{"id":22090429,"url":"https://github.com/ferreols/tipi4icy","last_synced_at":"2026-03-11T10:32:20.262Z","repository":{"id":22197098,"uuid":"25529468","full_name":"FerreolS/tipi4icy","owner":"FerreolS","description":"tipi4icy is a collection of Icy plugins based on TiPi","archived":false,"fork":false,"pushed_at":"2023-10-17T15:10:57.000Z","size":2309,"stargazers_count":11,"open_issues_count":0,"forks_count":2,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-07-24T23:15:46.390Z","etag":null,"topics":["blind-deconvolution","deconvolution","deconvolution-microscopy","icy-plugins","microscopy"],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/FerreolS.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,"zenodo":null}},"created_at":"2014-10-21T15:17:40.000Z","updated_at":"2024-07-22T17:49:23.000Z","dependencies_parsed_at":"2025-07-24T19:32:06.830Z","dependency_job_id":"33af7480-1f92-4ec0-be32-cda1592bbe98","html_url":"https://github.com/FerreolS/tipi4icy","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/FerreolS/tipi4icy","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FerreolS%2Ftipi4icy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FerreolS%2Ftipi4icy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FerreolS%2Ftipi4icy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FerreolS%2Ftipi4icy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/FerreolS","download_url":"https://codeload.github.com/FerreolS/tipi4icy/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/FerreolS%2Ftipi4icy/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30378084,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-11T06:09:32.197Z","status":"ssl_error","status_checked_at":"2026-03-11T06:09:17.086Z","response_time":84,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["blind-deconvolution","deconvolution","deconvolution-microscopy","icy-plugins","microscopy"],"created_at":"2024-12-01T02:16:25.179Z","updated_at":"2026-03-11T10:32:20.227Z","avatar_url":"https://github.com/FerreolS.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"tipi4icy\n========\n\nMaster: ![Travis build status](https://travis-ci.org/FerreolS/tipi4icy.svg?branch=master)  [![DOI](https://zenodo.org/badge/25529468.svg)](https://zenodo.org/badge/latestdoi/25529468)\n\n\ntipi4icy is a collection of classes to link  [Icy](http://icy.bioimageanalysis.org/)  and  [TiPi](https://github.com/emmt/TiPi), a Java *Toolkit for Inverse Problems and Imaging*. Along with [microTiPi](https://github.com/FerreolS/microTiPi) is mainly used to implements the DEconvolution MICroscopy Suite.\n\nDEconvolution MICroscopy Suite (DEMICS)\n========\n\nDEMICS is a collection of Icy plugins for deconvolution microscopy. It  provides user friendly and state of the art blind deconvolution methods for  fluorescence microscopy.\n\n**SimpleDEMIC**\n\nSimpleDEMIC is a simple non blind deconvolution plugin that uses total variation regularization. As it is non blind, it requires the knowledge of the PSF.\n\n**EpiDEMIC**\n\nEpiDEMIC stands for Epifluorescence DEconvolution MICroscopy. It is a blind deconvolution plugin for Epifluorescence / Widefield fluorescence microscopy. It requires only basic knowledge about the data (numerical aperture, wavelength, pixel size,...)\n\nAutomated batch processing\n========\n\n**Protocols**\n\nBoth plugins are compatible with Icy's protocols and can be easily added to any processing workflow.\n\n**DEMICS on server**\n\n\nDeconvolution is a memory and computation intensive task and it may not fit in end-users laptop. To process batches of large datasets, both plugins can be used without the Icy GUI on any server with [Docker](https://www.docker.com/). The docker images of [SimpleDEMIC](https://hub.docker.com/r/ferreol/simpledemic/) and [EpiDEMIC](https://hub.docker.com/r/ferreol/epidemic/) can be pulled from docker hub and executed using (for epidemic):\n```\ndocker run --rm -v FOLDER:/data -e NAME='DATAFILE'   -e XMS=MEMORY ferreol/epidemic'\n ```\n  where:\n  - `FOLDER` is the folder were the dataset is,\n  - `DATAFILE` is the name of the file and \n  - `MEMORY` is the memory size of the JVM (default: 10G). \n  \n All the parameters should be stored in an XML file `datafile-param.xml` in the same folder. This parameter file can be generated easily using the plugin in the Icy GUI. The result will be stored in the file `datafile-dec.tif`.\n\n\nDevelopers corner\n=======\n\n**Eclipse**\n\nThis project can be used in Eclipse, just copy/clone it into Eclipse workspace, then from Eclipse: \n\n```\nFile -\u003e import -\u003e Existing project in workspace and choose TiPi folder.\n```\n\nThen Eclipse should automatically accept it as a known project.\n\nTo add the needed libraries to TiPi Eclipse project, move all the jars into a folder. Then in eclipse:\n\n```\nRight clic on TiPi project in package explorer -\u003e Properties -\u003e Java Build Path -\u003e Libraries -\u003e Add External jar and select all Library jar\n```\n\n**Icy in Eclipse**\n\nThere is a plugin to launch quickly and easily Icy from eclipse [here](http://icy.bioimageanalysis.org/index.php?display=startDevWithIcy).\n\n\n## Javadoc\n\nThe javadoc is auto generated at each push and is [HERE](http://ferreols.github.io/tipi4icy)\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fferreols%2Ftipi4icy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fferreols%2Ftipi4icy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fferreols%2Ftipi4icy/lists"}