[{"dataset_id":"hair-2024-013","title":"Leishmania mexicana whole-cell dataset (SBF-SEM)","paper_title":"Whole cell reconstructions of Leishmania mexicana through the cell cycle.","year":2024,"source":"PLOS Pathogens","source_type":"paper","public_data_status":"partial","species":"Leishmania mexicana","cell_type":"Leishmania mexicana","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle; Other: Physiological relevance (in vitro vs sand fly-derived)","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":87.5,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","lipid droplets","golgi","flagella/cilia"],"organelle_pairs":["er:flagella/cilia","er:golgi","er:lipid droplets","er:mitochondria","er:nucleus","er:vacuole/lysosome","flagella/cilia:golgi","flagella/cilia:lipid droplets","flagella/cilia:mitochondria","flagella/cilia:nucleus","flagella/cilia:vacuole/lysosome","golgi:lipid droplets","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","lipid droplets:mitochondria","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area","density"],"sample_size":51,"sample_size_bucket":"51+","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 41 in vitro, 10 sand fly-derived","source_study_id":"Hair 2024","publication_pmid":"38416776","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/38416776/","public_locator_urls":["https://zenodo.org/records/10652021","https://www.ebi.ac.uk/empiar/EMPIAR-11826/"],"included_status":"included"},{"dataset_id":"mocaer-2023-002","title":"Ensiculifera tyrrhenica whole-cell dataset (FIB-SEM)","paper_title":"Targeted volume correlative light and electron microscopy of an environmental marine microorganism.","year":2023,"source":"Journal of Cell Science","source_type":"paper","public_data_status":"partial","species":"Ensiculifera tyrrhenica","cell_type":"Ensiculifera tyrrhenica","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":8.0,"axial_resolution_nm":8.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid","golgi","flagella/cilia"],"organelle_pairs":["chloroplast/plastid:flagella/cilia","chloroplast/plastid:golgi","chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","flagella/cilia:golgi","flagella/cilia:mitochondria","flagella/cilia:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Mocaer 2023","publication_pmid":"37455654","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37455654/","public_locator_urls":["https://github.com/mobie/environmentaldinoflagellate-vCLEM","https://www.ebi.ac.uk/empiar/EMPIAR-11399/"],"included_status":"included"},{"dataset_id":"tashyreva-2023-001","title":"Lacrimia vacuolata whole-cell dataset (SBF-SEM)","paper_title":"Ultrastructure and 3D reconstruction of a diplonemid protist (Diplonemea) and its novel membranous organelle.","year":2023,"source":"mBio","source_type":"paper","public_data_status":"none","species":"Lacrimia vacuolata","cell_type":"Lacrimia vacuolata","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":100.0,"isotropic":false,"organelles":["nucleus","mitochondria","lipid droplets","golgi","flagella/cilia"],"organelle_pairs":["flagella/cilia:golgi","flagella/cilia:lipid droplets","flagella/cilia:mitochondria","flagella/cilia:nucleus","golgi:lipid droplets","golgi:mitochondria","golgi:nucleus","lipid droplets:mitochondria","lipid droplets:nucleus","mitochondria:nucleus"],"metric_families":["dimensions","distance"],"sample_size":24,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Tashyreva 2023","publication_pmid":"37737610","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37737610/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"johkura-2022-090","title":"R. norvegicus, hepatocyte whole-cell dataset (SBF-SEM)","paper_title":"Whole-cell observation of ZIO-stained Golgi apparatus in rat hepatocytes with serial block-face scanning electron microscope, SBF-SEM.","year":2022,"source":"Microscopy","source_type":"paper","public_data_status":"none","species":"R. norvegicus","cell_type":"R. norvegicus, hepatocyte","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species; Other","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":10.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","golgi"],"organelle_pairs":["golgi:nucleus"],"metric_families":["volume","volume_fraction","count","surface_area"],"sample_size":8,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"4 single-nuc, 4 binuc","source_study_id":"Johkura 2022","publication_pmid":"35535544","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35535544/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"muller-2021-094","title":"M. musculus, beta cell whole-cell dataset (FIB-SEM)","paper_title":"3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse β cells.","year":2021,"source":"Journal of Cell Biology","source_type":"paper","public_data_status":"partial","species":"M. musculus","cell_type":"M. musculus, beta cell","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Other: High glucose v low