{"EMPIAR-12195":{"imagesets":[{"segmentations":[{"file":"data/annotation","description":"Each folder contains a mod file and an mrc file. The mrc file contains each label encoded as an integer. 0: outside of the segmentation region. 1: background of the segmentation region. 2: active zone. 10-maximum : synaptic vesicles.","original_files":null,"original_format":"MRC","entry":null}],"name":"Tilt series of rat synaptosomes","directory":"data/raw","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":9,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"SIGNED 16 BIT INTEGER","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"","image_width":"2048","image_height":"2048"},{"segmentations":[],"name":"tomograms of rat synaptosomes","directory":"data/tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":9,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"SIGNED 16 BIT INTEGER","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"One tomogram has another voxel type (spray_ctrl_6) : bytes - signed in file","image_width":null,"image_height":null},{"segmentations":[{"file":"data/annotation","description":"Each folder contains a mod file and an mrc file. The mod file contains the segmentation region, active zone, and synaptic vesicles. Everything has been segmented by hand.","original_files":null,"original_format":"MOD","entry":null}],"name":"tomograms that have been binned, trimmed, and denoised with non linear anisotropic diffusion","directory":"data/processed","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":9,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"SIGNED 16 BIT INTEGER","pixel_width":null,"pixel_height":null,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"","image_width":null,"image_height":null}],"workflow_file":null,"grant_references":[{"funding_body":"Swiss National Science Foundation","code":"179520","country":"Switzerland"}],"version_history":[],"title":"Training Set for CryoVesNet - Cryo-electron tomograms of rat synaptosomes and synaptic vesicle segmentation","principal_investigator":[{"author_orcid":"0000-0001-7725-5579","middle_name":null,"organization":"Institute of Anatomy, University of Bern","street":"Baltzerstrasse 2","town_or_city":"Bern","state_or_province":"BE","post_or_zip":"3012","telephone":null,"fax":null,"first_name":"Benoit","last_name":"Zuber","email":"benoit.zuber [at] unibe.ch","country":"Switzerland","entry":"EMPIAR-12195"}],"status":"REL","deposition_date":"2024-07-22","release_date":"2024-11-19","obsolete_date":null,"update_date":"2024-11-19","corresponding_author":{"author":{"author_orcid":"0000-0001-9480-5915","middle_name":null,"organization":"Institute of Anatomy, University of Bern","street":"Baltzerstrasse 2","town_or_city":"Bern","state_or_province":"BE","post_or_zip":"3012","first_name":"Amin","last_name":"Khosrozadeh","country":"Switzerland"}},"authors":[{"author":{"name":"Khosrozadeh A","author_orcid":"0000-0001-9480-5915"}},{"author":{"name":"Seeger R","author_orcid":"0000-0003-4461-3741"}},{"author":{"name":"Witz G","author_orcid":"0000-0003-1562-4265"}},{"author":{"name":"Radecke J","author_orcid":"0000-0002-5815-5537"}},{"author":{"name":"Sørensen JB","author_orcid":"0000-0001-5465-3769"}},{"author":{"name":"Zuber B","author_orcid":"0000-0001-7725-5579"}}],"cross_references":["EMD-18728"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Khosrozadeh A","author_orcid":"0000-0001-9480-5915"},{"name":"Seeger R","author_orcid":"0000-0003-4461-3741"},{"name":"Witz G","author_orcid":"0000-0003-1562-4265"},{"name":"Radecke J","author_orcid":"0000-0002-5815-5537"},{"name":"Sørensen JB","author_orcid":"0000-0001-5465-3769"},{"name":"Zuber B","author_orcid":"0000-0001-7725-5579"}],"editors":[],"published":false,"j_or_nj_citation":true,"title":"CryoVesNet: A Dedicated Framework for Synaptic Vesicle Segmentation in Cryo Electron Tomograms","volume":null,"country":"","first_page":null,"last_page":null,"year":"2024","language":null,"doi":null,"pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true},{"authors":[{"name":"Khosrozadeh A","author_orcid":"0000-0001-9480-5915"},{"name":"Seeger R","author_orcid":"0000-0003-4461-3741"},{"name":"Witz G","author_orcid":"0000-0003-1562-4265"},{"name":"Radecke J","author_orcid":"0000-0002-5815-5537"},{"name":"Sørensen JB","author_orcid":"0000-0001-5465-3769"},{"name":"Zuber B","author_orcid":"0000-0001-7725-5579"}],"editors":[{"name":" ","author_orcid":null}],"published":true,"j_or_nj_citation":true,"title":"CryoVesNet: A dedicated framework for synaptic vesicle segmentation in cryo-electron tomograms","volume":"224","country":"","first_page":null,"last_page":null,"year":"2024","language":"English","doi":"10.1083/jcb.202402169","pubmedid":"39446113","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"The Journal of cell biology","journal_abbreviation":"J Cell Biol","issue":"1","preprint":false}],"dataset_size":"8.9 GB","experiment_type":"EMDB","scale":"cell","entry_doi":"10.6019/EMPIAR-12195"}}