[{"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":"antao-2023-068","title":"Encephalitozoon intestinalis whole-cell dataset (SBF-SEM)","paper_title":"3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen Encephalitozoon intestinalis.","year":2023,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Encephalitozoon intestinalis","cell_type":"Encephalitozoon intestinalis","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Other: Developmental stages","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":2.0,"axial_resolution_nm":45.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome"],"organelle_pairs":["er:mitochondria","er:nucleus","er:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","contacts"],"sample_size":21,"sample_size_bucket":"11-50","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 21+ E.i. (\"A minimum of 7 parasites were segmented completely per condition\" [sporonts, sporoblasts, spores])","source_study_id":"Antao 2023","publication_pmid":"37996434","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37996434/","public_locator_urls":["https://doi.org/10.5281/zenodo.10009391","https://www.ebi.ac.uk/empiar/EMPIAR-11683/"],"included_status":"included"},{"dataset_id":"antao-2023-098","title":"Vero (Cercopithecus aethiops) whole-cell dataset (SBF-SEM)","paper_title":"3D reconstructions of parasite development and the intracellular niche of the microsporidian pathogen Encephalitozoon intestinalis.","year":2023,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"NHP","cell_type":"Vero (Cercopithecus aethiops)","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Other: Developmental stages","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":2.0,"axial_resolution_nm":45.0,"isotropic":false,"organelles":["nucleus","mito","er"],"organelle_pairs":["er:mito","er:nucleus","mito:nucleus"],"metric_families":["volume","volume_fraction","dimensions","contacts"],"sample_size":4,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 4 Vero (inc PV, Fig 5)","source_study_id":"Antao 2023","publication_pmid":"37996434","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37996434/","public_locator_urls":["https://doi.org/10.5281/zenodo.10009391","https://www.ebi.ac.uk/empiar/EMPIAR-11683/"],"included_status":"included"},{"dataset_id":"ezzedine-2023-035","title":"Sanguina nivaloides whole-cell dataset (FIB-SEM)","paper_title":"Adaptive traits of cysts of the snow alga Sanguina nivaloides unveiled by 3D subcellular imaging.","year":2023,"source":"Nature Communications","source_type":"paper","public_data_status":"complete","species":"Sanguina nivaloides","cell_type":"Sanguina nivaloides","tissue_or_system":null,"comparator_class":"methodology","comparator_detail":"Methodology","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":9.0,"axial_resolution_nm":9.0,"isotropic":true,"organelles":["nucleus","mitochondria","lipid droplets","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:lipid droplets","chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","lipid droplets:mitochondria","lipid droplets:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","dimensions","surface_area","contacts"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Public data available. 1 chemically fixed, 1 cryo-fixed","source_study_id":"Ezzedine 2023","publication_pmid":"37980360","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37980360/","public_locator_urls":["https://www.ebi.ac.uk/empiar/EMPIAR-11694/"],"included_status":"included"},{"dataset_id":"feng-2023-038","title":"Chlorella pyrenoidosa whole-cell dataset (FIB-SEM)","paper_title":"FIB-SEM analysis on three-dimensional structures of growing organelles in wild Chlorella pyrenoidosa cells.","year":2023,"source":"Protoplasma","source_type":"paper","public_data_status":"none","species":"Chlorella pyrenoidosa","cell_type":"Chlorella pyrenoidosa","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Other: photosynthetic growth, cell size (increases across cell growth stages)","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":2.44,"axial_resolution_nm":8.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","lipid droplets","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:er","chloroplast/plastid:lipid droplets","chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:vacuole/lysosome","er:lipid droplets","er:mitochondria","er:nucleus","er: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","distance","shape"],"sample_size":9,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"3+ per growth stage; 20 imaged, 15 segmented, but 3 per stage chosen for reconstruction","source_study_id":"Feng 2023","publication_pmid":"36416933","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/36416933/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"jadav-2023-111","title":"H446 (lung cancer) whole-cell dataset (SBF-SEM)","paper_title":"Beyond the surface: Investigation of tumorsphere morphology using volume electron microscopy.","year":2023,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"none","species":"Human (cancer)","cell_type":"H446 (lung