Quantcast

Zeiss Definite Focus does nothing in "apply" mode

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Zeiss Definite Focus does nothing in "apply" mode

Jim Valcourt
Hi all,

***Summary***
I am unable to use Definite Focus with multiple stage positions because nothing happens when Definite Focus is invoked in "apply" mode. This happens in both the beta (2.0.0-beta3 20170409) and a recent stable release (1.4.22).

***More details***
I'm experiencing a problem similar to ones described previously on this list (here and here), but I was unable to find a resolution in those threads. Briefly, I'm following the directions at https://micro-manager.org/wiki/ZeissCAN29. For each XY position, I set the definite focus position in "Measure" mode by clicking the autofocus button in the main window, then marking that position in the position list. (Each position ends up with a unique ZeissDefiniteFocusOffset and an XYStage position.) I then set "ZeissDefiniteFocus-Focus Method" to "Apply" and start the acquisition. The LCD screen on the Definite Focus box displays "Off" throughout the acquisition and the focus drifts, so I conclude that the Definite Focus is not running properly.

I know that micro-manager is able to talk to the Definite Focus module because it works perfectly if I attempt to take a timelapse of a single position using "Last Position" mode instead of "Apply" mode.

I have a log file (in debug mode) from a session in which this behavior occurs, if that's helpful.

Thanks very much for your help!

Best,
Jim

------------------------------------------------------------------------------
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
|  
Report Content as Inappropriate

Re: Zeiss Definite Focus does nothing in "apply" mode

PhilippeP
Hi Jim,

We are doing HCS using MM2 lists and Zeiss DF.
What we do is:
Set a 3 point plane covering the areas of interest;
Create our list of positions , the extrapolated z being calculated by MM
from the 3 point plane defined above;
Set DF focus manually ("Measure") on a random position, then switch DF
to "Last Position";
Start the acquisition.
As long as the 3 point plane z positions are within the DF searching
distance, everything works smoothly.
I have no idea what "Apply" is for.

Hope that helps...
Philippe


------------------------------------------------------------------------------
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
|  
Report Content as Inappropriate

Re: Zeiss Definite Focus does nothing in "apply" mode

Jun Liao
Hi Philippe,

Thank you for your reply.

I just found that change the trigger mode from internal trigger to software trigger allows me to use lower exposure time.

Best,
Jun

On Tue, Apr 11, 2017 at 9:33 AM, Philippe Pognonec <[hidden email]> wrote:
Hi Jim,

We are doing HCS using MM2 lists and Zeiss DF.
What we do is:
Set a 3 point plane covering the areas of interest;
Create our list of positions , the extrapolated z being calculated by MM
from the 3 point plane defined above;
Set DF focus manually ("Measure") on a random position, then switch DF
to "Last Position";
Start the acquisition.
As long as the 3 point plane z positions are within the DF searching
distance, everything works smoothly.
I have no idea what "Apply" is for.

Hope that helps...
Philippe


------------------------------------------------------------------------------
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
Reply | Threaded
Open this post in threaded view
|  
Report Content as Inappropriate

Re: Zeiss Definite Focus does nothing in "apply" mode

Jim Valcourt
In reply to this post by PhilippeP
Hi Philippe,

Thanks for your response. Unfortunately, my application requires imaging in slightly different planes in different wells; if I understand correctly what you're doing, I'm not sure that it will quite work without manually adding Z offsets to every position. I'll play around with it and see if I can get something to work.

Thanks,
Jim

On Tue, Apr 11, 2017 at 9:55 AM Philippe Pognonec <[hidden email]> wrote:
Hi Jim,

We are doing HCS using MM2 lists and Zeiss DF.
What we do is:
Set a 3 point plane covering the areas of interest;
Create our list of positions , the extrapolated z being calculated by MM
from the 3 point plane defined above;
Set DF focus manually ("Measure") on a random position, then switch DF
to "Last Position";
Start the acquisition.
As long as the 3 point plane z positions are within the DF searching
distance, everything works smoothly.
I have no idea what "Apply" is for.

Hope that helps...
Philippe


------------------------------------------------------------------------------
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
Loading...