https://github.com/UU-cellbiology/ZstackDepthColorCode

Z-stack Depth Colorcode ImageJ FIJI plugin
https://github.com/UU-cellbiology/ZstackDepthColorCode

colorcode fiji fiji-plugin imagej imagej-plugin microscopy utrecht-university

Last synced: 2 months ago
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Z-stack Depth Colorcode ImageJ FIJI plugin

• Host: GitHub
• URL: https://github.com/UU-cellbiology/ZstackDepthColorCode
• Owner: UU-cellbiology
• License: gpl-3.0
• Created: 2021-01-11T15:31:04.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2021-02-17T16:47:11.000Z (almost 4 years ago)
• Last Synced: 2024-08-23T19:23:12.777Z (5 months ago)
• Topics: colorcode, fiji, fiji-plugin, imagej, imagej-plugin, microscopy, utrecht-university
• Language: Java
• Homepage:
• Size: 56.6 KB
• Stars: 21
• Watchers: 3
• Forks: 7
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

• awesome-biological-image-analysis - Z-stack Depth Color Code - ImageJ/Fiji plugin to colorcode Z-stacks/hyperstacks. (Other)

README

        
# Z-stack Depth Color Code

[ImageJ](https://imagej.nih.gov/ij/)/[FIJI](http://fiji.sc/) 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](https://imagej.net/Temporal-Color_Code) macro (but does not create Z-projection) and it is rewritten version of Z_Code_Stack function from [FIJI Cookbook](https://github.com/fiji/cookbook).

Generated colorcoded stacks can be visualized by different 3D renders ([3D Viewer](https://imagej.nih.gov/ij/plugins/3d-viewer/) or [3Dscript](https://bene51.github.io/3Dscript/) plugin).

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

![EB BW](http://katpyxa.info/software/ZstackDepthColorCode/EB_colored_BW.gif "EB stack BW")

and coded with Thermal LUT, after:

![EB color](http://katpyxa.info/software/ZstackDepthColorCode/EB_colored_thermal.gif "EB stack color")

## 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 plugin](https://github.com/ekatrukha/ZstackDepthColorCode/raw/main/target/ZstackDepthColorCode_-0.0.2.jar) 

* plugin will appear in _Plugins->Stacks->Z-stack Depth Colorcode_ menu

## 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](http://cellbiology.science.uu.nl/) of Utrecht University.  

Email katpyxa @ gmail.com for any questions/comments/suggestions.