cancer)","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle; Methodology","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":9.0,"axial_resolution_nm":27.0,"isotropic":false,"organelles":["nucleus","mitochondria","vesicles"],"organelle_pairs":["mitochondria:nucleus","mitochondria:vesicles","nucleus:vesicles"],"metric_families":["volume","volume_fraction","count","surface_area","shape"],"sample_size":6,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Jadav 2023","publication_pmid":"37805154","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37805154/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"matharu-2023-105","title":"platelet whole-cell dataset (FIB-SEM)","paper_title":"Deep learning, 3D ultrastructural analysis reveals quantitative differences in platelet and organelle packing in COVID-19/SARSCoV2 patient-derived platelets.","year":2023,"source":"Platelets","source_type":"paper","public_data_status":"none","species":"Human","cell_type":"platelet","tissue_or_system":null,"comparator_class":"treatment","comparator_detail":"Stressors","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":7.0,"axial_resolution_nm":15.0,"isotropic":false,"organelles":["mitochondria"],"organelle_pairs":[],"metric_families":["volume","volume_fraction","count","surface_area"],"sample_size":64,"sample_size_bucket":"51+","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"63 including mito (606 total cell+AGl, 300 Ctrl, 306 COVID)","source_study_id":"Matharu 2023","publication_pmid":"37933490","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37933490/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"mcquate-2023-081","title":"Danio rerio, hair cells whole-cell dataset (SBF-SEM)","paper_title":"Activity regulates a cell type-specific mitochondrial phenotype in zebrafish lateral line hair cells.","year":2023,"source":"eLife","source_type":"paper","public_data_status":"partial","species":"Danio rerio","cell_type":"Danio rerio, hair cells","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Cell Type/Species; Other: development (young vs mature)","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":45.0,"isotropic":false,"organelles":["mitochondria","flagella/cilia"],"organelle_pairs":["flagella/cilia:mitochondria"],"metric_families":["volume","volume_fraction","dimensions","count","other"],"sample_size":134,"sample_size_bucket":"51+","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"McQuate 2023","publication_pmid":"36912880","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/36912880/","public_locator_urls":["https://elifesciences.org/articles/80468#data","http://demo.webknossos.org/"],"included_status":"included"},{"dataset_id":"mcquate-2023-082","title":"Danio rerio, supporting cells whole-cell dataset (SBF-SEM)","paper_title":"Activity regulates a cell type-specific mitochondrial phenotype in zebrafish lateral line hair cells.","year":2023,"source":"eLife","source_type":"paper","public_data_status":"partial","species":"Danio rerio","cell_type":"Danio rerio, supporting cells","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Cell Type/Species; Other: development (young vs mature)","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":45.0,"isotropic":false,"organelles":["mitochondria","flagella/cilia"],"organelle_pairs":["flagella/cilia:mitochondria"],"metric_families":["volume","volume_fraction","dimensions","count","other"],"sample_size":12,"sample_size_bucket":"11-50","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"McQuate 2023","publication_pmid":"36912880","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/36912880/","public_locator_urls":["https://elifesciences.org/articles/80468#data","http://demo.webknossos.org/"],"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":"attias-2022-004","title":"Trypanosoma sp. 858 whole-cell dataset (FIB-SEM)","paper_title":"Remarkable kinetoplast, cytostome-cytopharynx complex, and storage-related structures as dissected by three-dimensional reconstruction of Trypanosoma sp. 858 isolated from a toad (Amphibia: Anura)","year":2022,"source":"Micron","source_type":"paper","public_data_status":"none","species":"Protist (parasitic protozoan)","cell_type":"Trypanosoma sp. 858","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":null,"isotropic":null,"organelles":["nucleus","lipid droplets","flagella/cilia"],"organelle_pairs":["flagella/cilia:lipid droplets","flagella/cilia:nucleus","lipid droplets:nucleus"],"metric_families":["dimensions"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.85,"whole_cell_boundary_confirmed":"yes","notes":"Unclear","source_study_id":"Attias 2022","publication_pmid":"34798356","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/34798356/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"burrell-2022-014","title":"Eimeria tenella whole-cell dataset (SBF-SEM)","paper_title":"Cellular electron tomography of the apical complex in the apicomplexan parasite Eimeria tenella shows a highly organised gateway for regulated secretion.","year":2022,"source":"PLoS Pathogens","source_type":"paper","public_data_status":"none","species":"Eimeria tenella","cell_type":"Eimeria tenella","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":150.0,"isotropic":null,"organelles":["nucleus","mitochondria"],"organelle_pairs":["mitochondria:nucleus"],"metric_families":["volume","volume_fraction","count"],"sample_size":25,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Burrell 2022","publication_pmid":"35816515","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35816515/","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":"midorikawa-2022-049","title":"Arabidopsis thaliana, mesophyll whole-cell dataset (FESEM)","paper_title":"Three-dimensional nanoscale analysis of light-dependent organelle changes in Arabidopsis mesophyll cells","year":2022,"source":"PNAS Nexus","source_type":"paper","public_data_status":"none","species":"Arabidopsis thaliana","cell_type":"Arabidopsis thaliana, mesophyll","tissue_or_system":null,"comparator_class":"other","comparator_detail":"Light/Dark","modality":"FESEM","modality_family":"EM","lateral_resolution_nm":10.0,"axial_resolution_nm":100.