{"EMPIAR-12017":{"imagesets":[{"segmentations":[],"name":"9428 Lean Fasted Liver Dataset - FIB-SEM and Segmentations","directory":"data/9428 Lean Fasted","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":9501,"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":"Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.\nVoxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n9498 is Lean Fasted Liver (7984 x 6984 x 9501 pixels in x, y, z)\nThere are 9501 consecutive raw FIBSEM images and 9501 corresponding images in each segmentation class. \nRaw (8-bit): 493 Gb\nER (8-bit): 493 Gb (uncompressed size)\nMitochondria instance (32-bit): 1.9 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier\nLipid Droplet (8-bit): 493 Gb (uncompressed size)\nCell Membrane (8-bit): 493 Gb (uncompressed size) - each individual cell has a unique pixel intensity as an identifier\nNuclear membrane (8-bit): 493 Gb (uncompressed size)","image_width":"7984","image_height":"6984"},{"segmentations":[],"name":"8970 Obese Fasted Liver Dataset - FIB-SEM and Segmentations","directory":"data/8970 Obese Fasted","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":8450,"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":"Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.\nVoxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n8970 is Obese Fasted Liver (9402 x 6949 x 8450 pixels in x, y, z)\nThere are 8450 consecutive raw FIBSEM images and 8450 corresponding images in each segmentation class. \nRaw (8-bit): 514 Gb\nER (8-bit): 514 Gb (uncompressed size)\nMitochondria instance (32-bit): 2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier\nLipid Droplet (8-bit): 514 Gb (uncompressed size)\nCell Membrane (8-bit): 514 Gb (uncompressed size) - each individual cell has a unique pixel intensity as an identifier\nNuclear membrane (8-bit): 514 Gb (uncompressed size)","image_width":"9402","image_height":"6949"},{"segmentations":[],"name":"6461 Lean Fed Liver Dataset - Mitochondria instance segmentations","directory":"data/Lean Fed","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":"32 BIT FLOAT","pixel_width":8.0,"pixel_height":8.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes. Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n6461 is Lean Fed Liver (12000 x 8000 x 5638 pixels in x, y, z)\nMitochondria instance (32-bit): 2.16 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.\nRaw and other segmentation classes can be found at https://www.ebi.ac.uk/empiar/EMPIAR-10791/","image_width":"12000","image_height":"8000"},{"segmentations":[],"name":"6464 Obese Fed Liver Dataset - Mitochondria instance segmentations","directory":"data/Obese Fed","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":"32 BIT FLOAT","pixel_width":8.0,"pixel_height":8.0,"micrographs_file_pattern":"","picked_particles_file_pattern":"","picked_particles_directory":"","details":"Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes. Voxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n6464 is Obese Fed Liver (9112 x 10200 x 7896 pixels in x, y, z)\nMitochondria instance (32-bit): 3 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.\nRaw and other segmentation classes can be found at https://www.ebi.ac.uk/empiar/EMPIAR-10791/","image_width":"9112","image_height":"10200"},{"segmentations":[],"name":"1931 - Pericentral Liver Dataset - FIB-SEM images","directory":"data/Pericentral","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":10777,"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":"Raw FIBSEM images are not compressed and can be viewed online.\nVoxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n1931 - Pericentral (lean fed liver) (8125 x 8125 x 10777 pixels in x, y, z)\nThere are 10777 consecutive raw FIBSEM images.","image_width":"8125","image_height":"8125"},{"segmentations":[],"name":"1931 - Periportal Liver Dataset - FIB-SEM images","directory":"data/Periportal","category":"micrographs - multiframe","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":8982,"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":"Raw FIBSEM images are not compressed and can be viewed online.\nVoxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n1931 - Periportal (lean fed liver) (6500 x 6500 x 8982 pixels in x, y, z)\nThere are 8982 consecutive raw FIBSEM images.","image_width":"6500","image_height":"6500"},{"segmentations":[],"name":"2679 Obese LacZ Liver Dataset - FIB-SEM and Segmentations","directory":"data/Obese LacZ","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":7705,"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":"Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.\nVoxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n2679 is Obese liver expressing LacZ control (6500 x 6500 x 7705 pixels in x, y, z)\nThere are 7705 consecutive raw FIBSEM images and 3629 corresponding images in each segmentation class.\nRaw (8-bit): 303 Gb\nER (8-bit): 303 Gb (uncompressed size)\nMitochondria instance (32-bit): 1.2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier","image_width":"6500","image_height":"6500"},{"segmentations":[],"name":"1858 Obese RRBP1 (p180) Liver Dataset - FIB-SEM and Segmentations","directory":"data/Obese RRBP1","category":"reconstructed volumes","header_format":"TIFF","data_format":"TIFF","num_images_or_tilt_series":5860,"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":"Raw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.\nVoxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n1858 is Obese liver expressing RRBP1 (9375 x 10625 x 5860 pixels in x, y, z)\nPlease delete the first 65 images in each class (raw + segmentation). Firs 65 images contain the Durcupan resin.\nThere are 5860 consecutive raw FIBSEM images and 5860 corresponding images in each segmentation class.\nRaw (8-bit): 544 Gb\nER (8-bit): 544 Gb (uncompressed size)\nMitochondria instance (32-bit): 2.2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.","image_width":"9375","image_height":"10625"}],"workflow_file":null,"grant_references":[],"version_history":[],"title":"Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity","principal_investigator":[{"author_orcid":null,"middle_name":"S","organization":"Harvard TH Chan School of Public Health","street":"665 Huntington Ave SPH1 Rm610","town_or_city":"Boston","state_or_province":"MA","post_or_zip":"02115","telephone":"+18572049572","fax":null,"first_name":"Gokhan","last_name":"Hotamisligil","email":"ghotamis [at] hsph.harvard.edu","country":"United States","entry":"EMPIAR-12017"},{"author_orcid":null,"middle_name":null,"organization":"University of California, Berkeley","street":"129 Morgan Hall","town_or_city":"Berkeley","state_or_province":"CA","post_or_zip":"94720","telephone":"+1617-938-7158","fax":null,"first_name":"Ana Paula","last_name":"Arruda","email":"aarruda [at] berkeley.edu","country":"United States","entry":"EMPIAR-12017"}],"status":"REL","deposition_date":"2024-04-04","release_date":"2024-04-17","obsolete_date":null,"update_date":"2024-05-20","corresponding_author":{"author":{"author_orcid":null,"middle_name":null,"organization":"University of California, Berkeley","street":"119 Morgan Hall","town_or_city":"Berkeley","state_or_province":"CA","post_or_zip":"94720","first_name":"Gunes","last_name":"Parlakgul","country":"United States"}},"authors":[{"author":{"name":"Parlakgul G","author_orcid":"0000-0001-9365-7287"}}],"cross_references":[],"biostudies_references":[],"idr_references":[],"empiar_references":[{"name":"EMPIAR-10791"}],"citation":[{"authors":[{"name":"Parlakgül G","author_orcid":"0000-0001-9365-7287"},{"name":"Pang S","author_orcid":"0000-0002-7231-4151"},{"name":"Artico LL","author_orcid":"0000-0003-4691-2446"},{"name":"Min N","author_orcid":"0000-0002-7881-2514"},{"name":"Cagampan E","author_orcid":"0000-0003-2114-0267"},{"name":"Villa R","author_orcid":null},{"name":"Goncalves