{"id":31065793,"url":"https://github.com/henriqueslab/nanoj-core","last_synced_at":"2025-09-15T16:57:24.366Z","repository":{"id":79421555,"uuid":"114775425","full_name":"HenriquesLab/NanoJ-Core","owner":"HenriquesLab","description":"Core functionality of NanoJ","archived":false,"fork":false,"pushed_at":"2024-03-22T17:38:11.000Z","size":6981,"stargazers_count":14,"open_issues_count":4,"forks_count":3,"subscribers_count":6,"default_branch":"master","last_synced_at":"2024-03-22T18:56:35.762Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/HenriquesLab.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":"2017-12-19T14:34:28.000Z","updated_at":"2024-03-22T17:34:41.000Z","dependencies_parsed_at":"2023-04-18T03:18:13.427Z","dependency_job_id":null,"html_url":"https://github.com/HenriquesLab/NanoJ-Core","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/HenriquesLab/NanoJ-Core","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FNanoJ-Core","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FNanoJ-Core/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FNanoJ-Core/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FNanoJ-Core/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HenriquesLab","download_url":"https://codeload.github.com/HenriquesLab/NanoJ-Core/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HenriquesLab%2FNanoJ-Core/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":275289704,"owners_count":25438494,"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","status":"online","status_checked_at":"2025-09-15T02:00:09.272Z","response_time":75,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":"2025-09-15T16:57:22.565Z","updated_at":"2025-09-15T16:57:24.354Z","avatar_url":"https://github.com/HenriquesLab.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NanoJ-Core - ImageJ Plugin #\n\n**NanoJ-Core** is an open-source ImageJ and Fiji plugin that provide the base high-performance computing engine that other NanoJ plugins need to run: [NanoJ-SRRF](https://github.com/HenriquesLab/NanoJ-SRRF), [NanoJ-SQUIRREL](https://bitbucket.org/rhenriqueslab/nanoj-squirrel/wiki/Home), [NanoJ-VirusMapper](https://bitbucket.org/rhenriqueslab/nanoj-virusmapper/wiki/Home) and [NanoJ-Fluidics](https://github.com/HenriquesLab/NanoJ-Fluidics).\n\n**NanoJ-Core** also provides image analysis methods for **Drift Correction** and **Channel Alignment**. Check out our [**bioRxiv preprint**](https://www.biorxiv.org/content/early/2018/10/01/432674) for a full description of the NanoJ features, and the [**User Manual**](https://doi.org/10.6084/m9.figshare.7296767.v1) for an in-depth guide on how to use them.\n\n[![NanoJ Pre-Print](https://pbs.twimg.com/media/Doez3mnXsAA_RxN.jpg \"NanoJ Pre-Print\")](https://www.biorxiv.org/content/early/2018/10/01/432674)\n\n\n## Install NanoJ-Core ##\n\n\nNanoJ-Core is available as an ImageJ/Fiji (from here on ImageJ) plugin. The installation proceeds thought the ImageJ updater: open ImageJ and select “Update” in the “Help”-menu.  \n\n![alt text](https://user-images.githubusercontent.com/34708291/46486258-45659400-c7f5-11e8-9b31-acb07da686d4.png)  \nRegardless if other updates are available or not, press the “Manage update sites”-button on the Updater window (indicated in red).  \n![alt text](https://user-images.githubusercontent.com/34708291/46486262-47c7ee00-c7f5-11e8-9045-5fe2e10246c4.png)  \nThen, scroll down the list of update sites, click on the tick-box next to “NanoJ-Core\" and click the “Close” button (in red).  \n![alt text](https://user-images.githubusercontent.com/34708291/46486269-4c8ca200-c7f5-11e8-9585-0d64bd22276a.png)  \nFinally, click “Apply changes” (in red) in the Updater window, close and then restart ImageJ.  \n![alt text](https://user-images.githubusercontent.com/34708291/46486272-4e566580-c7f5-11e8-8304-c16d093bf883.png)  \nYou can find NanoJ-Core under the “Plugins” menu.  \n![alt text](https://user-images.githubusercontent.com/34708291/46486274-4f879280-c7f5-11e8-8947-d69e94d90004.png)\n\n## Image Registration methods in Python ##\n\nExciting news! Drift alignment and Channel registration are now accessible in Python through the [NanoPyx](https://github.com/HenriquesLab/NanoPyx) package. This integration brings the power and versatility of NanoJ-Core to Python users, opening up new possibilities for analysis and integration within Python-based workflows.\n\nNanoPyx seamlessly integrates NanoJ-Core's image registration capabilities into Python environments. With NanoPyx, users can now leverage NanoJ's high-performance analytical approach within their Python scripts, pipelines, and interactive sessions. Through NanoPyx, NanoJ-Core image registration methods are also available as \"codeless\" Jupyter Notebooks and a [napari plugin](https://github.com/HenriquesLab/napari-NanoPyx).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenriqueslab%2Fnanoj-core","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhenriqueslab%2Fnanoj-core","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenriqueslab%2Fnanoj-core/lists"}