{"EMPIAR-13270":{"imagesets":[{"segmentations":[{"file":"data/ERES_Paper/predictions","description":"Membranes were segmented using membrain-seg v2.","original_files":"data/ERES_Paper/frames","original_format":"MRC","entry":null}],"name":"Denoised tomograms containing COPII","directory":"data/ERES_Paper/denoised","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":63,"frames_per_image":42,"frame_range_min":1,"frame_range_max":42,"voxel_type":"16 BIT FLOAT","pixel_width":10.0,"pixel_height":10.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The 63 tilt series containing regions of interest were processed following the WarpTools pipeline, including motion correction, CTF and defocus handedness estimation (https://warpem.github.io/warp/). Tilt series were aligned using the WarpTools etomo patch tracking wrapper. Bad tilts were manually removed, and poorly aligned tilt series were manually improved with etomo. CTF-corrected tomograms were reconstructed at a pixel size of 10 Å and used to pick ribosomes for further improvement of alignments with Warp/M. Cryocare was used to denoise the tomograms.","image_width":"896","image_height":"896"},{"segmentations":[],"name":"Raw frames for the COPII containing tomograms","directory":"data/ERES_Paper/frames","category":"micrographs - multiframe","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":63,"frames_per_image":4,"frame_range_min":1,"frame_range_max":4,"voxel_type":"32 BIT FLOAT","pixel_width":2.24,"pixel_height":2.24,"micrographs_file_pattern":"data/ERES_Paper/frames/*.mrc","picked_particles_file_pattern":"data/ERES_Paper/job001/run_data.star","picked_particles_directory":"data/ERES_Paper/job001","details":"Raw frames of the 63 COPII containing tilt series. Each tilt series contains 42 tilts. Also included is the star file for the ribosome picking which yielded a 15A ribosome map that was further used to improve tilt series alignments for tomogram reconstruction via the Warp/M pipeline.","image_width":"3710","image_height":"3838"},{"segmentations":[],"name":"mdocs","directory":"data/ERES_Paper/mdoc_correctedFractions","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":63,"frames_per_image":4,"frame_range_min":1,"frame_range_max":4,"voxel_type":"BIT","pixel_width":2.24,"pixel_height":2.24,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"mdocs for the 63 COPII containing tomograms.","image_width":"3710","image_height":"3838"}],"workflow_file":null,"grant_references":[{"funding_body":"European Research Council (ERC)","code":"ERC-StG-2019 grant 852915","country":"United Kingdom"}],"version_history":[],"title":"Cryo electron tomography data presented in Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites","principal_investigator":[{"author_orcid":"0000-0003-1905-0342","middle_name":null,"organization":"Institute of Structural and Molecular Biology, Birkbeck, University of London","street":null,"town_or_city":"London","state_or_province":null,"post_or_zip":"WC1E 7HX","telephone":null,"fax":null,"first_name":"Giulia","last_name":"Zanetti","email":"giulia.zanetti [at] crick.ac.uk","country":"United Kingdom","entry":"EMPIAR-13270"}],"status":"REL","deposition_date":"2025-10-21","release_date":"2026-04-20","obsolete_date":null,"update_date":"2026-04-20","corresponding_author":{"author":{"author_orcid":"0000-0003-1905-0342","middle_name":null,"organization":"The Francis Crick Institute","street":"The Crick Institute, 1 Brill Place,","town_or_city":"London","state_or_province":null,"post_or_zip":"NW1 1BF","first_name":"Giulia","last_name":"Zanetti","country":"United Kingdom"}},"authors":[{"author":{"name":"Downes K","author_orcid":"0009-0000-1639-7960"}},{"author":{"name":"Zanetti G","author_orcid":"0000-0003-1905-0342"}}],"cross_references":["EMD-56951","EMD-56963","EMD-56606"],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Downes K","author_orcid":"0009-0000-1639-7960"},{"name":"Flood J","author_orcid":"0000-0001-6197-8406"},{"name":"Nans A","author_orcid":"0000-0002-3791-2447"},{"name":"Van der Verren S","author_orcid":"0000-0002-8783-1194"},{"name":"Audhya A","author_orcid":"0000-0002-7828-5152"},{"name":"Zanetti G","author_orcid":"0000-0003-1905-0342"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Multi-scale Molecular Imaging of Human Cells reveals COPI and COPII Vesicles at ER Exit Sites","volume":null,"country":"United Kingdom","first_page":null,"last_page":null,"year":"2025","language":"English","doi":"10.1101/2025.07.29.667472","pubmedid":null,"details":"This deposition contains all the raw tilt series (frames + mdocs), reconstructed tomograms, membrane segmentations and ribosome coordinates used and presented in the associated paper.","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"637.7 GB","experiment_type":"EMDB","scale":"cell","entry_doi":"10.6019/EMPIAR-13270"}}