{"EMPIAR-13056":{"imagesets":[{"segmentations":[],"name":"Raw unaligned frames and metadata for each tilt in tilt series acquired on lamellae from mouse embryonic fibroblasts","directory":"data/atpsynthase_structure/frames","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":410,"frames_per_image":10,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":1.663,"pixel_height":1.663,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw unaligned frames were preprocessed in Warp to generate tilt series stacks. Corresponding reference files in other directories under same base name (tilt series, mdocs, tomograms). Four directories included in subfolders.  MIM019_2 and MIM019_3 are from mtGFP mouse embryonic fibroblasts (untreated).  MIM029_3 and MIM032_1 are from mtGFP mouse embryonic fibroblasts treated with degraded Thapsigargin (500nm) for 8 hours- condition uncertain.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Unaligned tilt series stacks from lamellae from mouse embryonic fibroblasts","directory":"data/atpsynthase_structure/TiltSeries","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":41,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.663,"pixel_height":1.663,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The tilt series stacks (.st file) and rawtlt files (.rawtlt file) were created from Warp with the input of tilt-corrected mdoc files.  Raw mdoc files are listed in the Tilt_series_mdoc folder. Tilt series stacks are then aligned in IMOD. MIM019_2 and MIM019_3 are from mtGFP mouse embryonic fibroblasts (untreated).  MIM029_3 and MIM032_1 are from mtGFP mouse embryonic fibroblasts treated with degraded Thapsigargin (500nm) for 8 hours- condition uncertain.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Reconstructed tomograms of lamellae from mouse embryonic fibroblasts","directory":"data/atpsynthase_structure/Tomograms","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":41,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":6.65,"pixel_height":6.65,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Bin4 tomograms are reconstructed from Warp after IMOD alignment. Particle coordinates for ATP synthase are provided in particle_list folder","image_width":"1024","image_height":"1440"},{"segmentations":[],"name":"Reconstructed tomograms used for membrane thickness measurement of organelles in lamellae from mouse embryonic fibroblasts","directory":"data/morphometrics_thickness/Tomogram_bin6","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":41,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":9.98,"pixel_height":9.98,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Bin 6 Warp reconstructed tomograms. Subset of MIM19_2, MIM019_3 used in thickness measurement analysis.","image_width":"682","image_height":"960"},{"segmentations":[],"name":"Reconstructed tomograms used for segmentation of organelles in lamellae from mouse embryonic fibroblasts","directory":"data/morphometrics_thickness/Tomogram_bin8","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":41,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":13.3,"pixel_height":13.3,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Bin 8 Warp reconstructed tomograms. Subset of MIM19_2, MIM019_3 used to generated organelle membrane segmentation. Associated segmentations files can be found in data/morphometrics_thickness/Voxel_segmentations. Associated triangulated surface meshes can be found in /data/morphometrics_thickness/Triangulated_surface_mesh.","image_width":"512","image_height":"720"},{"segmentations":[],"name":"Raw unaligned frame and metadata for each tilt in tilt-series acquired on CHX-treated S. cerevisiae cryo-FIB lamellae","directory":"data/yeast/frames","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":462,"frames_per_image":11,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":1.663,"pixel_height":1.663,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Raw unaligned frames were preprocessed in Warp to generate tilt series stacks","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Unaligned tilt series stack of cryo-electron tomography acquired on CHX-treated S. cerevisiae cryo-FIB lamellae","directory":"data/yeast/TiltSeries","category":"tilt series","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":38,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":1.663,"pixel_height":1.663,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The tilt series stacks (.st file) and