glucose","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":4.0,"axial_resolution_nm":4.0,"isotropic":true,"organelles":["nucleus","mitochondria","golgi","centrosome/basal body","flagella","centriole","axomene"],"organelle_pairs":["axomene:centriole","axomene:centrosome/basal body","axomene:flagella","axomene:golgi","axomene:mitochondria","axomene:nucleus","centriole:centrosome/basal body","centriole:flagella","centriole:golgi","centriole:mitochondria","centriole:nucleus","centrosome/basal body:flagella","centrosome/basal body:golgi","centrosome/basal body:mitochondria","centrosome/basal body:nucleus","flagella:golgi","flagella:mitochondria","flagella:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area","contacts"],"sample_size":7,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 3 low-glucose, 4 high-glucose","source_study_id":"Muller 2021","publication_pmid":"33326005","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33326005/","public_locator_urls":["https://betaseg.github.io/","https://cloud.mpi-cbg.de/index.php/s/UJopHTRuh6f4wR8","https://sites.imagej.net/"],"included_status":"included"},{"dataset_id":"cui-2019-051","title":"Arabidopsis thaliana, cortical root whole-cell dataset (ET (cryo))","paper_title":"A whole-cell electron tomography model of vacuole biogenesis in Arabidopsis root cells.","year":2019,"source":"Nature Plants","source_type":"paper","public_data_status":"none","species":"Arabidopsis thaliana","cell_type":"Arabidopsis thaliana, cortical root","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"ET (cryo)","modality_family":"EM","lateral_resolution_nm":4.3,"axial_resolution_nm":300.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","chloroplast/plastid","golgi","mvb"],"organelle_pairs":["chloroplast/plastid:er","chloroplast/plastid:golgi","chloroplast/plastid:mitochondria","chloroplast/plastid:mvb","chloroplast/plastid:nucleus","chloroplast/plastid:vacuole/lysosome","er:golgi","er:mitochondria","er:mvb","er:nucleus","er:vacuole/lysosome","golgi:mitochondria","golgi:mvb","golgi:nucleus","golgi:vacuole/lysosome","mitochondria:mvb","mitochondria:nucleus","mitochondria:vacuole/lysosome","mvb:nucleus","mvb:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 whole cell w multiple organelles; 3 whole-cell vacuole only","source_study_id":"Cui 2019","publication_pmid":"30559414","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/30559414/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"laundon-2019-072","title":"Salpingoeca rosetta whole-cell dataset (ssTEM)","paper_title":"The architecture of cell differentiation in choanoflagellates and sponge choanocytes.","year":2019,"source":"PLOS Biology","source_type":"paper","public_data_status":"partial","species":"Salpingoeca rosetta","cell_type":"Salpingoeca rosetta","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Cell Type/Species; Other: Differentiation","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":110.0,"isotropic":null,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","golgi","flagella/cilia","centrosome/basal body","vesicles"],"organelle_pairs":["centrosome/basal body:er","centrosome/basal body:flagella/cilia","centrosome/basal body:golgi","centrosome/basal body:mitochondria","centrosome/basal body:nucleus","centrosome/basal body:vacuole/lysosome","centrosome/basal body:vesicles","er:flagella/cilia","er:golgi","er:mitochondria","er:nucleus","er:vacuole/lysosome","er:vesicles","flagella/cilia:golgi","flagella/cilia:mitochondria","flagella/cilia:nucleus","flagella/cilia:vacuole/lysosome","flagella/cilia:vesicles","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","golgi:vesicles","mitochondria:nucleus","mitochondria:vacuole/lysosome","mitochondria:vesicles","nucleus:vacuole/lysosome","nucleus:vesicles","vacuole/lysosome:vesicles"],"metric_families":["volume","volume_fraction","dimensions","count","distance","contacts","shape"],"sample_size":6,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 3 colonial, 3 single","source_study_id":"Laundon 2019","publication_pmid":"30978201","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/30978201/","public_locator_urls":["https://doi.org/10.6084/m9.figshare.7346750.v2"],"included_status":"included"},{"dataset_id":"laundon-2019-073","title":"Oscarella carmela, choanocytes whole-cell dataset (ssTEM)","paper_title":"The architecture of cell differentiation in choanoflagellates and sponge choanocytes.","year":2019,"source":"PLOS Biology","source_type":"paper","public_data_status":"partial","species":"Oscarella carmela","cell_type":"Oscarella carmela, choanocytes","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Cell Type/Species; Other: Differentiation","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":110.0,"isotropic":null,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","golgi","flagella/cilia","centrosome/basal body"],"organelle_pairs":["centrosome/basal body:er","centrosome/basal body:flagella/cilia","centrosome/basal body:golgi","centrosome/basal body:mitochondria","centrosome/basal body:nucleus","centrosome/basal