{"id":18964118,"url":"https://github.com/janeliascicomp/colormipsearch","last_synced_at":"2026-04-02T19:30:20.957Z","repository":{"id":38084988,"uuid":"98349943","full_name":"JaneliaSciComp/colormipsearch","owner":"JaneliaSciComp","description":"Distributed Color Depth MIP Search","archived":false,"fork":false,"pushed_at":"2024-05-22T17:59:47.000Z","size":4179,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":8,"default_branch":"main","last_synced_at":"2024-05-22T21:31:35.858Z","etag":null,"topics":["neuron","neuroscience","search-algorithm"],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","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":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-07-25T21:05:18.000Z","updated_at":"2024-05-28T22:10:34.272Z","dependencies_parsed_at":"2024-03-22T20:32:51.587Z","dependency_job_id":"b0315b48-afbd-4003-875e-a16730d83803","html_url":"https://github.com/JaneliaSciComp/colormipsearch","commit_stats":null,"previous_names":[],"tags_count":25,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fcolormipsearch","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fcolormipsearch/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fcolormipsearch/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JaneliaSciComp%2Fcolormipsearch/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JaneliaSciComp","download_url":"https://codeload.github.com/JaneliaSciComp/colormipsearch/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239959947,"owners_count":19725221,"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":["neuron","neuroscience","search-algorithm"],"created_at":"2024-11-08T14:22:52.987Z","updated_at":"2026-04-02T19:30:20.909Z","avatar_url":"https://github.com/JaneliaSciComp.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Color Depth MIP Search Tools\n\n[![DOI](https://zenodo.org/badge/98349943.svg)](https://zenodo.org/badge/latestdoi/98349943)\n[![Java CI with Maven](https://github.com/JaneliaSciComp/colormipsearch/actions/workflows/maven.yml/badge.svg)](https://github.com/JaneliaSciComp/colormipsearch/actions/workflows/maven.yml)\n\nThis is a set of tools for precomputing color depth searches using the same algorithms as [ColorMIP_Mask_Search](https://github.com/JaneliaSciComp/ColorMIP_Mask_Search) Fiji plugin. \nThe precomputed results are persisted in a Mongo database and can be exported to JSON in order to upload them to AWS for NeuronBridge. \n \n## Build\n\n```bash\n./mvnw install\n```\nor just\n```bash\n./mvnw package\n```\n\n### Build the docker container\n```bash\ndocker buildx build -t ghcr.io/janeliascicomp/colormipsearch-tools:\u003cVERSION\u003e . --push\n```\n\n\n## Release the artifacts to Janelia Nexus Repo:\n\nBefore running the release script make sure you have an server entry\nfor the janelia-repo in your default maven settings.xml, typically located\nat ~/.m2/settings.xml\n\n```xml\n\u003csettings xmlns=\"http://maven.apache.org/SETTINGS/1.0.0\"\n          xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n          xsi:schemaLocation=\"http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd\"\u003e\n\n  \u003cservers\u003e\n    \u003cserver\u003e\n      \u003cid\u003ejanelia-releases\u003c/id\u003e\n      \u003cusername\u003eyourusername\u003c/username\u003e\n      \u003cpassword\u003eyourpassword\u003c/password\u003e\n    \u003c/server\u003e\n  \u003c/servers\u003e\n\n\u003c/settings\u003e\n```\n\nIf you don't want the password in clear in settings.xml, maven offers a mechanism to encrypt it\nusing:\n```bash\nmvn --encrypt-master-password \u003cpassword\u003e\n```\nto create a master password and then use\n```bash\nmvn --encrypt-password \u003cpassword\u003e\n```\nwhich you can enter in place of your password. Check [maven documentation](https://maven.apache.org/guides/mini/guide-encryption.html)\nhow you can do this.\n\nTo release the artifacts simply run:\n\n```./release.sh \u003cversion\u003e```\n\nThis command will also tag the repository with the `\u003cversion\u003e`.\n\n\n## Run\n\n\n### Calculating the gradient score for a set of existing results\n```\njava -jar target/colormipsearch-2.8.0-jar-with-dependencies.jar \\\n    gradientScore \\\n    -rf local/testData/results/qq.json \\\n    -gp local/testData/flylight_40xMCFO_gradient_20px.zip \\\n    -rd local/testData/results.withscore\n```\n\n## Pre-computed color depth search data\n\nA more detailed description can be found in [PrecomputedData.md](PrecomputedData.md).\n\n### Generate EM - LM color depth search results\n\nThe steps to generate the precomputed color depth search results are the\nfollowing:\n\n* Run `createColorDepthSearchDataInput` to import color depth MIPs from JACS into the Mongo database \n* Run `colorDepthSearch` to calculate color depth matches between a mask library and a target library \n* Run `gradientScores` to calculate gradient based score for the matches from a selected mask library \n* If matching scores still need to be normalized after calculating gradient scores, run the `normalizeGradientScores` command\n* If Patch Per Pixel matches are available, those can be imported using `importPPPResults`\n* Run `exportData` command to export the results in order to be uploaded to NeuronBridge\n\nThese steps are typically handled by a set a [Nextflow](https://www.nextflow.io/) workflows from [Precompute github repository](https://github.com/JaneliaSciComp/neuronbridge-precompute)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Fcolormipsearch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjaneliascicomp%2Fcolormipsearch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjaneliascicomp%2Fcolormipsearch/lists"}