RLS","author_orcid":null},{"name":"Lee GY","author_orcid":null},{"name":"Xu CS","author_orcid":"0000-0002-8564-7836"},{"name":"Hotamışlıgil GS","author_orcid":"0000-0003-2906-1897"},{"name":"Arruda AP","author_orcid":"0000-0001-6179-2687"}],"editors":[],"published":true,"j_or_nj_citation":true,"title":"Spatial mapping of hepatic ER and mitochondria architecture reveals zonated remodeling in fasting and obesity","volume":"15","country":"United States","first_page":null,"last_page":null,"year":"2024","language":"English","doi":"10.1038/s41467-024-48272-7","pubmedid":"38729945","details":"Raw FIB-SEM imaging datasets and segmented classes from mouse liver tissues.\nRaw FIBSEM images are not compressed and can be viewed online. Segmentation images are compressed (.zip) and need to be downloaded, unzipped (uncompressed) and then viewed. The total uncompressed data size is 20 Terabytes. Compressed version of the data is around 2.9 Terabytes.\nVoxel size is 8nm isotropic (8nm x 8nm x 8nm in x, y, z).\n\n9498 is Lean Fasted Liver (7984 x 6984 x 9501 pixels in x, y, z)\nThere are 9501 consecutive raw FIBSEM images and 9501 corresponding images in each segmentation class. \nRaw (8-bit): 493 Gb\nER (8-bit): 493 Gb (uncompressed size)\nMitochondria instance (32-bit): 1.9 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier\nLipid Droplet (8-bit): 493 Gb (uncompressed size)\nCell Membrane (8-bit): 493 Gb (uncompressed size) - each individual cell has a unique pixel intensity as an identifier\nNuclear membrane (8-bit): 493 Gb (uncompressed size)\n\n8970 is Obese Fasted Liver (9402 x 6949 x 8450 pixels in x, y, z)\nThere are 8450 consecutive raw FIBSEM images and 8450 corresponding images in each segmentation class. \nRaw (8-bit): 514 Gb\nER (8-bit): 514 Gb (uncompressed size)\nMitochondria instance (32-bit): 2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier\nLipid Droplet (8-bit): 514 Gb (uncompressed size)\nCell Membrane (8-bit): 514 Gb (uncompressed size) - each individual cell has a unique pixel intensity as an identifier\nNuclear membrane (8-bit): 514 Gb (uncompressed size)\n\n6461 is Lean Fed Liver (12000 x 8000 x 5638 pixels in x, y, z)\nMitochondria instance (32-bit): 2.16 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.\nRaw and other segmentation classes can be found at https://www.ebi.ac.uk/empiar/EMPIAR-10791/ \n\n6464 is Obese Fed Liver (9112 x 10200 x 7896 pixels in x, y, z)\nMitochondria instance (32-bit): 3 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier.\nRaw and other segmentation classes can be found at https://www.ebi.ac.uk/empiar/EMPIAR-10791/\n\n2679 is Obese liver expressing LacZ control (6500 x 6500 x 7705 pixels in x, y, z)\nThere are 7705 consecutive raw FIBSEM images and 3629 corresponding images in each segmentation class.\nRaw (8-bit): 303 Gb\nER (8-bit): 303 Gb (uncompressed size)\nMitochondria instance (32-bit): 1.2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier\n\n1858 is Obese liver expressing RRBP1 (9375 x 10625 x 5860 pixels in x, y, z)\nPlease delete the first 65 images in each class (raw + segmentation). Firs 65 images contain the Durcupan resin.\nThere are 5860 consecutive raw FIBSEM images and 5860 corresponding images in each segmentation class.\nRaw (8-bit): 544 Gb\nER (8-bit): 544 Gb (uncompressed size)\nMitochondria instance (32-bit): 2.2 Tb (uncompressed size) - each individual mito has a unique pixel intensity as an identifier\n\n1931 - Pericentral (lean fed liver) (8125 x 8125 x 10777 pixels in x, y, z)\nThere are 10777 consecutive raw FIBSEM images.\n\n1931 - Periportal (lean fed liver) (6500 x 6500 x 8982 pixels in x, y, z)\nThere are 8982 consecutive raw FIBSEM images.","book_chapter_title":null,"publisher":null,"publication_location":null,"journal":"Nature communications","journal_abbreviation":"Nat Commun","issue":"1","preprint":false}],"dataset_size":"2.9 TB","experiment_type":"FIB-SEM","scale":"tissue","entry_doi":"10.6019/EMPIAR-12017"}}