Depth color code time series to make a movie!

Lorna_Young · 2017-04-14 01:35:34 UTC

Hi! I know how to color code my time series, but I’d like to depth color code my movie (the color being the depth, Z section). Is there a plug in to do this?

etarena · 2017-04-17 14:28:36 UTC

Hi @Lorna_Young

Take a look at this Depth Coding info… perhaps that can help you?

It’s Image > Hyperstacks > Temporal-Color Code that should do the trick.

eta

Lorna_Young · 2017-04-17 14:41:20 UTC

Thank you. I’ve used that, but it doesn’t give me a color coded time series… just the max projection of the time series, if that makes sense?

etarena · 2017-04-17 14:46:41 UTC

Hi @Lorna_Young

Ok. You are right. So … a little ‘hack’ you could try is to first Image > Hyperstacks > Re-Order Hyperstack - switching the frame and time-series. Then run the Temporal-Color Code.

Does that work?!

eta

Lorna_Young · 2017-04-17 15:22:58 UTC

Thanks… It didn’t work, but I tried making each Z a different color and then max projecting that as a time series… the problem with that is I am restricted to the colours that are preset (red/green/cyan etc?), and have to make my own “color scale bar” ??

emartini · 2017-04-19 08:43:16 UTC

Dear @Lorna_Young,
I don’t know if I have got fully your request but you could also try this one:

github.com

fiji/cookbook/blob/master/src/main/java/sc/fiji/cookbook/Z_Code_Stack.java

package sc.fiji.cookbook;

import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.gui.ImageWindow;
import ij.measure.Calibration;
import ij.plugin.PlugIn;
import ij.process.ColorProcessor;
import ij.process.ImageProcessor;

public class Z_Code_Stack implements PlugIn {

	ImageStack depthCoded;
	ImageProcessor ipc3;

	@Override
	public void run(final String arg) {
		final ImagePlus imp1 = WindowManager.getCurrentImage();

This file has been truncated. show original

I think you can also download it with the fiji cookbook update site or just dowload
it and put it in the plugins folder.

Emanuele Martini