New ImageJ plugin for Z-stack (or hyperstack) color-coding

Hello everybody,

I’ve written simple plugin to colorcode Z-stacks (or hyperstacks, Z+T, (8-,16-,32 bit)).

It allows to use all available LUTs + invert them. The plugin creates output as Composite or RGB stack.
It is loosely based on Temporal-Color Code macro (but does not create Z-projection) and it is rewritten version of Z_Code_Stack function from FIJI Cookbook.
I hope you find it useful.

Any feedback/comments are welcome.



This is the real shit! Thank you!! Works much better than temporal LUT and you can leave you z-slices as Z in the properties :smiley:

Q: how could I make a LUT next to the image which shows me the corresponding Z depth in µm, taken from the image voxel values?

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Hello Sarah,

I’ve added this colorbar option to a new version of plugin (0.0.2).
It will generate a new image (with 256 colors or only with number of z-slices), see options.

I didn’t format this colorbar plot, since usually everybody want to choose specific font, or do it later in some other program.
Also, I didn’t add Z-depth in um, since sometimes voxel depth in stacks is wrong, so it is up to user to do it, making sure what is going on. Do you think it is ok? Or you prefer to have it (maybe in frames)? Let me know.

Hope it helps.

You can find new version on github or just update FIJI.