Live image treatment during acquisition

[thomas...@gmail.com]

Hello,

I guess this is a question for the micromanager people in the icy team.

Is it possible to call another plugin to treat images during the acquisition and save only the processed image? My case of interest would be similar to doing a max projection of a bright field stack (eg 24 or 32 planes) and saving only this single plane picture (although the transformation is more complex than a max projection).

Thank you in advance for your help. Regards,

Thomas Julou

[Stephane]

Hello,

I would say yes, it is possible to call any plugin and process your image freshly acquired. Still beware that doing acquisition can consume a bit of time on your computer so be sure that processing your image at same time don't introduce any lag in your acquisition (it should be ok as soon you have 2 cores on your computer). Of course it's free to you to handle the way you are saving the result image but anything is possible ;)

- Stephane

[Thomas Julou]

Thank you Stephane for your answer.

Glad to know it’s doable. Maybe I should rephrase a bit my question now: does icy make that easier than MM itself, or is it going to be the same than writing it for MM embedded in ImageJ for instance?

Also, is there any documentation related to MM in Icy? Or could you give me hints on how to start? (do I need to write another plugin? what kind of API functions are to be used?)

-- Thomas

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[Stephane]

Hi Thomas,

Icy provides some methods to make the image acquisition easier and return image in the appropriate format for Icy but there is currently any documentation to use it.
You have to look in the sources and in the javadoc from the original Micro-Manager plugin for Icy.
You can extends MicroscopePlugin or even MicroscopePluginAcquisition so your plugin will automatically load the micro manager engine at starting.

You can retrieve the Micro Manager core by doing :

MicroscopeCore core = MicroscopeCore.getCore();

And you have some classes utilities as ImageGetter for easier acquisition or StageMover to control XYZ position of the microscope.