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Image Pipeline

The Micro-Manager image pipeline is designed to allow programmers to provide code to analyze images as they are acquired.

To take advantage of this, you will need to write a class (in a Java Micro-Manager plugin or Beanshell script) that overrides the “analyze” method in the org.micromanager.api.TaggedImageAnalyzer abstract class.

The analyze method takes a TaggedImage as it arrives from acquisition. Each TaggedImage consists of raw pixels (either an array of bytes or shorts, depending on the pixel bit depth) and a JSON Object of Metadata.

In a plugin or script you can provide your class derived from TaggedImageAnalyzer to the acquisition engine:


It will then analyze the images as soon as they are available, before sending them to be saved and displayed.