same Java install involving JVM 1.8. They launch flawlessly and are running JVM 1.6.0_35. This all suggests some environment variable or something is weird on the other laptop. However, the fact that ImageJ runs fine has me baffled.

Can anyone provide some advice? I mainly want to open Micro-Manager datasets on the laptops; we use Windows machines to control hardware.

Thanks in advance for your help!
Cheers,
Jeff
__________________________
Jeff Hardin
Raymond E. Keller Professor and Chair
Department of Zoology
Faculty Director, Biology Core Curriculum
University of Wisconsin
1117 W. Johnson St.
Madison, WI 53706
voice: (608) 262-9634
fax: (608) 262-7319
email: [hidden email]
web page: http://worms.zoology.wisc.edu

On Mar 18, 2016, at 2:08 PM, Mark Tsuchida <[hidden email]> wrote:

Hi Dave,

On Fri, Mar 18, 2016 at 7:05 AM, Knecht, David <[hidden email]> wrote:
Hi Austin- Are any of the Macs you have working running El Capitan?  My

One more thing which I should have mentioned earlier:
Java 6 (from Apple), which Micro-Manager currently uses, is not
supported on El Capitan.
We will work on migrating to Java 8 (from Oracle) (as ImageJ has done
recently) over the next months, but until then, we recommend sticking
to Yosemite or Mavericks.

(This is independent of any Arduino or FTDI issues.)

Best,
Mark

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