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome","chloroplast/plastid","peroxisome"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:peroxisome","chloroplast/plastid:vacuole/lysosome","mitochondria:nucleus","mitochondria:peroxisome","mitochondria:vacuole/lysosome","nucleus:peroxisome","nucleus:vacuole/lysosome","peroxisome:vacuole/lysosome"],"metric_families":["volume","volume_fraction","count","surface_area","distance","contacts","shape","other"],"sample_size":6,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"3L, 3D","source_study_id":"Midorikawa 2022","publication_pmid":"36712360","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/36712360/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"zechmann-2022-045","title":"Nicotiana tabacum whole-cell dataset (FIB-SEM)","paper_title":"Volumetric 3D reconstruction of plant leaf cells using SEM, ion milling, TEM, and serial sectioning.","year":2022,"source":"Planta","source_type":"paper","public_data_status":"none","species":"Nicotiana tabacum","cell_type":"Nicotiana tabacum","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":80.0,"isotropic":null,"organelles":["nucleus","mitochondria","vacuole/lysosome","chloroplast/plastid","peroxisome"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:peroxisome","chloroplast/plastid:vacuole/lysosome","mitochondria:nucleus","mitochondria:peroxisome","mitochondria:vacuole/lysosome","nucleus:peroxisome","nucleus:vacuole/lysosome","peroxisome:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Zechmann 2022","publication_pmid":"35522384","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35522384/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"zechmann-2022-046","title":"Nicotiana tabacum whole-cell dataset (ssTEM)","paper_title":"Volumetric 3D reconstruction of plant leaf cells using SEM, ion milling, TEM, and serial sectioning.","year":2022,"source":"Planta","source_type":"paper","public_data_status":"none","species":"Nicotiana tabacum","cell_type":"Nicotiana tabacum","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":80.0,"isotropic":null,"organelles":["nucleus","mitochondria","vacuole/lysosome","chloroplast/plastid","peroxisome"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:peroxisome","chloroplast/plastid:vacuole/lysosome","mitochondria:nucleus","mitochondria:peroxisome","mitochondria:vacuole/lysosome","nucleus:peroxisome","nucleus:vacuole/lysosome","peroxisome:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Zechmann 2022","publication_pmid":"35522384","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35522384/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"zechmann-2022-047","title":"Cucurbita pepo whole-cell dataset (FIB-SEM)","paper_title":"Volumetric 3D reconstruction of plant leaf cells using SEM, ion milling, TEM, and serial sectioning.","year":2022,"source":"Planta","source_type":"paper","public_data_status":"none","species":"Cucurbita pepo","cell_type":"Cucurbita pepo","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":80.0,"isotropic":null,"organelles":["nucleus","mitochondria","vacuole/lysosome","chloroplast/plastid","peroxisome"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:peroxisome","chloroplast/plastid:vacuole/lysosome","mitochondria:nucleus","mitochondria:peroxisome","mitochondria:vacuole/lysosome","nucleus:peroxisome","nucleus:vacuole/lysosome","peroxisome:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Zechmann 2022","publication_pmid":"35522384","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35522384/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"zechmann-2022-048","title":"Cucurbita pepo whole-cell dataset (ssTEM)","paper_title":"Volumetric 3D reconstruction of plant leaf cells using SEM, ion milling, TEM, and serial sectioning.","year":2022,"source":"Planta","source_type":"paper","public_data_status":"none","species":"Cucurbita pepo","cell_type":"Cucurbita pepo","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":80.0,"isotropic":null,"organelles":["nucleus","mitochondria","vacuole/lysosome","chloroplast/plastid","peroxisome"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:peroxisome","chloroplast/plastid:vacuole/lysosome","mitochondria:nucleus","mitochondria:peroxisome","mitochondria:vacuole/lysosome","nucleus:peroxisome","nucleus:vacuole/lysosome","peroxisome:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Zechmann 