Z-stack Depth Color Code

ImageJ/FIJI plugin to colorcode Z-stacks/hyperstacks (8-,16-,32 bit). Allows to uses available LUTs + invert them.

The plugin creates an output as Composite or RGB stack. So there is conversion to 8-bit, depending on the current Brightness/Contrast settings.

NB: After installation plugin appears in Plugins->Stacks->Z-stack Depth Colorcode menu.

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.

Generated colorcoded stacks can be visualized by different 3D renders (3D Viewer or 3Dscript plugin).

Example: EB comets (by Boris Shneyer), grayscale before:

and coded with Thermal LUT, after:

How to install plugin

To install plugin in FIJI:

• add https://sites.imagej.net/Ekatrukha/ to the list of update sites, as follows
• go to Help -> Update and press "Manage update sites" button
• press "Add update site" button and put the following link there https://sites.imagej.net/Ekatrukha/

To install plugin manually in ImageJ:

• download and copy the latest version of jar plugin file to the plugins folder of FIJI/ImageJ
• plugin will appear in Plugins->Stacks->Z-stack Depth Colorcode menu

How to cite the plugin

1. You can cite it by providing a direct link to the code, pointing out the version, like this:

"visualization was made using ZstackDepthColorCode v.X.X.X plugin for FIJI (https://github.com/UU-cellbiology/ZstackDepthColorCode)."

and specify the parameters used.

2. Alternatively, you can use Zenodo DOI for the link to the specific release:

Katrukha E. 2021, ZstackDepthColorCode plugin for ImageJ, vX.X.X, Zenodo, doi:10.5281/zenodo.17027115

Updates history

2021.02.17 (v.0.0.2) Added LUT image generation option. Fixed colors for inverted LUT and some window appearance.

2021.01.11 (v.0.0.1) First version.

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Developed in Cell Biology group of Utrecht University.
Email katpyxa @ gmail.com for any questions/comments/suggestions.