Script

Micro-Manager Z stack acquisition

Stephane Dallongeville
Publication ID: ICY-T6D4J7
Short Description Documentation Articles on this Review this Dependencies Changelog

Short Description

This java script show how to perform a small Z-Stack acquisition trough Micro-Manager. WARNING: You need to start Micro-Manager for Icy plugin before executing the script.

Versions

  • Version 1 • Released on: 2017-08-16 15:48:14
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    Description:

    initial version

    importClass(Packages.icy.sequence.Sequence)
importClass(Packages.plugins.tprovoost.Microscopy.MicroManager.MicroManager)
importClass(Packages.plugins.tprovoost.Microscopy.MicroManager.tools.StageMover)

z = 0
 // create the result sequence
sequence = new Sequence()

 // move to position (5, 5, 5)
 StageMover.moveXYAbsolute(5, 5)
StageMover.moveZAbsolute(5)

 // acquire 1 image
 image = MicroManager.snapImage()
 // set it in resulting sequence at position 0
 sequence.setImage(0, z++, image)
 // shift microscope Z position by 10
 StageMover.moveZRelative(10)

 // acquire 1 image
 image = MicroManager.snapImage()
 // set it in resulting sequence at position 0
 sequence.setImage(0, z++, image)
 // shift microscope Z position by 10
 StageMover.moveZRelative(10)

  // acquire last image
 image = MicroManager.snapImage()
 // set it in resulting sequence at position 0
 sequence.setImage(0, z, image)

 // show the sequence in Icy
gui.addSequence(sequence)

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