2022","publication_pmid":"35522384","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35522384/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"decelle-2021-003","title":"Brandtodinium nutricula whole-cell dataset (FIB-SEM)","paper_title":"Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae.","year":2021,"source":"Environmental Microbiology","source_type":"paper","public_data_status":"none","species":"Brandtodinium nutricula","cell_type":"Brandtodinium nutricula","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Other: metabolism/trophy - free-living vs symbiotic (radiolarians - collodaria Collozoum host)","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":8.0,"axial_resolution_nm":8.0,"isotropic":true,"organelles":["nucleus","mitochondria","vacuole/lysosome","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","surface_area","other"],"sample_size":7,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"3 free-living, 4 symbiotic","source_study_id":"Decelle 2021","publication_pmid":"34499794","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/34499794/","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":"pokrovskaya-2021-086","title":"C57BL/6 (M. musculus) whole-cell dataset (SBF-SEM)","paper_title":"Structural analysis of resting mouse platelets by 3D-EM reveals an unexpected variation in α-granule shape.","year":2021,"source":"Platelets","source_type":"paper","public_data_status":"none","species":"Rodent","cell_type":"C57BL/6 (M. musculus)","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":6.7,"axial_resolution_nm":35.0,"isotropic":false,"organelles":["mitochondria"],"organelle_pairs":[],"metric_families":["volume","volume_fraction","dimensions","count"],"sample_size":10,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Pokrovskaya 2021","publication_pmid":"32815431","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/32815431/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"uwizeye-2021a-026","title":"Micromonas whole-cell dataset (FIB-SEM)","paper_title":"Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.","year":2021,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Protist (plankton)","cell_type":"Micromonas","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Light/Dark; Cell Type/Species; Other: Trophic conditions","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":6.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","contacts"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 3 cells per species","source_study_id":"Uwizeye 2021a","publication_pmid":"33594064","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33594064/","public_locator_urls":["https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST575","https://www.ebi.ac.uk/biostudies/studies/S-BSST575"],"included_status":"included"},{"dataset_id":"uwizeye-2021a-027","title":"Emiliana whole-cell dataset (FIB-SEM)","paper_title":"Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.","year":2021,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Protist (plankton)","cell_type":"Emiliana","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Light/Dark; Cell Type/Species; Other: Trophic conditions","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":6.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","contacts"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Uwizeye 2021a","publication_pmid":"33594064","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33594064/","public_locator_urls":["https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST575","https://www.ebi.ac.uk/biostudies/studies/S-BSST575"],"included_status":"included"},{"dataset_id":"uwizeye-2021a-030","title":"Symbiodinium whole-cell dataset (FIB-SEM)","paper_title":"Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.","year":2021,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Protist (plankton)","cell_type":"Symbiodinium","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Light/Dark; Cell Type/Species; Other: Trophic conditions","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":6.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","contacts"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Uwizeye 2021a","publication_pmid":"33594064","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33594064/","public_locator_urls":["https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST575","https://www.ebi.ac.uk/biostudies/studies/S-BSST575"],"included_status":"included"},{"dataset_id":"uwizeye-2021a-031","title":"Galdieria whole-cell dataset (FIB-SEM)","paper_title":"Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.","year":2021,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Protist (plankton)","cell_type":"Galdieria","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Light/Dark; Cell Type/Species; Other: Trophic conditions","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":6.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","contacts"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Uwizeye 2021a","publication_pmid":"33594064","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33594064/","public_locator_urls":["https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST575","https://www.ebi.ac.uk/biostudies/studies/S-BSST575"],"included_status":"included"},{"dataset_id":"uwizeye-2021a-032","title":"Phaeodactylum whole-cell dataset (FIB-SEM)","paper_title":"Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.","year":2021,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Protist (plankton)","cell_type":"Phaeodactylum","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Light/Dark; Cell Type/Species; Other: Trophic conditions","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":6.