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A Micro-Manager 2 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 was inspired by 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. This plugin is not compatible with earlier versions of Micro-Manager.


  • Launch Micro-manager.
  • Execute the plugin with Plugin ▶ On-The-Fly Image Processing ▶ Frame Processor.
  • Launch a live or MDA acquisition.
  • Set the number of frames you want to process and the algorithm you want to apply on the stack such as mean, max, min, or sum.
  • The acquisition window displays the processed images (mean image of the last 10 images by default).

Please report any issue to https://github.com/micro-manager/micro-manager/issues.


  • This plugin can perform several classic operations during live or MDA such as mean, sum, max and min on a user-specified number of frames.
  • 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.




FrameCombiner was written by Hadrien Mary.

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