{"id":18964005,"url":"https://github.com/JaneliaSciComp/ColorMIP_Mask_Search","last_synced_at":"2025-04-16T05:31:48.396Z","repository":{"id":82954056,"uuid":"122373444","full_name":"JaneliaSciComp/ColorMIP_Mask_Search","owner":"JaneliaSciComp","description":"ColorMIP_Mask_Search plugin for Fiji","archived":false,"fork":false,"pushed_at":"2023-11-08T20:36:21.000Z","size":55921,"stargazers_count":4,"open_issues_count":6,"forks_count":12,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-04-07T01:49:28.191Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"ImageJ Macro","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JaneliaSciComp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-02-21T18:06:33.000Z","updated_at":"2023-01-17T18:24:23.000Z","dependencies_parsed_at":"2023-10-21T11:56:44.171Z","dependency_job_id":null,"html_url":"https://github.com/JaneliaSciComp/ColorMIP_Mask_Search","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FColorMIP_Mask_Search","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FColorMIP_Mask_Search/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FColorMIP_Mask_Search/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2FColorMIP_Mask_Search/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/ColorMIP_Mask_Search/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223697482,"owners_count":17187811,"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":[],"created_at":"2024-11-08T14:22:37.829Z","updated_at":"2025-04-16T05:31:48.380Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"ImageJ Macro","readme":"# Color-MIP Mask Search [![LinkToJanelia](../images/jrc_logo_180x40.png)](https://www.janelia.org)\nThe algorithm created by Hideo Otsuna.  \nFIJI plugins created by Hideo Otsuna and Takashi Kawase.  \nThis manual is modified based on the instruction developed by Justine X Chia (UCSF).  \n\n***For EM MIP search please use this EM search [plugin](https://github.com/JaneliaSciComp/EM_MIP_search)\n\n***Downloading the Color Depth MIPs are [here](https://open.quiltdata.com/b/janelia-flylight-color-depth/tree/Color_Depth_MIPs_For_Download/)\n\n***The unisex brain template for the CDM resolution can be found [here](https://open.quiltdata.com/b/janelia-flylight-color-depth/tree/alignment_templates/JRC2018_UNISEX_20x_HR.nrrd)\n\n## Before starting\n 1. Launch and update FIJI.\n 2. Drag and drop `ColorMIP_Mask_Search.jar` on FIJI then quit (the plugin installation).  \n (you can get the .jar file from [here](https://github.com/JaneliaSciComp/ColorMIP_Mask_Search/blob/master/Color_MIP_Mask_Search.jar)) \n\n## Startup\nDrag the folder (containing Gal4 color depth MIPs) into fiji, use virtual stack option. \n\n## Create mask of neuron of interest\n 1. Duplicate a single slice that containing the neuron from the Gal4 image (⌘⇧ D).\n 2. Trace area of interest on a duplicated slice (use polygon tool and try to be as accurate as possible).\n 3. Edit \u003e Clear Outside.\n\n## Search stacks with mask\nPlugins \u003e ColorMIP Mask search  \n![ScreenShot0](../images/scr0.png)\n### considerations/ tips:\n - Show log // -\u003e show NaN for log may be useful for a first pass, just to keep track of all slices.\n - Threshold for data: 30-60 is a good place to start for searching Gal4.\n - If background is too high, increase threshold (max value is 255).  \n - If too many hits, can try increasing % of Positive PX Threshold 5-10%.\n - The search can stop by pushing escape.\n\n## Synchronize windows\nTo make sure the position between the mask (the neuron) and hits (Gal4 lines), synchronizing the wingdows is useful function.\n 1. Analyze \u003e Tools \u003e Synchronize Windows.  \n 2. Select the two windows to synchronize.  \n\u003c!-- dummy --\u003e\n![ScreenShot1](../images/scr1.png)  \n\u003cbr /\u003e\nA red x (cross-hair) will now appear at the same position in both images.\n![ScreenShot2](../images/scr3.jpg)\n\n## Create a list of candidate lines\n`realtime_Result_ctrl_click_substack.ijm` is useful for quickly making a list of lines and the substack while scrolling through the stack of potential hits. \n 1. Open `realtime_Result_ctrl_click_substack.ijm`.\n 2. Click window with colorMIP search result stacks.\n 3. Run macro (only accepts one open window). Then Result window will be open.\n 4. Shift + click on the result stack will add the image name into the Result table.\n 5. ctrl + click will create a substack with the Result table from the result stack.\n \n ## Demo movie\n [![Demomovie](../images/MIPsearchDemo.jpg)](https://youtu.be/JVZs19yvEqY)\n","funding_links":[],"categories":["Fiji Plugins"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FJaneliaSciComp%2FColorMIP_Mask_Search","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FJaneliaSciComp%2FColorMIP_Mask_Search","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FJaneliaSciComp%2FColorMIP_Mask_Search/lists"}