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","contacts"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Uwizeye 2021a","publication_pmid":"33594064","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33594064/","public_locator_urls":["https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST575","https://www.ebi.ac.uk/biostudies/studies/S-BSST575"],"included_status":"included"},{"dataset_id":"uwizeye-2021a-033","title":"Nannochloropsis whole-cell dataset (FIB-SEM)","paper_title":"Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.","year":2021,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Protist (plankton)","cell_type":"Nannochloropsis","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Light/Dark; Cell Type/Species; Other: Trophic conditions","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":6.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","contacts"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Uwizeye 2021a","publication_pmid":"33594064","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33594064/","public_locator_urls":["https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST575","https://www.ebi.ac.uk/biostudies/studies/S-BSST575"],"included_status":"included"},{"dataset_id":"uwizeye-2021a-039","title":"Pelagomonas whole-cell dataset (FIB-SEM)","paper_title":"Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.","year":2021,"source":"Nature Communications","source_type":"paper","public_data_status":"partial","species":"Protist (plankton)","cell_type":"Pelagomonas","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Light/Dark; Cell Type/Species; Other: Trophic conditions","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":6.0,"axial_resolution_nm":6.0,"isotropic":true,"organelles":["nucleus","mitochondria","chloroplast/plastid","vesicles"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:vesicles","mitochondria:nucleus","mitochondria:vesicles","nucleus:vesicles"],"metric_families":["volume","volume_fraction","surface_area","contacts"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Uwizeye 2021a","publication_pmid":"33594064","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33594064/","public_locator_urls":["https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BSST575","https://www.ebi.ac.uk/biostudies/studies/S-BSST575"],"included_status":"included"},{"dataset_id":"uwizeye-2021b-029","title":"Phaeocystis cordata whole-cell dataset (FIB-SEM)","paper_title":"Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae.","year":2021,"source":"PNAS","source_type":"paper","public_data_status":"partial","species":"Phaeocystis cordata","cell_type":"Phaeocystis cordata","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Other: free-living vs symbiotic","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":7.5,"axial_resolution_nm":7.5,"isotropic":true,"organelles":["nucleus","mitochondria","vacuole/lysosome","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","surface_area","distance","contacts","shape"],"sample_size":27,"sample_size_bucket":"11-50","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 20 free-living + 7 symbiotic (w/  and w/o host Acantharia (radiolarian protozoa, marine microplankton))","source_study_id":"Uwizeye 2021b","publication_pmid":"34215695","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/34215695/","public_locator_urls":["https://www.ebi.ac.uk/empiar/EMPIAR-10672/"],"included_status":"included"},{"dataset_id":"hoffman-2020-099","title":"COS-7 (Cercopithecus aethiops) whole-cell dataset (FIB-SEM)","paper_title":"Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells.","year":2020,"source":"Science","source_type":"paper","public_data_status":"none","species":"NHP","cell_type":"COS-7 (Cercopithecus aethiops)","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","er","mitochondria"],"organelle_pairs":["er:mitochondria","er:nucleus","mitochondria:nucleus"],"metric_families":["volume","dimensions"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Hoffman 2020","publication_pmid":"31949053","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/31949053/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"pollreisz-2020-104","title":"RPE (retinal epithelia) whole-cell dataset (SBF-SEM)","paper_title":"Atlas of Human Retinal Pigment Epithelium Organelles Significant for Clinical Imaging.","year":2020,"source":"Invest Ophthalmol Vis Sci.","source_type":"paper","public_data_status":"none","species":"Human","cell_type":"RPE (retinal epithelia)","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus"],"organelle_pairs":[],"metric_families":["volume","volume_fraction","dimensions","count","distance"],"sample_size":17,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Pollreisz 