{"EMPIAR-10791":{"imagesets":[{"segmentations":[],"name":"6461 Lean Liver Dataset - FIB-SEM and Segmentation","directory":"data/Parlakgul et al - Regulation of liver subcellular architecture controls metabolic homeostasis/FIB-SEM Raw and Segmentation Data/6461 - Lean Liver","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5638,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":8.0,"pixel_height":8.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"6461 is Lean liver dataset - 12000 x 8000 x 5638 voxel, 8nm isotropic resolution.\nThere are 5638 consecutive raw FIBSEM images \nand 5638 corresponding images in each segmentation class \n(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane, Nuclear membrane)","image_width":"12000","image_height":"8000"},{"segmentations":[],"name":"6464 Obese1 Liver Dataset - FIB-SEM and Segmentation","directory":"data/Parlakgul et al - Regulation of liver subcellular architecture controls metabolic homeostasis/FIB-SEM Raw and Segmentation Data/6464 - Obese1 Liver","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":7896,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":8.0,"pixel_height":8.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"6464 is Obese1 liver dataset, 9112 x 10200 x 7896 voxel, 8nm isotropic resolution\nThere are 7896 consecutive raw FIBSEM images \nand 7896 corresponding images in each segmentation class \n(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane, Nuclear membrane)","image_width":"9112","image_height":"10200"},{"segmentations":[],"name":"9430 Obese2 Liver Dataset - FIB-SEM and Segmentation","directory":"data/Parlakgul et al - Regulation of liver subcellular architecture controls metabolic homeostasis/FIB-SEM Raw and Segmentation Data/9430 - Obese2 Liver","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":8501,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":8.0,"pixel_height":8.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"9430 is Obese2 liver dataset, 8000 x 8050 x 8501 voxel, 8nm isotropic resolution\nThere are 8501 consecutive raw FIBSEM images \nand 8501 corresponding images in each segmentation class \n(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane, Nuclear membrane)","image_width":"8000","image_height":"8050"},{"segmentations":[],"name":"1857 Obese Climp63 Liver Dataset - FIB-SEM and Segmentation","directory":"data/Parlakgul et al - Regulation of liver subcellular architecture controls metabolic homeostasis/FIB-SEM Raw and Segmentation Data/1857 - Obese Climp-63 Liver","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":3629,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":8.0,"pixel_height":8.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"1857 is Obese Climp63 liver dataset, 9700 x 9650 x 3629 voxel, 8nm isotropic resolution\nThere are 3629 consecutive raw FIBSEM images \nand 3629 corresponding images in each segmentation class \n(ER, ER sheets, ER Tubules, Mitochondria, Lipid Droplet, Cell Membrane)","image_width":"9700","image_height":"9650"},{"segmentations":[],"name":"Segmentation Evaluation files - Manual annotation, prediction, raw data files","directory":"data/Parlakgul et al - Regulation of liver subcellular architecture controls metabolic homeostasis/FIB-SEM Raw and Segmentation Data/Segmentation Evaluation","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":25,"frames_per_image":1,"frame_range_min":null,"frame_range_max":null,"voxel_type":"UNSIGNED BYTE","pixel_width":16.0,"pixel_height":16.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"The evaluation was performed on down-sampled data. A down-sampled version of the raw data is provided as well. Raw data, manual annotation data and predictions are provided as tiff stacks (8bit or 32bit, compressed, packaged in a .zip container). For lipid droplets, mitochondria, nuclear membrane and ER, we selected 3 test volumes of 300×300×50 voxels at random locations. Object based scores were only calculated for mitochondria and lipid droplets. For ER sheet and tubule evaluation, we randomly choose an area of 750x750 pixel^2 at 4 different locations in each dataset. Raw data, manual annotations and predictions are provided.","image_width":"150","image_height":"150"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"High resolution 3D imaging of liver subcellular architecture and its link to metabolic function","principal_investigator":[{"author_orcid":null,"middle_name":"S","organization":"Harvard TH Chan School of Public Health","street":"665 Huntington Ave SPH1 Room610","town_or_city":"Boston","state_or_province":"MA","post_or_zip":"02115","telephone":null,"fax":null,"first_name":"Gokhan","last_name":"Hotamisligil","email":"ghotamis [at] hsph.harvard.edu","country":"United States","entry":"EMPIAR-10791"}],"status":"REL","deposition_date":"2021-08-13","release_date":"2022-01-14","obsolete_date":null,"update_date":"2026-03-12","corresponding_author":{"author":{"author_orcid":"0000-0001-9365-7287","middle_name":null,"organization":"Harvard TH Chan School of Public Health","street":"665 Huntington Ave SPH1 Room610","town_or_city":"Boston","state_or_province":"MA","post_or_zip":"02115","first_name":"Gunes","last_name":"Parlakgul","country":"United States"}},"authors":[{"author":{"name":"Parlakgul G","author_orcid":"0000-0001-9365-7287"}},{"author":{"name":"Hotamisligil GS","author_orcid":null}}],"cross_references":[],"biostudies_references":[],"idr_references":[],"empiar_references":[],"citation":[{"authors":[{"name":"Parlakgul G","author_orcid":"0000-0001-9365-7287"},{"name":"Arruda AP","author_orcid":null},{"name":"Pang S","author_orcid":null},{"name":"Cagampan E","author_orcid":null},{"name":"Min N","author_orcid":null},{"name":"Guney E","author_orcid":null},{"name":"Lee Y","author_orcid":null},{"name":"Inouye K","author_orcid":null},{"name":"Hess HF","author_orcid":null},{"name":"Xu CS","author_orcid":null},{"name":"Hotamisligil GS","author_orcid":null}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Regulation of liver subcellular architecture controls metabolic homeostasis","volume":null,"country":"United States","first_page":null,"last_page":null,"year":"2022","language":"English","doi":"10.1038/s41586-022-04488-5","pubmedid":"35264794","details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Nature","journal_abbreviation":"Nature","issue":null,"preprint":false},{"authors":[{"name":"Parlakgül G","author_orcid":"0000-0001-9365-7287"},{"name":"Arruda AP","author_orcid":"0000-0001-6179-2687"},{"name":"Cagampan E","author_orcid":null},{"name":"Pang S","author_orcid":null},{"name":"Güney E","author_orcid":null},{"name":"Lee Y","author_orcid":null},{"name":"Hess HF","author_orcid":null},{"name":"Xu CS","author_orcid":"0000-0002-8564-7836"},{"name":"Hotamışlıgil GS","author_orcid":null}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"High resolution 3D imaging of liver reveals a central role for subcellular architectural organization in metabolism","volume":null,"country":"","first_page":null,"last_page":null,"year":"2020","language":"English","doi":"10.1101/2020.11.18.387803","pubmedid":null,"details":null,"book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"bioRxiv","journal_abbreviation":"","issue":null,"preprint":true}],"dataset_size":"2.8 TB","experiment_type":"FIB-SEM","scale":null,"entry_doi":"10.6019/EMPIAR-10791"}}