Multidimensonal Acquisition not working?

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

Multidimensonal Acquisition not working?

Micro-Manager mailing list

Hi everyone,

I'm running into trouble acquiring MultiD images with micromanager. Everything seems to be working -- the stage is moving, shutters are activating and filters are changing -- but I don't get an image viewer and it doesn't save any images. I don't have any problems with saving or viewing images with the Snap, Live, or Album buttons; it's just the MultiD Acquisition that's giving me trouble.


This is with a Nikon eclipse TI microscope, an Andor Zyla sCMOS camera, Micromanager 1.4.22 and ImageJ 1.52b on Windows 10.


Looking at the log file, I see a few errors during the acquisition process:

2018-05-25T16:10:24.075263 tid8340 [IFO,App] 
                                   [       ] org.json.JSONException: JSONObject["ChannelIndex"] not found. in Thread[tagged image sink thread,6,main]
                                   [       ]   at org.json.JSONObject.get(JSONObject.java:498)
                                   [       ]   at org.json.JSONObject.getInt(JSONObject.java:559)
                                   [       ]   at org.micromanager.utils.MDUtils.getChannelIndex(MDUtils.java:112)
                                   [       ]   at org.micromanager.utils.MDUtils.getLabel(MDUtils.java:408)
                                   [       ]   at org.micromanager.acquisition.TaggedImageStorageRamFast.putImage(TaggedImageStorageRamFast.java:96)
                                   [       ]   at org.micromanager.acquisition.MMImageCache.putImage(MMImageCache.java:198)
                                   [       ]   at org.micromanager.acquisition.DefaultTaggedImageSink$1.run(DefaultTaggedImageSink.java:49)
2018-05-25T16:10:24.080268 tid8340 [IFO,App] 
                                   [       ] java.lang.NullPointerException in Thread[tagged image sink thread,6,main]
                                   [       ]   at org.micromanager.utils.ImageLabelComparator.compare(ImageLabelComparator.java:52)
                                   [       ]   at org.micromanager.utils.ImageLabelComparator.compare(ImageLabelComparator.java:26)
                                   [       ]   at java.util.TreeMap.compare(TreeMap.java:1291)
                                   [       ]   at java.util.TreeMap.put(TreeMap.java:538)
                                   [       ]   at org.micromanager.acquisition.TaggedImageStorageRamFast.putImage(TaggedImageStorageRamFast.java:104)
                                   [       ]   at org.micromanager.acquisition.MMImageCache.putImage(MMImageCache.java:198)
                                   [       ]   at org.micromanager.acquisition.DefaultTaggedImageSink$1.run(DefaultTaggedImageSink.java:49)
2018-05-25T16:10:24.080268 tid8340 [IFO,App] 
                                   [       ] org.json.JSONException: JSONObject["FrameIndex"] not found. in Thread[tagged image sink thread,6,main]
                                   [       ]   at org.json.JSONObject.get(JSONObject.java:498)
                                   [       ]   at org.json.JSONObject.getInt(JSONObject.java:559)
                                   [       ]   at org.micromanager.utils.MDUtils.getFrameIndex(MDUtils.java:123)
                                   [       ]   at org.micromanager.acquisition.MMImageCache.putImage(MMImageCache.java:201)
                                   [       ]   at org.micromanager.acquisition.DefaultTaggedImageSink$1.run(DefaultTaggedImageSink.java:49)

Honestly not even sure where to start with this one so any advice would be appreciated.
Thanks,
Taylor 


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Multidimensonal Acquisition not working?

JonD
Administrator
Micro-Manager mailing list wrote
> I'm running into trouble acquiring MultiD images with micromanager.
> [snip]
> This is with a Nikon eclipse TI microscope, an Andor Zyla sCMOS camera,
> Micromanager 1.4.22 and ImageJ 1.52b on Windows 10.

The first thing to try is updating to a recent nightly build... 1.4.22 is
pretty old now and there have been lots of bugfixes and improvements.

-------------------------------------------
Jon Daniels
Applied Scientific Instrumentation
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
-------------------------------------------



--
Sent from: http://micro-manager.3463995.n2.nabble.com/

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general
Reply | Threaded
Open this post in threaded view
|

Re: Multidimensonal Acquisition not working?

Micro-Manager mailing list
That seems to have fixed it. I didn't realize our version of Micromanager was so old. Thanks Jon!

Taylor

-----Original Message-----
From: JonD <[hidden email]>
Sent: Friday, May 25, 2018 4:48 PM
To: [hidden email]
Subject: Re: [micro-manager-general] Multidimensonal Acquisition not working?

Micro-Manager mailing list wrote
> I'm running into trouble acquiring MultiD images with micromanager.
> [snip]
> This is with a Nikon eclipse TI microscope, an Andor Zyla sCMOS
> camera, Micromanager 1.4.22 and ImageJ 1.52b on Windows 10.

The first thing to try is updating to a recent nightly build... 1.4.22 is pretty old now and there have been lots of bugfixes and improvements.

-------------------------------------------
Jon Daniels
Applied Scientific Instrumentation
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
-------------------------------------------



--
Sent from: http://micro-manager.3463995.n2.nabble.com/

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general

------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
micro-manager-general mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/micro-manager-general