2020","publication_pmid":"32648890","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/32648890/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"rudlaff-2020-023","title":"Plasmodium falciparum whole-cell dataset (FIB-SEM)","paper_title":"Three-dimensional ultrastructure of Plasmodium falciparum throughout cytokinesis.","year":2020,"source":"PLOS Pathogens","source_type":"paper","public_data_status":"partial","species":"Plasmodium falciparum","cell_type":"Plasmodium falciparum","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle; Stressors; Other: stressor - E64 protease inhibitor treatment","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":20.0,"isotropic":false,"organelles":["nucleus","vacuole/lysosome","centrosome/basal body"],"organelle_pairs":["centrosome/basal body:nucleus","centrosome/basal body:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["count","contacts","other"],"sample_size":11,"sample_size_bucket":"11-50","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available.","source_study_id":"Rudlaff 2020","publication_pmid":"32511279","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/32511279/","public_locator_urls":["https://www.ebi.ac.uk/pdbe/","https://www.ebi.ac.uk/empiar/EMPIAR-10392/"],"included_status":"included"},{"dataset_id":"wu-2020-066","title":"Saccharomyces cerevisiae whole-cell dataset (FIB-SEM)","paper_title":"Multi-scale 3D Cryo-Correlative Microscopy for Vitrified Cells.","year":2020,"source":"Structure","source_type":"paper","public_data_status":"none","species":"Saccharomyces cerevisiae","cell_type":"Saccharomyces cerevisiae","tissue_or_system":null,"comparator_class":"methodology","comparator_detail":"Stressors; Methodology","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":17.39,"axial_resolution_nm":17.39,"isotropic":true,"organelles":["nucleus","mitochondria","vacuole/lysosome","lipid droplets","vesicles"],"organelle_pairs":["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":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"comparing 3 modalities on 1 cell, FIB-SEM produces the only \"whole cell\"","source_study_id":"Wu 2020","publication_pmid":"32814034","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/32814034/","public_locator_urls":[],"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":"decelle-2019-028","title":"Phaeocystis cordata whole-cell dataset (FIB-SEM)","paper_title":"Algal Remodeling in a Ubiquitous Planktonic Photosymbiosis.","year":2019,"source":"Current Biology","source_type":"paper","public_data_status":"none","species":"Phaeocystis cordata","cell_type":"Phaeocystis cordata","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":8.0,"axial_resolution_nm":8.0,"isotropic":true,"organelles":["nucleus","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:nucleus"],"metric_families":["volume","count","surface_area"],"sample_size":18,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"8 symbiotic, 10 free-living; 2 representative cells shown","source_study_id":"Decelle 2019","publication_pmid":"30827917","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/30827917/","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":"pokrovskaya-2020-106","title":"platelet whole-cell dataset (SBF-SEM)","paper_title":"3D ultrastructural analysis of α‐granule, dense granule, mitochondria, and canalicular system arrangement in resting human platelets","year":2019,"source":"Res Pract Thromb Haemost","source_type":"paper","public_data_status":"none","species":"Human","cell_type":"platelet","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":6.8,"axial_resolution_nm":30.0,"isotropic":false,"organelles":["mitochondria"],"organelle_pairs":[],"metric_families":["volume_fraction"],"sample_size":30,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Pokrovskaya 2020","publication_pmid":"31989087","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/31989087/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"okumura-2018-097","title":"Mm2T (Muntiacus muntjak) whole-cell dataset (ET)","paper_title":"Electron tomography of whole cultured cells using novel transmission electron imaging technique.","year":2018,"source":"Micron","source_type":"paper","public_data_status":"none","species":"Mammal","cell_type":"Mm2T (Muntiacus muntjak)","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"ET","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":70.0,"isotropic":null,"organelles":["mitochondria","lipid droplets"],"organelle_pairs":["lipid droplets:mitochondria"],"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":"Okumura 2018","publication_pmid":"29049927","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/29049927/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"cooper-2017-010","title":"Trypanosoma (currawong) whole-cell dataset (FIB-SEM)","paper_title":"A comparative molecular and 3-dimensional structural investigation into cross-continental and novel avian Trypanosoma spp. in Australia.","year":2017,"source":"Parasites & Vectors","source_type":"paper","public_data_status":"none","species":"Protist (parasitic protozoan)","cell_type":"Trypanosoma (currawong)","tissue_or_system":null,"comparator_class":"other","comparator_detail":"Other: a large and a small