{"id":25895633,"url":"https://github.com/diamondlightsource/python-epuanalysis","last_synced_at":"2025-03-02T22:32:16.173Z","repository":{"id":44789997,"uuid":"328954830","full_name":"DiamondLightSource/python-epuanalysis","owner":"DiamondLightSource","description":null,"archived":false,"fork":false,"pushed_at":"2022-03-31T15:56:20.000Z","size":289865,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2023-03-23T01:26:20.102Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Shell","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/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}},"created_at":"2021-01-12T10:45:32.000Z","updated_at":"2022-01-25T09:00:42.000Z","dependencies_parsed_at":"2022-07-25T23:17:27.370Z","dependency_job_id":null,"html_url":"https://github.com/DiamondLightSource/python-epuanalysis","commit_stats":null,"previous_names":[],"tags_count":null,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-epuanalysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-epuanalysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-epuanalysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DiamondLightSource%2Fpython-epuanalysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DiamondLightSource","download_url":"https://codeload.github.com/DiamondLightSource/python-epuanalysis/tar.gz/refs/heads/main","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":"2025-03-02T22:32:15.520Z","updated_at":"2025-03-02T22:32:16.142Z","avatar_url":"https://github.com/DiamondLightSource.png","language":"Shell","readme":"# epubrowser\n\n## Quick start\n\nOpen the EPU browser\n```bash\n$ epu.browser.py\n```\n\nBrowse and select a star file from a Relion refinement\n\nBrowse and select an EPU directory at its top level\nThis should contain 'Images-disc', 'Metadata' and 'EpuSession.dm'\n\nEnter the Relion star file Micrograph column name\nNormally: '_rlnMicrographName'\n\nEnter the Data Suffix which is added due to image processing\nNormally: '_Fractions'\nOriginal image name: FoilHole_5871221_Data_5860229_5860231_20210808_185028\nAs found in the star file: FoilHole_5871221_Data_5860229_5860231_20210808_185028_Fractions.mrc\n\nRun the analysis by clicking Run\nNote the first time you run this epu.browser will call a shell script to find each microgrpah and associated hole and square image, this runs line by line and can take some time.\n\nClick Inpsect EPU Images\nThis will open a new window in whcih you can interactively explore what the micrograph, foil hole and square images looked like for data that was used in the star file versus data that ultimately was not used.\n\n## Demo\n\nWatch the video EPU\\_browser.mp4 for a quick visual representation of what you might expect to find. Note this is performed on a subset of data in a Relion star file for speed.\n\n## Description\n\nPython and shell scripts for analysing EPU directories based on a Relion format particle star file. The analysis will allow you to visualise which micrographs were ultimately utilised in Relion processing and further to inspect what the foilhole and grid square looked like from which useful particles were identified. If particle coordinates are present in the star file then they can be shown on the micrograph for further understanding on trends in the data.\n\n## Motivation\n\nI would expect the develops of EPU are writing this functionality but it was necessary to write this code to troubleshoot a data set where 99% of the particles were being thrown away, without an obvious reason.\n\nThis framework can find and display square images that led to productive 3D reconstruction in SPA and as such holds the potential to be able to guide SPA set up on new targets, based on the output of real time SPA analyses.\n\n## FAQ\n\nPlease watch the short movie 'EPU\\_browser.mp4' to familiarise yourself with the functionality of this software.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdiamondlightsource%2Fpython-epuanalysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdiamondlightsource%2Fpython-epuanalysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdiamondlightsource%2Fpython-epuanalysis/lists"}