Latest release of Micro-manager 2.0 gamma problem

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Latest release of Micro-manager 2.0 gamma problem

Knecht, David
I downloaded the latest Mac OS release (the last two- 2-9 and 2-10) and in both cases, they boot ImageJ but not Micro-manager.  Micro-manager does not even show up in the Plugins menu.  Dave

Dr. David Knecht
Professor, Department of Molecular and Cell Biology 
University of Connecticut
91 N. Eagleville Rd.
U-3125
Storrs, CT 06269-3125
860-486-2200



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Re: Latest release of Micro-manager 2.0 gamma problem

Nico Stuurman-2

On 2/11/2020 1:11 PM, Knecht, David wrote:
> I downloaded the latest Mac OS release (the last two- 2-9 and 2-10)
> and in both cases, they boot ImageJ but not Micro-manager.
>  Micro-manager does not even show up in the Plugins menu.  Dave

MacOS makes it very difficult for applications like ImageJ and
Micro-Manager to operate.  Did you see a menu entry like "Why are
plugins missing" in the ImageJ plugin menu?  If so, follow its instructions.

Another possible explanation is that you do not have Java 8 installed
(MM 2.0-gamma needs Java 8, whereas ImageJ will still work with Java 6).

There are some more instructions here:
https://micro-manager.org/wiki/Micro-Manager_Installation_Notes

Additions to that documentation are highly appreciated.


Best,


  Nico





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Re: Latest release of Micro-manager 2.0 gamma problem

Knecht, David
Hi Nico- See below

Dr. David Knecht
Professor, Department of Molecular and Cell Biology 
University of Connecticut
91 N. Eagleville Rd.
U-3125
Storrs, CT 06269-3125
860-486-2200

On Feb 11, 2020, at 6:20 PM, Stuurman, Nico <[hidden email]> wrote:


On 2/11/2020 1:11 PM, Knecht, David wrote:
I downloaded the latest Mac OS release (the last two- 2-9 and 2-10)
and in both cases, they boot ImageJ but not Micro-manager.
 Micro-manager does not even show up in the Plugins menu.  Dave

MacOS makes it very difficult for applications like ImageJ and
Micro-Manager to operate.  Did you see a menu entry like "Why are
plugins missing" in the ImageJ plugin menu?  If so, follow its instructions.
Nothing like that

Another possible explanation is that you do not have Java 8 installed
(MM 2.0-gamma needs Java 8, whereas ImageJ will still work with Java 6).
Was running Java 1.8.0 already.  Updated to latest version 8 and same issue.

There are some more instructions here:
<a href="https://nam10.safelinks.protection.outlook.com/?url=https://micro-manager.org/wiki/Micro-Manager_Installation_Notes&amp;amp;data=02|01|david.knecht@uconn.edu|674cf73828ef48ac64ab08d7af491c4a|17f1a87e2a254eaab9df9d439034b080|0|0|637170600854002586&amp;amp;sdata=gs/zxHc6k4LxJRe5e0oenY8CFlb7ogYhxY5/iqj8Grg=&amp;amp;reserved=0" class="">https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicro-manager.org%2Fwiki%2FMicro-Manager_Installation_Notes&amp;data=02%7C01%7Cdavid.knecht%40uconn.edu%7C674cf73828ef48ac64ab08d7af491c4a%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637170600854002586&amp;sdata=gs%2FzxHc6k4LxJRe5e0oenY8CFlb7ogYhxY5%2Fiqj8Grg%3D&amp;reserved=0
Tried copying to desktop and back and no difference.
Any other ideas?

Also, given someone’s comments on the confusions of MacOS, I should note that I switched from Mac OS to Windows this year and I could spend the next hour venting about my frustrations with getting MM to work there.  Still having COM ports changing and losing contact with the Arduino boards at random times.  
Also, we could not get the pixel size calibration to work for a long time with the MM1.4 we are currently running (the cameras require that version).  We could not enter the objectives in the hardware config.  The hardware config wizard did not appear to have a demo objective turret option in the hardware config list.  I only found it by switching from “by vendor” to “by type” and it was in an obscurely named folder there.  I never did find it in the “by vendor” list.  Perhaps I missed it, and maybe it is fixed in the latest version (which is why I was trying to download and run it) but if not,  I suggest moving all the demo items to a folder or the utilities folder.

Additions to that documentation are highly appreciated.


Best,


 Nico





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Re: Latest release of Micro-manager 2.0 gamma problem

Knecht, David
In reply to this post by Nico Stuurman-2
Hi Nico- Was going to play around with this some more.  What plugin file does Micro-manager use for the startup.  I am wondering if I can tell it to run that plugin from the plugins menu and see if that works.  Dave
Dr. David Knecht
Professor, Department of Molecular and Cell Biology 
University of Connecticut
91 N. Eagleville Rd.
U-3125
Storrs, CT 06269-3125
860-486-2200

On Feb 11, 2020, at 6:20 PM, Stuurman, Nico <[hidden email]> wrote:


On 2/11/2020 1:11 PM, Knecht, David wrote:
I downloaded the latest Mac OS release (the last two- 2-9 and 2-10)
and in both cases, they boot ImageJ but not Micro-manager.
 Micro-manager does not even show up in the Plugins menu.  Dave

MacOS makes it very difficult for applications like ImageJ and
Micro-Manager to operate.  Did you see a menu entry like "Why are
plugins missing" in the ImageJ plugin menu?  If so, follow its instructions.

Another possible explanation is that you do not have Java 8 installed
(MM 2.0-gamma needs Java 8, whereas ImageJ will still work with Java 6).

There are some more instructions here:
https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmicro-manager.org%2Fwiki%2FMicro-Manager_Installation_Notes&amp;data=02%7C01%7Cdavid.knecht%40uconn.edu%7C674cf73828ef48ac64ab08d7af491c4a%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C637170600854002586&amp;sdata=gs%2FzxHc6k4LxJRe5e0oenY8CFlb7ogYhxY5%2Fiqj8Grg%3D&amp;reserved=0

Additions to that documentation are highly appreciated.


Best,


 Nico





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