body:vacuole/lysosome","er:flagella/cilia","er:golgi","er:mitochondria","er:nucleus","er:vacuole/lysosome","flagella/cilia:golgi","flagella/cilia:mitochondria","flagella/cilia:nucleus","flagella/cilia:vacuole/lysosome","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","count","distance","contacts","shape"],"sample_size":5,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Laundon 2019","publication_pmid":"30978201","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/30978201/","public_locator_urls":["https://doi.org/10.6084/m9.figshare.7346750.v2"],"included_status":"included"},{"dataset_id":"liu-2018-078","title":"Danio rerio, neural progenitor cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, neural progenitor cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 of each cell type (see below); 3 time points for zebrafish neural progenitor","source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"liu-2018-079","title":"Danio rerio, lens cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, lens cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"liu-2018-080","title":"Danio rerio, skin cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, skin cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"liu-2018-083","title":"Danio rerio, retinal neuroepithelial cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, retinal neuroepithelial cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"hughes-2017-009","title":"Trypanosoma brucei whole-cell dataset (SBF-SEM)","paper_title":"Patterns of organelle ontogeny through a cell cycle revealed by whole-cell reconstructions using 3D electron microscopy.","year":2017,"source":"Journal of Cell Science","source_type":"paper","public_data_status":"none","species":"Trypanosoma brucei","cell_type":"Trypanosoma brucei","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":6.1,"axial_resolution_nm":100.0,"isotropic":false,"organelles":["nucleus","mitochondria","golgi","flagella/cilia","centrosome/basal body"],"organelle_pairs":["centrosome/basal body:flagella/cilia","centrosome/basal body:golgi","centrosome/basal body:mitochondria","centrosome/basal body:nucleus","flagella/cilia:golgi","flagella/cilia:mitochondria","flagella/cilia:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","dimensions","count","distance"],"sample_size":79,"sample_size_bucket":"51+","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"(different n's for each quant)","source_study_id":"Hughes 2017","publication_pmid":"28049718","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28049718/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"valm-2017-100","title":"COS-7 (Cercopithecus aethiops) whole-cell dataset (Fluorescence (LLS))","paper_title":"Applying systems-level spectral imaging and analysis to reveal the organelle interactome","year":2017,"source":"Nature","source_type":"paper","public_data_status":"none","species":"NHP","cell_type":"COS-7 (Cercopithecus aethiops)","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Stressors; Methodology","modality":"Fluorescence (LLS)","modality_family":"optical","lateral_resolution_nm":334.5,"axial_resolution_nm":798.0,"isotropic":false,"organelles":["er","mitochondria","vacuole/lysosome","lipid droplets","peroxisome","golgi"],"organelle_pairs":["er:golgi","er:lipid droplets","er:mitochondria","er:peroxisome","er:vacuole/lysosome","golgi:lipid droplets","golgi:mitochondria","golgi:peroxisome","golgi:vacuole/lysosome","lipid droplets:mitochondria","lipid droplets:peroxisome","lipid droplets:vacuole/lysosome","mitochondria:peroxisome","mitochondria:vacuole/lysosome","peroxisome:vacuole/lysosome"],"metric_families":["volume","volume_fraction","count","distance","contacts"],"sample_size":10,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Valm 2017","publication_pmid":"28538724","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28538724/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wacker-2015-075","title":"Danio rerio, \"long process\" cell whole-cell dataset (SEM-AT)","paper_title":"Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.","year":2015,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, \"long process\" cell","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"SEM-AT","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome","golgi"],"organelle_pairs":["golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Wacker 2015","publication_pmid":"25611576","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/25611576/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wacker-2015-076","title":"Danio rerio, \"cogwheel\" cell whole-cell dataset (SEM-AT)","paper_title":"Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.","year":2015,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, \"cogwheel\" cell","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"SEM-AT","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome","golgi"],"organelle_pairs":["golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Wacker 