Nikon Perfect Focus crash -- stuck Z stacks

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Nikon Perfect Focus crash -- stuck Z stacks

Maxime Woringer-2

Hi µManager community!

I would like to submit a problem we are encountering regularly, for which we've been stuck for days now. We perform multi-position, 4D acquisitions (Z-stacks at several timepoints). We usually program ~10 positions and acquire ~20 Z planes in two channels. The total acquisition time is typically 2-8 hours.

To avoid axial drift, we activate the Nikon Perfect Focus system. It works well most of the time, and finds the focus at the beginning of almost every single Z-stacks. However, sometimes, it will not find the focus and will output the following error message in the logs:

2019-11-08T18:57:34.867275 tid1256 [IFO,dev:iXon888] PrepareSnap();
2019-11-08T18:57:35.602317 tid1256 [IFO,Core] Default autofocus set to PFS
2019-11-08T18:57:35.619318 tid1256 [ERR,Core] Error occurred in device PFS: Error in device "PFS": Unknown error in the device (1)
2019-11-08T18:57:35.619318 tid1256 [IFO,App] Autofocus failed.
                                   [       ] java.lang.RuntimeException: org.micromanager.internal.utils.MMException: Error in device "PFS": Unknown error in the device (1) in Thread[AcquisitionEngine2010 Thread (Clojure),6,main]
                                   [       ]   at clojure.lang.Util.runtimeException(Util.java:165)
                                   [       ]   at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:97)
                                   [       ]   at clojure.lang.Reflector.invokeNoArgInstanceMember(Reflector.java:316)
                                   [       ]   at org.micromanager.acq_engine$run_autofocus.invoke(acq_engine.clj:271)
                                   [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1268.invoke(acq_engine.clj:746)
                                   [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:773)
                                   [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:787)
                                   [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:976)
                                   [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                   [       ]   at java.lang.Thread.run(Unknown Source)
                                   [       ] Caused by: org.micromanager.internal.utils.MMException: Error in device "PFS": Unknown error in the device (1)
                                   [       ]   at org.micromanager.internal.utils.CoreAutofocus.fullFocus(CoreAutofocus.java:33)
                                   [       ]   at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
                                   [       ]   at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
                                   [       ]   at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
                                   [       ]   at java.lang.reflect.Method.invoke(Unknown Source)
                                   [       ]   at clojure.lang.Reflector.invokeMatchingMethod(Reflector.java:92)
                                   [       ]   at clojure.lang.Reflector.invokeNoArgInstanceMember(Reflector.java:316)
                                   [       ]   at org.micromanager.acq_engine$run_autofocus.invoke(acq_engine.clj:271)
                                   [       ]   at org.micromanager.acq_engine$make_event_fns$fn__1268.invoke(acq_engine.clj:746)
                                   [       ]   at org.micromanager.acq_engine$execute.invoke(acq_engine.clj:773)
                                   [       ]   at org.micromanager.acq_engine$run_acquisition.invoke(acq_engine.clj:787)
                                   [       ]   at org.micromanager.acq_engine$run$fn__1412.invoke(acq_engine.clj:976)
                                   [       ]   at clojure.lang.AFn.run(AFn.java:24)
                                   [       ]   at java.lang.Thread.run(Unknown Source)
2019-11-08T18:57:35.863332 tid1256 [IFO,dev:iXon888] [Snap Image] called...

In our case, we can afford having the PFS not finding the focus once in a while, but a major issue is that after this bug, the stage always stop scanning in z, and all the subsequent images are acquired with the stage stuck at the same Z position.

Is this an expected or at least documented behaviour? Would you have any advice about how to circumvent it? How could we recover Z-scanning after this issue?

Many thanks!

Maxime Woringer

Antoine Coulon lab, UMR1664

Institut Curie, 26 rue d'Ulm, Paris

FRANCE



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