Overlay Channels

This simple command can be used to combine several individual videos into one. It creates a combined video in which each of the original videos is categorized with a different value for ‘Channel’ (C). The output is a combined video in which the channel can be selected by using the slider at the bottom. Make sure to adjust the contrast for each channel separately to obtain a proper visualization.

Input

• Add To Me - Select the video to which the other video should be added.
• Transform Me - Select the video to be added to the other video.
• Keep originals - Tick box in case the original video documents should be saved (preffered option).

Affine2D Transformation Matrix: coordinates found with the Affine2D calculation (see tutorial)

• m00
• m01
• m02
• m10
• m11

• m12

• Thread count - Determines how much computing power of your computer will be devoted to this calculation. A higher thread count decreases computing time.

Output

• A single video with individual channels representing the input videos.

How to run this Command from a groovy script

#@ ImagePlus image
#@ ImageJ ij

import de.mpg.biochem.mars.ImageProcessing.*

//Make an instance of the Command you want to run...
final OverlayChannelsCommand overlayChannels = new OverlayChannelsCommand();

//Set the parameters required for the command
overlayChannels.setAddToMe(img1.tif);
overlayChannels.setKeepOriginals(True);
overlayChannels.setTransformMe(img2.tif);
overlayChannels.setM00(1);
overlayChannels.setM01(0);
overlayChannels.setM02(0);
overlayChannels.setM10(0);
overlayChannels.setM20(1);
overlayChannels.setM12(0);

//Run the Command
overlayChannels.run();