{"EMPIAR-10812":{"imagesets":[{"segmentations":[],"name":"2D class averages for training neural network in region_class_ranker","directory":"data","category":"class averages","header_format":"MRCS","data_format":"MRCS","num_images_or_tilt_series":18051,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Each subdirectory with 12 random characters contains a single 2D classification run, with an image file run_class.mrcs that contains the actual 2D class averages, the files run_model.star, run_data.star, run_sampling.star and run_optimiser.star with the corresponding metadata from RELION's 2D classification run (see RELION documentation for details), a file job_score.txt that contains the manually assigned job score for that 2D classification run, a backup_selection.star file that contains the different categories of assigned classes, which are converted to individual class scores in the class_ranker program (see function ClassRanker::getClassScoreFromJobScore inside src/class_ranker.cpp), and a file features_normalized.star that contains the features calculated by the region_class_ranker program.\n\nOne can visualise the images for each class, e.g. in directory cahg4Zo4Goos, with the following command: \n\nrelion_display --sort rlnClassDistribution --reverse --class --i cahg4Zo4Goos/run_optimiser.star --fn_imgs cahg4Zo4Goos/backup_selection.star \n\nClasses shown in red (1 in backup_selection.star) are the best according to the manually assigned class labels in backup_selection.star; magenta (5) are second-best; green (2) third-best; and blue (3) or cyan (4) fourth-best. Yellow classes (6) or non-coloured classes (0) are the worst (score=0).\n\nThe normalised_features.star file was calculated in RELION-4.0, running the following command in csh from the main directory:\n\nforeach opt (*/run_optimiser.star)\n set dir=`echo ${opt} | awk -F\"/\" '{print $1}'`\n echo $dir\n relion_class_ranker --train --do_granularity_features --extract_subimages --subimage_boxsize 64 --nr_subimages 25 --opt ${dir}/run_optimiser.star --select ${dir}/backup_selection.star --fn_score ${dir}/job_score.txt --o ${dir} --write_normalized_features\nend","image_width":null,"image_height":null}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Training data set for automated 2D class selection","principal_investigator":[{"author_orcid":"0000-0002-0462-6540","middle_name":"H.W.","organization":"MRC Laboratory of Molecular Biology","street":"Francis Crick Avenue","town_or_city":"Cambridge","state_or_province":"Cambridgeshire","post_or_zip":"CB2 0QH","telephone":null,"fax":null,"first_name":"Sjors","last_name":"Scheres","email":"scheres [at] mrc-lmb.cam.ac.uk","country":"United Kingdom","entry":"EMPIAR-10812"}],"status":"REL","deposition_date":"2021-09-20","release_date":"2021-10-01","obsolete_date":null,"update_date":"2022-02-28","corresponding_author":{"author":{"author_orcid":"0000-0002-0462-6540","middle_name":"H.W.","organization":"MRC laboratory of molecular biology","street":"Francis Crick Avenue","town_or_city":"Cambridge","state_or_province":"Cambridgeshire","post_or_zip":"CB2 0QH","first_name":"Sjors","last_name":"Scheres","country":"United Kingdom"}},"authors":[{"author":{"name":"Kimanius D","author_orcid":"0000-0002-2662-6373"}},{"author":{"name":"Dong L","author_orcid":null}},{"author":{"name":"Sharov G","author_orcid":"0000-0002-6930-4999"}},{"author":{"name":"Nakane T","author_orcid":"0000-0003-2697-2767"}},{"author":{"name":"Scheres SHW","author_orcid":"0000-0002-0462-6540"}}],"cross_references":[],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Kimanius D","author_orcid":"0000-0002-2662-6373"},{"name":"Dong L","author_orcid":null},{"name":"Sharov G","author_orcid":"0000-0002-6930-4999"},{"name":"Nakane T","author_orcid":"0000-0003-2697-2767"},{"name":"Scheres SHW","author_orcid":"0000-0002-0462-6540"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"New tools for automated cryo-EM single-particle analysis in RELION-4.0","volume":"478","country":"","first_page":"4169","last_page":"4185","year":"2021","language":"English","doi":"10.1042/bcj20210708","pubmedid":"34783343","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"The Biochemical journal","journal_abbreviation":"Biochem J","issue":"24","preprint":false},{"authors":[{"name":"Kimanius D","author_orcid":"0000-0002-2662-6373"},{"name":"Dong L","author_orcid":null},{"name":"Sharov G","author_orcid":"0000-0002-6930-4999"},{"name":"Nakane T","author_orcid":"0000-0003-2697-2767"},{"name":"Scheres SHW","author_orcid":"0000-0002-0462-6540"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"New tools for automated cryo-EM single-particle analysis in RELION-4.0","volume":null,"country":"","first_page":null,"last_page":null,"year":null,"language":null,"doi":"10.1101/2021.09.30.462538","pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"20.7 GB","experiment_type":"Exception","scale":null,"entry_doi":"10.6019/EMPIAR-10812"}}