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 pligin).
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 plugin
- plugin will appear in Plugins->Stacks->Z-stack Depth Colorcode menu
2021.01.11 First version.
Developed in Cell Biology group of Utrecht University.
Email katpyxa @ gmail.com for any questions/comments/suggestions.