Runnables in bean shell, finding current frame, slice, colour index

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cr4
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Runnables in bean shell, finding current frame, slice, colour index

cr4
Hi all,

I have written a beanshell script which attaches a runnable to run every frame and collect 9 images then montage them. Currently I'm saving this seperately however I rather use the snap and add function to integrate it properly with micromanager. For this the runnable needs to know what the current slice frame colour etc index is. How is this done? Is there a workaround?

Best

Craig

Following the recent revision to the International System of Units (SI), we will be looking at one of the seven SI base units each month. This month it’s the kelvin.


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Re: Runnables in bean shell, finding current frame, slice, colour index

julou
Dear Craig,

As far as I know, you have to take care of incrementing counters
manually… this is indeed cumbersome!
see e.g.
https://github.com/vanNimwegenLab/MiM_NikonTi/blob/master/Scripts/scripts_1.4/multipos_multiexp.bsh

I'd love to hear from MM devs in case there has been any progress on this
front. Best,
Thomas

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Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University
of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 207 16 21
|  https://julou.github.io/




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Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21

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Thomas Julou  |  Computational & Systems Biology  |  Biozentrum – University of Basel  |  Klingelbergstrasse 50/70 CH-4056 Basel  |  +41 (0)61 267 16 21
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Re: Runnables in bean shell, finding current frame, slice, colour index

nanthony
Unfortunately I think that Thomas is correct. There are a few things about
the acquisition manager that would be great to have added including access
to the current coordinates.

I took a look at the acquisition manager code once to see if I could work on
it a bit, but unfortunately it is written in Clojure and I had a hard time
understanding the flow of the code.

If there's anyone around that is less Clojure illiterate than me I'm sure
many people would appreciate your help in cleaning up the acquisition
manager code.

--Nick



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