epimastigote","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":25.0,"isotropic":null,"organelles":["mitochondria","endosome","reservosome (late endosome)"],"organelle_pairs":["endosome:mitochondria","endosome:reservosome (late endosome)","mitochondria:reservosome (late endosome)"],"metric_families":["volume","dimensions","surface_area"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"2 full reconstructions; quants from 25 cells, only kinetoplasts segmented","source_study_id":"Cooper 2017","publication_pmid":"28499405","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28499405/","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":"oi-2017-044","title":"Oryza sativa, mesophyll whole-cell dataset (FIB-SEM)","paper_title":"Three-dimensional intracellular structure of a whole rice mesophyll cell observed with FIB-SEM.","year":2017,"source":"Annals of Botany","source_type":"paper","public_data_status":"none","species":"Oryza sativa","cell_type":"Oryza sativa, mesophyll","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":25.0,"axial_resolution_nm":50.0,"isotropic":false,"organelles":["nucleus","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 visible 3D reconstruction, 2 addtl in supp movies (chloroplast counts)","source_study_id":"Oi 2017","publication_pmid":"28444369","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28444369/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"feng-2016-074","title":"Penaeus monodon whole-cell dataset (SBF-SEM)","paper_title":"Three-dimensional reconstruction of black tiger prawn (Penaeus monodon) spermatozoa using serial block-face scanning electron microscopy.","year":2016,"source":"Journal of Morphology","source_type":"paper","public_data_status":"none","species":"Penaeus monodon","cell_type":"Penaeus monodon","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":8.7,"axial_resolution_nm":50.0,"isotropic":false,"organelles":["nucleus","mitochondria"],"organelle_pairs":["mitochondria:nucleus"],"metric_families":["volume","dimensions","count"],"sample_size":9,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"Randomly selected spermatozoa","source_study_id":"Feng 2016","publication_pmid":"26877112","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/26877112/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"ota-2016-036","title":"Parachlorella kessleri whole-cell dataset (ssTEM)","paper_title":"Highly efficient lipid production in the green alga Parachlorella kessleri: draft genome and transcriptome endorsed by whole-cell 3D ultrastructure.","year":2016,"source":"Biotechnology for Biofuels","source_type":"paper","public_data_status":"none","species":"Parachlorella kessleri","cell_type":"Parachlorella kessleri","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Stressors","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":null,"isotropic":null,"organelles":["nucleus","mitochondria","vacuole/lysosome","lipid droplets","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:lipid droplets","chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid: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"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":0.85,"whole_cell_boundary_confirmed":"yes","notes":"1 per condition","source_study_id":"Ota 2016","publication_pmid":"26811738","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/26811738/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"sakaguchi-2016-024","title":"Plasmodium falciparum whole-cell dataset (SBF-SEM)","paper_title":"Three-dimensional analysis of morphological changes in the malaria parasite infected red blood cell by serial block-face scanning electron microscopy.","year":2016,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"partial","species":"Plasmodium falciparum","cell_type":"Plasmodium falciparum","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Other: developmental/life cycle stages","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":8.22,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome","vesicles"],"organelle_pairs":["mitochondria:nucleus","mitochondria:vacuole/lysosome","mitochondria:vesicles","nucleus:vacuole/lysosome","nucleus:vesicles","vacuole/lysosome:vesicles"],"metric_families":["volume","volume_fraction","surface_area"],"sample_size":22,"sample_size_bucket":"11-50","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 22 iRBCs, as well as 10 non-iRBCs which don't count becase they don't have organelles","source_study_id":"Sakaguchi 2016","publication_pmid":"26772147","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/26772147/","public_locator_urls":["https://www.ebi.ac.uk/empiar/EMPIAR-10052/","https://www.ebi.ac.uk/empiar/EMPIAR-10053/","https://www.ebi.ac.uk/empiar/EMPIAR-10054/","https://www.ebi.ac.uk/empiar/EMPIAR-10055/"],"included_status":"included"},{"dataset_id":"gluenz-2015-008","title":"Trypanosoma brucei whole-cell dataset (SBF-SEM)","paper_title":"Scanning and three-dimensional electron microscopy methods for the study of Trypanosoma brucei and Leishmania mexicana flagella.","year":2015,"source":"Methods in Cell Biology","source_type":"paper","public_data_status":"none","species":"Trypanosoma brucei","cell_type":"Trypanosoma