FrameCombiner

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.

Usage

• 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.

Features

• 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.

Screenshot

Authors

FrameCombiner was written by Hadrien Mary.

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