Depth color code time series to make a movie!


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?


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 :slight_smile:


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?


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?!



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” ??


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

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