Hyperspectral imaging in Multi-Dimensional Acquisition

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Hyperspectral imaging in Multi-Dimensional Acquisition

nanthony
I would like to use the multi-dimensional acquisition engine to take
hyperspectral "data cubes" rather than just a single image at each frame,
slice, time, channel, etc.

This means that rather than passing a single image from the acquisition
engine to the processor stack I would pass ~100 images each image is taken
at a different wavelength.

I have looked into the documentation here:
https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming
https://micro-manager.org/wiki/Writing_image_processors_for_Micro-Manager

and I have tested one of the example "runnables"

Is it possible to due this just using a custom acquisition runnable and
custom data processor or will I need to dig deeper in order to pass data
cubes rather than single images?

Thanks,
  Nick



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Re: Hyperspectral imaging in Multi-Dimensional Acquisition

julou
Hi Nick,

I'm a strong advocate of using runnables rather than rewriting a script /
GUI for MDA with minor customisations… What is not clear to me in your case
is what would be the dimensions of your "cube" at each acquisition.

Obviously the challenge will be data storage. If you can compress your cube
to 1 plane, then it should be fairly straightforward. Otherwise, you will
have to handle the storage by yourself anyway (the only added value of a
runnable that I can think of in this case would be the GUI to specify the
acquisition parameters).

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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Re: Hyperspectral imaging in Multi-Dimensional Acquisition

nanthony
julou wrote

> I'm a strong advocate of using runnables rather than rewriting a script /
> GUI for MDA with minor customisations… What is not clear to me in your
> case
> is what would be the dimensions of your "cube" at each acquisition.
>
> Obviously the challenge will be data storage. If you can compress your
> cube
> to 1 plane, then it should be fairly straightforward. Otherwise, you will
> have to handle the storage by yourself anyway (the only added value of a
> runnable that I can think of in this case would be the GUI to specify the
> acquisition parameters).
>
> Best,
> Thomas

Hi Thomas,

Each acquisition would be 3 dimensional (x,y,wavelength). I'm really hoping
that this can be achieved with runnables since the existing MDA gui is
already so nice to use.

I can't be sure but based on the diagram here:
https://micro-manager.org/wiki/Multi-Dimensional_Acquisition_Programming
It looks like you can only pass Tagged Images from the acquisition engine.

If I can get each acquisition to capture and pass ~100 Tagged Images instead
of just one then I could write a data processor to save the images into a
single data file. I'm hoping that someone can point me in the write
direction on how to do this though, I haven't been able to find many
acquisition runnable examples.

Thanks,
  Nick




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Re: Hyperspectral imaging in Multi-Dimensional Acquisition

julou
Sorry to be dense on this one but I still dont get it fully :-/

Do you want to acquire time (100 frames) x pos x channels and repeat n times
at fixed interval?
in this case, you would be better of starting consecutive MDAs from a
script…

It'd help if you could describe more precisely what you want to achieve.
Best,

Thomas



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Re: Hyperspectral imaging in Multi-Dimensional Acquisition

nanthony
julou wrote

> Sorry to be dense on this one but I still dont get it fully :-/
>
> Do you want to acquire time (100 frames) x pos x channels and repeat n
> times
> at fixed interval?
> in this case, you would be better of starting consecutive MDAs from a
> script…
>
> It'd help if you could describe more precisely what you want to achieve.
> Best,
>
> Thomas

Hi Thomas,

Sorry I haven't explained it clearly. I think I may have found an example of
how to do this in the "Frame Averager" plugin:
https://openpolscope.org/pages/MMPlugin_Frame_Averager.htm

Basically, every time that micromanager would normally just acquire a single
image, I want to replace that with a routine that snaps a series of images
and adjusts a spectral filter between each one so that each image is at a
different wavelength.

I'm going to try modifying the frame averaging plugin to fit my application.
I'll post an update if I make progress.

--Nick



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