2015","publication_pmid":"25611576","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/25611576/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wacker-2015-077","title":"Danio rerio, thymus whole-cell dataset (SEM-AT)","paper_title":"Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.","year":2015,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, thymus","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"SEM-AT","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","er:vacuole/lysosome","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 thymus, 1 cytotoxic t cell, 1 adrenal medulla neutrophil, 1 ea of unknown cell types (cogwheel and longer process)","source_study_id":"Wacker 2015","publication_pmid":"25611576","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/25611576/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wacker-2015-084","title":"Danio rerio, cytotoxic T cell whole-cell dataset (SEM-AT)","paper_title":"Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.","year":2015,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, cytotoxic T cell","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"SEM-AT","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","er:vacuole/lysosome","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Wacker 2015","publication_pmid":"25611576","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/25611576/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wacker-2015-085","title":"Danio rerio, adrenal medulla neutrophil whole-cell dataset (SEM-AT)","paper_title":"Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.","year":2015,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, adrenal medulla neutrophil","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"SEM-AT","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome","golgi"],"organelle_pairs":["golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Wacker 2015","publication_pmid":"25611576","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/25611576/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wayama-2013-037","title":"Haematococcus pluvialis whole-cell dataset (ssTEM)","paper_title":"Three-dimensional ultrastructural study of oil and astaxanthin accumulation during encystment in the green alga Haematococcus pluvialis.","year":2013,"source":"PLoS ONE","source_type":"paper","public_data_status":"none","species":"Haematococcus pluvialis","cell_type":"Haematococcus pluvialis","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Stressors","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":4.0,"axial_resolution_nm":4.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid","golgi"],"organelle_pairs":["chloroplast/plastid:golgi","chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 coccoid cell, 1 cyst cell","source_study_id":"Wayama 2013","publication_pmid":"23326471","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/23326471/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wei-2012-063","title":"Saccharomyces cerevisiae whole-cell dataset (FIB-SEM)","paper_title":"High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy.","year":2012,"source":"Biotechniques","source_type":"paper","public_data_status":"none","species":"Saccharomyces cerevisiae","cell_type":"Saccharomyces cerevisiae","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":3.0,"axial_resolution_nm":3.0,"isotropic":true,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","lipid droplets","golgi","vesicles"],"organelle_pairs":["er:golgi","er:lipid droplets","er:mitochondria","er:nucleus","er:vacuole/lysosome","er:vesicles","golgi:lipid droplets","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","golgi:vesicles","lipid droplets:mitochondria","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","lipid droplets:vesicles","mitochondria:nucleus","mitochondria:vacuole/lysosome","mitochondria:vesicles","nucleus:vacuole/lysosome","nucleus:vesicles","vacuole/lysosome:vesicles"],"metric_families":["volume","volume_fraction","dimensions"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 cell per resolution","source_study_id":"Wei 2012","publication_pmid":"22780318","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/22780318/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wei-2012-064","title":"Saccharomyces cerevisiae whole-cell dataset (FIB-SEM)","paper_title":"High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy.","year":2012,"source":"Biotechniques","source_type":"paper","public_data_status":"none","species":"Saccharomyces cerevisiae","cell_type":"Saccharomyces cerevisiae","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":5.0,"isotropic":true,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","lipid droplets","golgi","vesicles"],"organelle_pairs":["er:golgi","er:lipid droplets","er:mitochondria","er:nucleus","er:vacuole/lysosome","er:vesicles","golgi:lipid droplets","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","golgi:vesicles","lipid