{"id":13717280,"url":"https://github.com/UU-cellbiology/ZstackDepthColorCode","last_synced_at":"2025-05-07T07:30:55.586Z","repository":{"id":54692054,"uuid":"328708769","full_name":"UU-cellbiology/ZstackDepthColorCode","owner":"UU-cellbiology","description":"Z-stack Depth Colorcode ImageJ FIJI plugin","archived":false,"fork":false,"pushed_at":"2021-02-17T16:47:11.000Z","size":58,"stargazers_count":21,"open_issues_count":0,"forks_count":7,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-08-23T19:23:12.777Z","etag":null,"topics":["colorcode","fiji","fiji-plugin","imagej","imagej-plugin","microscopy","utrecht-university"],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/UU-cellbiology.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-01-11T15:31:04.000Z","updated_at":"2024-04-03T04:03:12.000Z","dependencies_parsed_at":"2022-08-14T00:10:37.429Z","dependency_job_id":null,"html_url":"https://github.com/UU-cellbiology/ZstackDepthColorCode","commit_stats":null,"previous_names":["ekatrukha/zstackdepthcolorcode"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UU-cellbiology%2FZstackDepthColorCode","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UU-cellbiology%2FZstackDepthColorCode/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UU-cellbiology%2FZstackDepthColorCode/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/UU-cellbiology%2FZstackDepthColorCode/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/UU-cellbiology","download_url":"https://codeload.github.com/UU-cellbiology/ZstackDepthColorCode/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224573437,"owners_count":17333804,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["colorcode","fiji","fiji-plugin","imagej","imagej-plugin","microscopy","utrecht-university"],"created_at":"2024-08-03T00:01:20.226Z","updated_at":"2024-11-14T05:31:20.244Z","avatar_url":"https://github.com/UU-cellbiology.png","language":"Java","funding_links":[],"categories":["Other"],"sub_categories":[],"readme":"# Z-stack Depth Color Code\n\n[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. \n\nThe plugin creates an output as Composite or RGB stack. So there is conversion to 8-bit, depending on the current Brightness/Contrast settings.\n\n**NB:** After installation plugin appears in *Plugins-\u003eStacks-\u003eZ-stack Depth Colorcode* menu.\n\nIt 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).\n\nGenerated 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).\n\nExample: EB comets (by Boris Shneyer), grayscale before: \n\n\n![EB BW](http://katpyxa.info/software/ZstackDepthColorCode/EB_colored_BW.gif \"EB stack BW\")\n\n\nand coded with Thermal LUT, after:\n\n\n![EB color](http://katpyxa.info/software/ZstackDepthColorCode/EB_colored_thermal.gif \"EB stack color\")\n\n\n\n## How to install plugin\n\nTo install plugin in FIJI:\n\n* add https://sites.imagej.net/Ekatrukha/ to the list of update sites, as follows\n* go to Help -\u003e Update and press \"Manage update sites\" button\n* press \"Add update site\" button and put the following link there https://sites.imagej.net/Ekatrukha/\n\nTo install plugin manually in ImageJ:\n\n* download and copy the [latest version of plugin](https://github.com/ekatrukha/ZstackDepthColorCode/raw/main/target/ZstackDepthColorCode_-0.0.2.jar) \n* plugin will appear in _Plugins-\u003eStacks-\u003eZ-stack Depth Colorcode_ menu\n\n## Updates history\n2021.02.17 (v.0.0.2) Added LUT image generation option. Fixed colors for inverted LUT and some window appearance. \n \n2021.01.11 (v.0.0.1) First version. \n\n---\nDeveloped in [Cell Biology group](http://cellbiology.science.uu.nl/) of Utrecht University.  \nEmail katpyxa @ gmail.com for any questions/comments/suggestions.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FUU-cellbiology%2FZstackDepthColorCode","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FUU-cellbiology%2FZstackDepthColorCode","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FUU-cellbiology%2FZstackDepthColorCode/lists"}