{"id":25895432,"url":"https://github.com/diamondlightsource/python-icebreaker","last_synced_at":"2025-09-12T04:34:17.684Z","repository":{"id":45601409,"uuid":"382045527","full_name":"DiamondLightSource/python-icebreaker","owner":"DiamondLightSource","description":"Ice gradient estimation for cryoEM","archived":false,"fork":false,"pushed_at":"2024-10-11T09:49:30.000Z","size":105,"stargazers_count":9,"open_issues_count":5,"forks_count":6,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-02-17T23:17:39.593Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"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/DiamondLightSource.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":"2021-07-01T13:39:18.000Z","updated_at":"2024-08-29T02:45:37.000Z","dependencies_parsed_at":"2023-01-21T21:02:47.323Z","dependency_job_id":"0ea33330-6e94-4909-ac4b-46eadb3fa7de","html_url":"https://github.com/DiamondLightSource/python-icebreaker","commit_stats":null,"previous_names":[],"tags_count":11,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-icebreaker","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-icebreaker/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-icebreaker/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-icebreaker/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DiamondLightSource","download_url":"https://codeload.github.com/DiamondLightSource/python-icebreaker/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":241582515,"owners_count":19985845,"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":"2025-03-02T22:31:20.120Z","updated_at":"2025-03-02T22:31:42.022Z","avatar_url":"https://github.com/DiamondLightSource.png","language":"Python","readme":"# ICEBREAKER\n\nThe Icebreaker software for ice gradient estimation and removal on cryoEM micrographs.\n\nExternal job for calling IceBreaker grouping within Relion 3.1\nin_parts is input star file from relion picking job \nin_mics is previous grouping job directory\n \nRun in main Relion project directory\n\n## Running as a RELION External job\n\nIcebreaker provides a number of command line tools that wrap the core functionality in a way that is friendly for the RELION External job. These tools are:\n\n```\nib_job\nib_group\nib_5fig\n```\n\nIf Icebreaker is installed in your Python environment then these can be used directly as the executables for a RELION External job. \n\n## Processing the micrographs\n\nTo process the micrographs use the `ib_job` command line tool \n\nAs an input, it takes a .star file with a list of micrographs to process, e.g. micrographs_ctf.star\n\nIn the 'Params' tab, you have to add a label **mode** which can take values **group** (it will group areas with similar ice thickness) or **flatten** (it will improve contrasts locally trying to remove the ice gradient). \n\nIn the Running tab use the slider to select the number of threads. \n\nThe output from this job is a new set of micrographs.\n\n\n## Processing the particles\n\nThis is done using the `ib_group` command line tool. As 'Input micrographs' it takes micrographs 'grouped' with the previous script. As 'Input particles' any star file with particles from jobs like Extract particles, 2D classes, etc. As a result, additional parameter column (\\_ibIceGroup) with estimated ice thickness value for each particle will be added.\n\n\n## Using the job templates\n\nTo make it easier to get started running Icebreaker from Relion, you can use one of the template star files *ib\\_job\\_template\\_GROUP\\_MODE.star*, *ib\\_job\\_template\\_FLATTEN\\_MODE.star* or *ib\\_group\\_template.star*. To use a template:\n\n1. Copy one of the templates to your Relion project directory as *.gui\\_externaljob.py*\n2. Select the External job type\n3. Click Jobs -\u003e Load job settings\n4. Change the placeholder input names to select your input files\n5. Choose your running options and run the job as normal\n\n## Runnnig outside of RELION\n\nThere are a number of command line tools which can be used outside of the RELION context. These are:\n\n```\nib.micrographs_group \nib.micrographs_flatten \nib.particles_group\nib.five_fig \n```\n\nThe functionality of these tools correspond, respectively, to `ib_job` in **group** mode, `ib_job` in **flatten** mode, `ib_group` and `ib_5fig`. \nThe required command line options can be seen by using the `--help` flag.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdiamondlightsource%2Fpython-icebreaker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdiamondlightsource%2Fpython-icebreaker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdiamondlightsource%2Fpython-icebreaker/lists"}