Process multi-channel time-lapse data

This notebook demonstrates how image data can be processed that has multiple channels and time points.

Source

Let’s start by cleaaning up and opening an example dataset.

For cleaning up and loading the image, we use ImageJ-functions:

// clean up first
run("Close All");
run("Clear Results");

// open a the Mitosis example image
open("http://imagej.nih.gov/ij/images/Spindly-GFP.zip");

We now initialize the GPU and push the image as explained in the basics of clij tutorial.

run("CLIJ2 Macro Extensions", "cl_device=");
Ext.CLIJ2_clear();

Processing multiple channels

Pushing an image to GPU means in this context, that only the currently selected channel and time point are pushed.

// push current Z-stack image to GPU memory
input = getTitle();
Stack.setChannel(1);
Ext.CLIJ2_pushCurrentZStack(input);

We can then process the channel, e.g. by projecting it in Z:

Ext.CLIJ2_maximumZProjection(input, max_projection_c1);
Ext.CLIJ2_pull(max_projection_c1);
run("Red");

Afterwards, we can do the same with the other channel:

selectWindow(input);
Stack.setChannel(2);
Ext.CLIJ2_pushCurrentZStack(input);
Ext.CLIJ2_maximumZProjection(input, max_projection_c2);
Ext.CLIJ2_pull(max_projection_c2);
run("Green");

Channels can then be merged using ImageJs functionality

run("Merge Channels...", "c1=" + max_projection_c1 + " c2=" + max_projection_c2 + " create");

Processing time-lapse data

We can apply the same procedure to the whole time-lapse using a for-loop:

selectWindow(input);
// find out how many frames the time-lapse has
getDimensions(_, _, _, _, frames);

// loop over time points
for (t = 0; t < frames; t += 5) {
	// move forward in time in the dataset
	selectWindow(input);
	Stack.setFrame(t + 1); // ImageJ's frame-counter is 1-based
	
	// process channel 1
	Stack.setChannel(1);
	Ext.CLIJ2_pushCurrentZStack(input);
	Ext.CLIJ2_maximumZProjection(input, max_projection_c1);
	Ext.CLIJ2_pull(max_projection_c1);
	run("Red");
	
	// process channel 2
	selectWindow(input);
	Stack.setChannel(2);
	Ext.CLIJ2_pushCurrentZStack(input);
	Ext.CLIJ2_maximumZProjection(input, max_projection_c2);
	Ext.CLIJ2_pull(max_projection_c2);
	run("Green");

	// merge channels
	run("Merge Channels...", "c1=" + max_projection_c1 + " c2=" + max_projection_c2 + " create");
}

Depending on how large data is, you may not want to show all results on screen. Instead, consider saving results of a 3D stack:

Ext.CLIJ2_saveAsTIF(max_projection_c2, "max_projection_c2_f" + t + ".tif");

Clean up by the end

Ext.CLIJ2_clear();