droplets:mitochondria","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","lipid droplets:vesicles","mitochondria:nucleus","mitochondria:vacuole/lysosome","mitochondria:vesicles","nucleus:vacuole/lysosome","nucleus:vesicles","vacuole/lysosome:vesicles"],"metric_families":["volume","volume_fraction","dimensions"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 cell per resolution","source_study_id":"Wei 2012","publication_pmid":"22780318","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/22780318/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wei-2012-065","title":"Saccharomyces cerevisiae whole-cell dataset (FIB-SEM)","paper_title":"High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy.","year":2012,"source":"Biotechniques","source_type":"paper","public_data_status":"none","species":"Saccharomyces cerevisiae","cell_type":"Saccharomyces cerevisiae","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":3.72,"axial_resolution_nm":15.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","lipid droplets","golgi","vesicles"],"organelle_pairs":["er:golgi","er:lipid droplets","er:mitochondria","er:nucleus","er:vacuole/lysosome","er:vesicles","golgi:lipid droplets","golgi:mitochondria","golgi:nucleus","golgi:vacuole/lysosome","golgi:vesicles","lipid droplets:mitochondria","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","lipid droplets:vesicles","mitochondria:nucleus","mitochondria:vacuole/lysosome","mitochondria:vesicles","nucleus:vacuole/lysosome","nucleus:vesicles","vacuole/lysosome:vesicles"],"metric_families":["volume","volume_fraction","dimensions"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 cell per resolution","source_study_id":"Wei 2012","publication_pmid":"22780318","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/22780318/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"hohmann-marriott-2009-022","title":"Plasmodium falciparum whole-cell dataset (STEM)","paper_title":"Nanoscale 3D cellular imaging by axial scanning transmission electron tomography.","year":2009,"source":"Nature Methods","source_type":"paper","public_data_status":"none","species":"Plasmodium falciparum","cell_type":"Plasmodium falciparum","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"STEM","modality_family":"EM","lateral_resolution_nm":1.9,"axial_resolution_nm":20.0,"isotropic":false,"organelles":["nucleus","vacuole/lysosome","lipid droplets","golgi"],"organelle_pairs":["golgi:lipid droplets","golgi:nucleus","golgi:vacuole/lysosome","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Hohmann-Marriott 2009","publication_pmid":"19718033","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/19718033/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"noske-2008-095","title":"M. musculus, beta cell whole-cell dataset (ET (Cryo))","paper_title":"Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets.","year":2008,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"none","species":"M. musculus","cell_type":"M. musculus, beta cell","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"ET (Cryo)","modality_family":"EM","lateral_resolution_nm":17.5,"axial_resolution_nm":17.5,"isotropic":true,"organelles":["nucleus","mitochondria","golgi","mvb"],"organelle_pairs":["golgi:mitochondria","golgi:mvb","golgi:nucleus","mitochondria:mvb","mitochondria:nucleus","mvb:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area","distance","contacts"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Noske 2008","publication_pmid":"18069000","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/18069000/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"henderson-2007-025","title":"Ostreococcus tauri whole-cell dataset (ET (cryo))","paper_title":"3-D ultrastructure of O. tauri: electron cryotomography of an entire eukaryotic cell.","year":2007,"source":"PLoS One","source_type":"paper","public_data_status":"none","species":"Ostreococcus tauri","cell_type":"Ostreococcus tauri","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle; Light/Dark","modality":"ET (cryo)","modality_family":"EM","lateral_resolution_nm":1.2,"axial_resolution_nm":1.2,"isotropic":true,"organelles":["nucleus","er","mitochondria","chloroplast/plastid","peroxisome","golgi"],"organelle_pairs":["chloroplast/plastid:er","chloroplast/plastid:golgi","chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:peroxisome","er:golgi","er:mitochondria","er:nucleus","er:peroxisome","golgi:mitochondria","golgi:nucleus","golgi:peroxisome","mitochondria:nucleus","mitochondria:peroxisome","nucleus:peroxisome"],"metric_families":["volume","volume_fraction","dimensions","surface_area"],"sample_size":10,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"10 (6 best cells used for quantitation) (52 imaged total); 23 dark-to-light transition; 29 light-to-dark transition;","source_study_id":"Henderson 2007","publication_pmid":"17710148","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/17710148/","public_locator_urls":[],"included_status":"included"}]