fluorescence exposure in situ control in MultiD acquisition

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fluorescence exposure in situ control in MultiD acquisition

nathalieqbb@gmail.com
Hi,

The MultiD acquisition of MM performs a set of tasks on all locations equally. We would like to be able to visit some specific locations from the locations list every frame for one mode(phase-contrast) and once every 10 frames for the other modes (fluorescence). This is needed in order to monitor in situ the physiology, bleaching etc.  of cells exposed to 10 times less fluorescence. 

Has anyone implemented a similar procedure? Can it be done from with MM or only by external control?
Thanks,
Nathalie

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Re: fluorescence exposure in situ control in MultiD acquisition

Nico Stuurman-2
Hi Nathalie,

> The MultiD acquisition of MM performs a set of tasks on all locations
> equally. We would like to be able to visit some specific locations
> from the locations list every frame for one mode(phase-contrast) and
> once every 10 frames for the other modes (fluorescence). This is
> needed in order to monitor in situ the physiology, bleaching etc.  of
> cells exposed to 10 times less fluorescence.
>
> Has anyone implemented a similar procedure? Can it be done from with
> MM or only by external control?

This can be done in Micro-Manager, but needs writing a script.

Best,

Nico



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Re: fluorescence exposure in situ control in MultiD acquisition

JonD
Administrator
In reply to this post by nathalieqbb@gmail.com
Hi Nathalie,


[hidden email] wrote
> The MultiD acquisition of MM performs a set of tasks on all locations
> equally. We would like to be able to visit some specific locations from
> the
> locations list every frame for one mode(phase-contrast) and once every 10
> frames for the other modes (fluorescence). This is needed in order to
> monitor in situ the physiology, bleaching etc.  of cells exposed to 10
> times less fluorescence.

To my knowledge this cannot be done directly from the MDA interface but
should be relatively straightforward if you write a Beanshell script.  You
could have 2 different position lists and switch between them.  I don't know
if there are "high-level" ways to use the MDA via a script, but certainly
you can replicate the behavior of the MDA with a more verbose script.  This
link has some information you may find useful:
https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming.

Jon

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Jon Daniels
Applied Scientific Instrumentation
29391 West Enid Rd, Eugene, OR 97402
Phone: (541) 461-8181 x118
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Re: fluorescence exposure in situ control in MultiD acquisition

StevenF
In reply to this post by nathalieqbb@gmail.com
Hello Natahlie,

I'm not sure this exact script has been implemented before, but if you want
to do "complexe" things like what you are suggesting you need to script
things. Micromanager has a few ways you can script things:
-C++
-Beanshell (java)
-Python
-Matlab

so if you are familiar with any of these programming languages it won't be
too difficult to achieve what you want to do!

this page in the wiki contains a lot of useful information for anything
programming to get you started and you should definitively check it out if
you haven't seen it before!
https://micro-manager.org/wiki/Micro-Manager_Programming%20Guide

this second link can give you an idea of the functions accessible from the
various wrappers!
https://valelab4.ucsf.edu/~MM/doc/MMCore/html/class_c_m_m_core.html

Hope this helped!
Cheers,
Steven




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Re: fluorescence exposure in situ control in MultiD acquisition

nathalieqbb@gmail.com
In reply to this post by Nico Stuurman-2
Thanks Nico, Jon and Steven for the feedback.. We hope to write a script with a proper GUI so that other people use it. In our experience, having an in-situ control for whether the fluorescent imaging affects the physiology of cells is a must.

On Wed, Jul 25, 2018 at 6:51 AM, Nico Stuurman <[hidden email]> wrote:
Hi Nathalie,

The MultiD acquisition of MM performs a set of tasks on all locations equally. We would like to be able to visit some specific locations from the locations list every frame for one mode(phase-contrast) and once every 10 frames for the other modes (fluorescence). This is needed in order to monitor in situ the physiology, bleaching etc.  of cells exposed to 10 times less fluorescence.

Has anyone implemented a similar procedure? Can it be done from with MM or only by external control?

This can be done in Micro-Manager, but needs writing a script.

Best,

Nico



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Re: fluorescence exposure in situ control in MultiD acquisition

JonD
Administrator
[hidden email] wrote
> We hope to write a script
> with a proper GUI so that other people use it. In our experience, having
> an
> in-situ control for whether the fluorescent imaging affects the physiology
> of cells is a must.

If you want a GUI then you need to write a (Java) plugin, which in its
simplest form is a Beanshell script turned into proper Java (Beanshell lets
you take some shortcuts) plus some boilerplate code so the main application
properly loads the plugin.  Note there are some differences in the
boilerplate for 2.0.

You'll find lots of examples if you look at the source code under "plugins"
plus a page in the wiki at
https://micro-manager.org/wiki/Writing_plugins_for_Micro-Manager.  Many use
GUIs created by the Netbeans GUI builder but I suggest using Miglayout
instead (you'll find examples of those too).

Jon



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Re: fluorescence exposure in situ control in MultiD acquisition

julou
In reply to this post by nathalieqbb@gmail.com
Hi Nathalie,

We achieve very similar task using "runnables" i.e. small script that you
can attach to the MDA before running it. Because writing GUI is really a
pain ;)
For instance this script allows to use custom channels and exposure time at
every position for a given channel:
https://github.com/vanNimwegenLab/MiM_NikonTi/blob/master/Scripts/scripts_1.4/multipos_multiexp.bsh

The main drawback in my opinion is that the metadata are the one
corresponding to the MDA settings (so we always store the runnable script
along the dataset). In your case, you could for instance modify it so that
fluorescence is replaced by phase contrast 9 frames out of 10th at given
positions.

Let me know if anything is unclear. Best,
Thomas


PS: I also wrote one for MM2 where one can monitor one extra position in a
given channel that is recorded in its dedicated dataset… We use it to
monitor microfluidic flow at critical position of our chips during MDA
experiments
https://github.com/vanNimwegenLab/MiM_NikonTi/blob/master/Scripts/MDAextraPos.bsh



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Re: fluorescence exposure in situ control in MultiD acquisition

nathalieqbb@gmail.com
Merci Thomas!

On Wed, Jul 25, 2018 at 3:19 PM, julou <[hidden email]> wrote:
Hi Nathalie,

We achieve very similar task using "runnables" i.e. small script that you
can attach to the MDA before running it. Because writing GUI is really a
pain ;)
For instance this script allows to use custom channels and exposure time at
every position for a given channel:
https://github.com/vanNimwegenLab/MiM_NikonTi/blob/master/Scripts/scripts_1.4/multipos_multiexp.bsh

The main drawback in my opinion is that the metadata are the one
corresponding to the MDA settings (so we always store the runnable script
along the dataset). In your case, you could for instance modify it so that
fluorescence is replaced by phase contrast 9 frames out of 10th at given
positions.

Let me know if anything is unclear. Best,
Thomas


PS: I also wrote one for MM2 where one can monitor one extra position in a
given channel that is recorded in its dedicated dataset… We use it to
monitor microfluidic flow at critical position of our chips during MDA
experiments
https://github.com/vanNimwegenLab/MiM_NikonTi/blob/master/Scripts/MDAextraPos.bsh



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