Taking Images at Multiple Positions & Accessing Location of Images Later

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Taking Images at Multiple Positions & Accessing Location of Images Later

kianago
Hi,

   Has anyone taken multiple images at multiple positions and been able to access these images and its correlating location on the stage afterwards using Micro-Manager? 

   Essentially, I want to be able to set up the program, leave as Micro-manager takes images at multiple positions, and come back later to access these images and their corresponding location so I may go back to that location. 

   I am familiar with Multi-D Acquisition, but it is limiting in its functions of what I want it to specifically do (for instance, its always does time then slice, but I want slice then time; or we want 10 images from one position).

   Thanks in advance!

Much Appreciated,
Kiana 

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Re: Taking Images at Multiple Positions & Accessing Location of Images Later

AustinBlanco
If the position list is the same (e.g. a generated grid spacing from a start point) this may be something to do in a script. 

Austin Blanco
Advanced Research Consulting Corporation
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On Jul 23, 2018, at 5:28 PM, Kiana Go <[hidden email]> wrote:

Hi,

   Has anyone taken multiple images at multiple positions and been able to access these images and its correlating location on the stage afterwards using Micro-Manager? 

   Essentially, I want to be able to set up the program, leave as Micro-manager takes images at multiple positions, and come back later to access these images and their corresponding location so I may go back to that location. 

   I am familiar with Multi-D Acquisition, but it is limiting in its functions of what I want it to specifically do (for instance, its always does time then slice, but I want slice then time; or we want 10 images from one position).

   Thanks in advance!

Much Appreciated,
Kiana 

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Re: Taking Images at Multiple Positions & Accessing Location of Images Later

JonD
Administrator
In reply to this post by kianago
Hi Kiana,


kianago wrote
>    Has anyone taken multiple images at multiple positions and been able to
> access these images and its correlating location on the stage afterwards
> using Micro-Manager?
>
>    Essentially, I want to be able to set up the program, leave as
> Micro-manager takes images at multiple positions, and come back later to
> access these images and their corresponding location so I may go back to
> that location.

The positions are stored in per-image metadata under the keys "XPositionUm"
"YPositonUm" and "ZPositionUm".  It seems that the label of the position in
the Position List is also stored as "PositionName".  You can view these
properties on the metadata tab of the main window in 1.4.x, and I know
accessing it is easy in 2.0 too.

You can write a short script that will read positions from the metadata and
then move to that position again.  You can find an example script for
accessing metadata in this thread:
http://micro-manager.3463995.n2.nabble.com/accessing-Micro-manager-metadata-from-Beanshell-script-td7583558.html
(incidentally in response to a question I asked).  There are API calls in
both MMCore and the GUI/ScriptInterface for moving stages.

Jon



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