{"EMPIAR-12794":{"imagesets":[{"segmentations":[],"name":"Source unaligned micrographs (.tif) of synaptic vesicles isolated from mouse brain (part I)","directory":"data/frames_1","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":48,"frames_per_image":10,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":0.84,"pixel_height":0.84,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The naming correspondence between raw micrographs and tilt series/tomograms can be found in frames2tomos.txt.\nThe respective gain-reference file is SuperCDSRef_A_000_0.0.dm4\nFor this dataset raw micrographs were collected in 10 frames with a total dose per tilt view of 4.1391 e−/Å2 and the total dose distributed equally among all tilt images.\nSee top-level README.txt for contents location details.","image_width":"11520","image_height":"8184"},{"segmentations":[],"name":"Source unaligned micrographs (.tif) of synaptic vesicles isolated from mouse brain (part II)","directory":"data/frames_2","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":64,"frames_per_image":10,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":0.84,"pixel_height":0.84,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The naming correspondence between raw micrographs and tilt series/tomograms can be found in frames2tomos.txt.\nThe respective gain-reference file is SuperCDSRef_ts_051_000_-0.0.dm4\nFor this dataset raw micrographs were collected using high-dose zero-tilt scheme. Thus, a zero-tilt micrographs were collected in 75 frames with a total dose per image of 31.077 e−/Å2 and other tilt micrographs were collected in 10 frames with a total dose per image of 4.1391 e−/Å2.\nSee top-level README.txt for contents location details.","image_width":"11520","image_height":"8184"},{"segmentations":[],"name":"Unaligned unbinned tilt stacks (.st) with metadata (.xf, .tlt, .defocus) of synaptic vesicles isolated from mouse brain","directory":"data/Stacks","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":99,"frames_per_image":10,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":0.84,"pixel_height":0.84,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The metadata files could be used to align tilt stacks (.tlt and .xf), correct CTF (.defocus) and perform 3D reconstruction (.tlt), e.g. using IMOD.","image_width":"11520","image_height":"8184"},{"segmentations":[],"name":"CTF-corrected binned tomograms (.rec) of synaptic vesicles isolated from mouse brain","directory":"data/tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":99,"frames_per_image":10,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":13.44,"pixel_height":13.44,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Particle coordinates and orientations could be found in the subfolder \"/data/particle_tables/\" of this deposition.\nFor additional info see file prtcls_description_dataset_1.txt","image_width":"512","image_height":"720"}],"workflow_file":null,"grant_references":[{"funding_body":"German Research Foundation (DFG)","code":"KU3222/3-1","country":"Germany"},{"funding_body":"German Research Foundation (DFG)","code":"458275811","country":"Germany"},{"funding_body":"German Research Foundation (DFG)","code":"436260754","country":"Germany"},{"funding_body":"European Research Council (ERC)","code":"ERC-STG No. 949184","country":"Germany"}],"version_history":[],"title":"Cryo-electron tomography on synaptic vesicles isolated from mouse brain (part 1)","principal_investigator":[{"author_orcid":"0000-0003-3550-6274","middle_name":null,"organization":"Max Delbrück Center for Molecular Medicine","street":null,"town_or_city":"Berlin","state_or_province":null,"post_or_zip":"13125","telephone":null,"fax":null,"first_name":"Mikhail","last_name":"Kudryashev","email":"Mikhail.Kudryashev [at] mdc-berlin.de","country":"Germany","entry":"EMPIAR-12794"}],"status":"REL","deposition_date":"2025-01-27","release_date":"2025-07-25","obsolete_date":null,"update_date":"2025-07-25","corresponding_author":{"author":{"author_orcid":"0000-0003-3550-6274","middle_name":null,"organization":"Max Delbrück Center for Molecular Medicine","street":null,"town_or_city":"Berlin","state_or_province":null,"post_or_zip":"13125","first_name":"Mikhail","last_name":"Kudryashev","country":"Germany"}},"authors":[{"author":{"name":"Kravcenko U","author_orcid":"0009-0004-7176-8444"}},{"author":{"name":"Ruwolt M","author_orcid":"0009-0000-7220-406X"}},{"author":{"name":"Kroll J","author_orcid":"0000-0003-4243-4088"}},{"author":{"name":"Yushkevich A","author_orcid":"0000-0002-8729-9281"}},{"author":{"name":"Zenkner M","author_orcid":null}},{"author":{"name":"Ruta J","author_orcid":"0009-0007-0524-6885"}},{"author":{"name":"Lotfy R","author_orcid":null}},{"author":{"name":"Wanker EE","author_orcid":"0000-0001-8072-1630"}},{"author":{"name":"Rosenmund C","author_orcid":"0000-0002-3905-2444"}},{"author":{"name":"Liu F","author_orcid":null}},{"author":{"name":"Kudryashev M","author_orcid":"0000-0003-3550-6274"}}],"cross_references":["EMD-18572","EMD-18568","EMD-18578","EMD-18557","EMD-18556"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Kravcenko U","author_orcid":"0009-0004-7176-8444"},{"name":"Kudryashev M","author_orcid":"0000-0003-3550-6274"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Molecular architecture of synaptic vesicles","volume":"121","country":"United States","first_page":null,"last_page":null,"year":"2024","language":"English","doi":"10.1073/pnas.2407375121","pubmedid":"39602275","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Proceedings of the National Academy of Sciences","journal_abbreviation":"PNAS","issue":"49","preprint":false}],"dataset_size":"1.4 TB","experiment_type":"EMDB","scale":"molecule","entry_doi":"10.6019/EMPIAR-12794"}}