{"EMPIAR-10994":{"imagesets":[{"segmentations":[{"file":"data/160621_HeLa_Control/03_models","description":"Two models, one (CellOutlineModel_TIF and Labels_cell_outlines.mask) for outlines of the metaphase cell, and the other (OrganelleModel_TIF and Labels_160621_HeLa_OrganelleModel.model) includes segmentation of mitochondria, chromosomes, centrioles, and ER from a quadrant of the cell and insides of the spindle area.\nZ voxel size is 30 nm\nLabels_cell_outlines.mask and Labels_160621_HeLa_OrganelleModel.model are a mask and a model files for Microscopy Image Browser\n\nDescription of materials is available in readme.txt file and shown below:\n\nModel of one quadrant of a metaphase HeLa cell\n\nLabels_160621_HeLa_OrganelleModel.model -> model file of segmented organelles in Microscopy Image Browser format\nOrganelleModel_TIF -> the same model in TIF format\nIndices of materials:\n0 -> Exterior\n1 -> Mitochondria\n2 -> ER\n3 -> ER at the close proximity to chromosomes (at 320 nm distance)\n4 -> Chromosomes \n5 -> Centrioles\n6 -> Peripheral ER\n\nLabels_cell_outlines.mask -> model mask file of segmented cell outline\nCellOutlineModel_TIF -> the same model in TIF format","original_files":"data/160621_HeLa_Control/03_models","original_format":"TIFF","entry":null},{"file":"data/161107_HeLa_REEP3-4_KD_LBR/03_models","description":"A model (Model_TIF and Labels_161107_HeLa_REEP3-4_KD_LBR.model) includes segmentation of mitochondria, chromosomes, lipid droplets, and ER from a quadrant of the cell and insides of the spindle area.\nZ voxel size is 30 nm\nLabels_161107_HeLa_REEP3-4_KD_LBR.model is a model file for Microscopy Image Browser\n\nDescription of materials is available in readme.txt file and shown below:\n\nModel of one quadrant of a metaphase HeLa REEP 3/4 KD LBR cell\n\nLabels_161107_HeLa_REEP3-4_KD_LBR.model -> model file of segmented organelles in Microscopy Image Browser format\nModel_TIF -> the same model in TIF format\nIndices of materials:\n0 -> Exterior\n1 -> Mitochondria\n2 -> Lipid Droplets\n3 -> ER \n4 -> Chromosomes","original_files":"data/161107_HeLa_REEP3-4_KD_LBR/03_models","original_format":"TIFF","entry":null}],"name":"HeLa Control metaphase cell, raw data","directory":"data/160621_HeLa_Control/01_original_images","category":"micrographs - single frame","header_format":"DM4","data_format":"DM4","num_images_or_tilt_series":578,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":151.884,"pixel_height":151.884,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Z voxel size is 30 nm","image_width":"1280","image_height":"1280"},{"segmentations":[],"name":"HeLa Control metaphase cell, processed data","directory":"data/160621_HeLa_Control/02_processed_dataset","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":578,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":151.884,"pixel_height":151.884,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Z voxel size is 30 nm","image_width":"1453","image_height":"1477"},{"segmentations":[],"name":"HeLa REEP3/4 KD metaphase cell, raw datasets","directory":"data/161107_HeLa_REEP3-4_KD_LBR/01_original_images","category":"micrographs - single frame","header_format":"DM4","data_format":"DM4","num_images_or_tilt_series":474,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED 16 BIT INTEGER","pixel_width":148.183,"pixel_height":148.183,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Z voxel size is 30 nm","image_width":"1400","image_height":"1400"},{"segmentations":[],"name":"HeLa REEP3/4 KD metaphase cell, processed datasets","directory":"data/161107_HeLa_REEP3-4_KD_LBR/02_processed_dataset","category":"micrographs - single frame","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":471,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":148.183,"pixel_height":148.183,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Z voxel size is 30 nm","image_width":"1600","image_height":"1586"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"REEP3 and REEP4 determine the tubular morphology of the endoplasmic reticulum during mitosis","principal_investigator":[{"author_orcid":"0000-0002-4159-6934","middle_name":null,"organization":"Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki","street":"PL56 (Viikinkaari 9)","town_or_city":"Helsinki","state_or_province":"Uusimaa","post_or_zip":"00014","telephone":"+358 50 4696799","fax":null,"first_name":"Eija","last_name":"Jokitalo","email":"eija.jokitalo [at] helsinki.fi","country":"Finland","entry":"EMPIAR-10994"}],"status":"REL","deposition_date":"2022-04-01","release_date":"2024-01-16","obsolete_date":null,"update_date":"2024-01-16","corresponding_author":{"author":{"author_orcid":"0000-0002-4159-6934","middle_name":null,"organization":"Electron Microscopy Unit, Institute of Biotechnology, University of Helsinki","street":"PL56 (Viikinkaari 9)","town_or_city":"Helsinki","state_or_province":"Uusimaa","post_or_zip":"00014","first_name":"Eija","last_name":"Jokitalo","country":"Finland"}},"authors":[{"author":{"name":"Belevich I","author_orcid":"0000-0003-2190-4909"}},{"author":{"name":"Jokitalo E","author_orcid":"0000-0002-4159-6934"}}],"cross_references":[],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Kumar D","author_orcid":"0000-0001-5371-1779"},{"name":"Golchoubian B","author_orcid":"0000-0003-0854-710X"},{"name":"Belevich I","author_orcid":"0000-0003-2190-4909"},{"name":"Jokitalo E","author_orcid":"0000-0002-4159-6934"},{"name":"Schlaitz AL","author_orcid":"0000-0002-8737-9556"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"REEP3 and REEP4 determine the tubular morphology of the endoplasmic reticulum during mitosis","volume":"30","country":"","first_page":"1377","last_page":"1389","year":"2019","language":"English","doi":"10.1091/mbc.e18-11-0698","pubmedid":"30995177","details":"SBF-SEM datasets of control and REEP3/4 KD HeLa cells in metaphase","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Molecular biology of the cell","journal_abbreviation":"Mol Biol Cell","issue":"12","preprint":false}],"dataset_size":"8.7 GB","experiment_type":"SBF-SEM","scale":"cell","entry_doi":"10.6019/EMPIAR-10994"}}