rawtlt files (in Tilt_series_rawtlt) were created from Warp with the input of tilt-corrected mdoc files. Raw mdoc files are listed in the yeast/tilt_series_mdocs folder. Tilt series stacks are then aligned in IMOD.","image_width":"5760","image_height":"4092"},{"segmentations":[],"name":"Reconstructed tomograms of CHX-treated S. cerevisiae lamellae used for segmentation of organelle membranes","directory":"data/yeast/Tomogram_bin6","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":38,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":9.98,"pixel_height":9.98,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Bin 6 tomograms are reconstructed from Warp after IMOD alignment.","image_width":"682","image_height":"960"},{"segmentations":[],"name":"Voxel segmentation of organelle membranes within in lamellae from mouse embryonic fibroblasts","directory":"data/morphometrics_thickness/Voxel_segmentations","category":"reconstructed volumes","header_format":"MRC","data_format":"MRC","num_images_or_tilt_series":1,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"32 BIT FLOAT","pixel_width":13.3,"pixel_height":13.3,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"voxel segmentations from reconstructed tomograms at bin 8. These voxel segmentations were then input into surface morphometrics to generate triangulated surface meshes.","image_width":"512","image_height":"720"}],"workflow_file":null,"grant_references":[{"funding_body":"Damon Runyon Cancer Research Foundation","code":"DRR-65-21","country":"United States"},{"funding_body":"National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)","code":"RF1NS125674","country":"United States"},{"funding_body":"Collins Medical Trust","code":"N/A","country":"United States"},{"funding_body":"Pew Biomedical Scholars","code":"N/A","country":"United States"},{"funding_body":"Achievement Rewards for College Scientists Foundation","code":"N/A","country":"United States"}],"version_history":[],"title":"Surface morphometrics reveals local membrane thickness variation in organellar subcompartments","principal_investigator":[{"author_orcid":"0000-0001-6346-5137","middle_name":null,"organization":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute","street":"10550 N Torrey Pines Rd","town_or_city":"La Jolla","state_or_province":"California","post_or_zip":"92037","telephone":"(858) 784-8761","fax":null,"first_name":"Michaela","last_name":"Medina","email":"mmedina300kv [at] gmail.com","country":"United States","entry":"EMPIAR-13056"}],"status":"REL","deposition_date":"2025-08-26","release_date":"2025-11-19","obsolete_date":null,"update_date":"2025-11-19","corresponding_author":{"author":{"author_orcid":"0000-0001-6346-5137","middle_name":null,"organization":"Department of Integrative Structural and Computational Biology, The Scripps Research Institute","street":"10550 N Torrey Pines Rd","town_or_city":"La Jolla","state_or_province":"California","post_or_zip":"92037","first_name":"Michaela","last_name":"Medina","country":"United States"}},"authors":[{"author":{"name":"Medina M","author_orcid":"0000-0001-6346-5137"}},{"author":{"name":"Chang YT","author_orcid":"0000-0003-2580-4622"}},{"author":{"name":"Rahmani H","author_orcid":"0000-0003-0222-6989"}},{"author":{"name":"Fuentes D","author_orcid":"0000-0002-9687-0902"}},{"author":{"name":"Barad BA","author_orcid":"0000-0002-1016-862X"}},{"author":{"name":"Grotjahn DA","author_orcid":"0000-0001-5908-7882"}}],"cross_references":["EMD-72321"],"biostudies_references":[],"idr_references":[],"empiar_references":[{"name":"EMPIAR-12534"}],"citation":[{"authors":[{"name":"Medina M","author_orcid":"0000-0001-6346-5137"},{"name":"Chang YT","author_orcid":"0000-0003-2580-4622"},{"name":"Rahmani H","author_orcid":"0000-0003-0222-6989"},{"name":"Fuentes D","author_orcid":"0000-0002-9687-0902"},{"name":"Barad BA","author_orcid":"0000-0002-1016-862X"},{"name":"Grotjahn DA","author_orcid":"0000-0001-5908-7882"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Surface morphometrics reveals local membrane thickness variation in organellar subcompartments","volume":null,"country":"United States","first_page":null,"last_page":null,"year":"2025","language":null,"doi":"10.1101/2025.04.30.651574","pubmedid":"40654968","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"BioRxiv","journal_abbreviation":"BioRxiv","issue":null,"preprint":true}],"dataset_size":"575.4 GB","experiment_type":"EMDB","scale":"cell","entry_doi":"10.6019/EMPIAR-13056"}}