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