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THIS PLUGIN IS NOW INTEGRATED TO MICRO-MANAGER. SEE https://micro-manager.org/wiki/FrameProcessor FOR ANYMORE DETAILS.


FrameProcessor

A Micro-Manager plugin that can process stack images in time. The processing can be applied in real-time (live mode) or during an acquisition (MDA).

This plugin has been inspired from the excellent FrameAverager plugin from OpenPolScope available on github at https://github.com/LC-PolScope/Micro-Manager-Addons.

The motivation to create this plugin was to make it compatible with Micro-Manager 2 and also add more processing operations.

Install

  • Download the JAR file at https://github.com/hadim/FrameProcessor/releases.
  • Copy it to YOUR_MICRO_MANAGER_FOLDER/mmplugins/.
  • Launch Micromanager.
  • Execute the plugin with Plugin On-The-Fly Image Processing Frame Processor.
  • Launch a live or MDA acquisition.
  • The acquisition window should display the processed images (mean image of the last 10 images by default).

Please report any issue to https://github.com/hadim/FrameProcessor/issues.

Features

  • This plugin can perform several classic operations during live or MDA such as mean, sum, max and min on a certain number of frames defined by the user.
  • Images are processed for each combinations of Z, Channel and Stage Position.
  • User can choose a set of channels to be ignored by the processor.

Screenshot of the Frame Processor plugin

Develop

  • Import the project into Netbeans/Eclipse (Ant project).
  • Add the appropriate MM JAR files to the properties of the project (follow theses instructions).
  • Hack it !
  • Launch Micromanager directly from Eclipse/Netbeans by running Debug.

Authors

FrameProcessor has been created by Hadrien Mary.

This work started in 2016 at the Gary Brouhard laboratory at the University of McGill.

License

GPLv3. See LICENSE

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Live frame processing during acquisition (Micro-Manager plugin)

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