brucei","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":6.1,"axial_resolution_nm":100.0,"isotropic":false,"organelles":["nucleus","mitochondria","vesicles","flagella/cilia"],"organelle_pairs":["flagella/cilia:mitochondria","flagella/cilia:nucleus","flagella/cilia:vesicles","mitochondria:nucleus","mitochondria:vesicles","nucleus:vesicles"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"Fig 9. original data","source_study_id":"Gluenz 2015","publication_pmid":"25837406","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/25837406/","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":"murata-2014-060","title":"Saccharomyces cerevisiae whole-cell dataset (STEM)","paper_title":"Whole-cell imaging of the budding yeast Saccharomyces cerevisiae by high-voltage scanning transmission electron tomography","year":2014,"source":"Ultramicroscopy","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":"STEM","modality_family":"EM","lateral_resolution_nm":5.0,"axial_resolution_nm":25.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome"],"organelle_pairs":["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":"Murata 2014","publication_pmid":"24935612","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/24935612/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"hanssen-2013-021","title":"Plasmodium falciparum whole-cell dataset (ET (chemical))","paper_title":"Electron tomography of Plasmodium falciparum merozoites reveals core cellular events that underpin erythrocyte invasion.","year":2013,"source":"Cellular Microbiology","source_type":"paper","public_data_status":"none","species":"Plasmodium falciparum","cell_type":"Plasmodium falciparum","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Methodology; Other: stages of RBC invasion","modality":"ET (chemical)","modality_family":"EM","lateral_resolution_nm":130.0,"axial_resolution_nm":130.0,"isotropic":true,"organelles":["nucleus","mitochondria","rhoptry","cystosomal ring","apicoplast","polar rings"],"organelle_pairs":["apicoplast:cystosomal ring","apicoplast:mitochondria","apicoplast:nucleus","apicoplast:polar rings","apicoplast:rhoptry","cystosomal ring:mitochondria","cystosomal ring:nucleus","cystosomal ring:polar rings","cystosomal ring:rhoptry","mitochondria:nucleus","mitochondria:polar rings","mitochondria:rhoptry","nucleus:polar rings","nucleus:rhoptry","polar rings:rhoptry"],"metric_families":["volume","volume_fraction"],"sample_size":17,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"17","source_study_id":"Hanssen 2013","publication_pmid":"23461734","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/23461734/","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":"girard-dias-2012-006","title":"Trypanosoma cruzi whole-cell dataset (ET (cryo))","paper_title":"On the ultrastructural organization of Trypanosoma cruzi using cryopreparation methods and electron tomography.","year":2012,"source":"Histochemistry and Cell Biology","source_type":"paper","public_data_status":"none","species":"Trypanosoma cruzi","cell_type":"Trypanosoma cruzi","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"ET (cryo)","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":135.0,"isotropic":null,"organelles":["nucleus","vacuole/lysosome","flagella/cilia"],"organelle_pairs":["flagella/cilia:nucleus","flagella/cilia:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["count"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"(M&M mentions \"35 tomograms (appox. 25 from epimastigotes and 10 from amastigotes and epimastigotes)\"","source_study_id":"Girard-Dias 2012","publication_pmid":"22872316","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/22872316/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"medeiros-2012-011","title":"Plasmodium chaubadi whole-cell dataset (FIB-SEM)","paper_title":"Visualizing the 3D architecture of multiple erythrocytes infected with Plasmodium at nanoscale by focused ion beam-scanning electron microscopy.","year":2012,"source":"PLoS One","source_type":"paper","public_data_status":"none","species":"Plasmodium chaubadi","cell_type":"Plasmodium chaubadi","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":4.785,"axial_resolution_nm":4.785,"isotropic":true,"organelles":["nucleus","vacuole/lysosome"],"organelle_pairs":["nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","count","surface_area"],"sample_size":10,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"10 quantified (Table 1); 1 or 2 whole cell images","source_study_id":"Medeiros 2012","publication_pmid":"22432024","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/22432024/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"paredes-santos-2012-018","title":"Toxoplasma gondii whole-cell dataset (FIB-SEM)","paper_title":"Dynamics and 3D organization of secretory organelles of Toxoplasma gondii.","year":2012,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"none","species":"Toxoplasma gondii","cell_type":"Toxoplasma gondii","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":25.0,"axial_resolution_nm":25.0,"isotropic":true,"organelles":["other: secretory organelles (microneme","rhoptry","dense granules)","conoid"],"organelle_pairs":["conoid:dense granules)","conoid:other: secretory organelles (microneme","conoid:rhoptry","dense granules):other: secretory organelles (microneme","dense granules):rhoptry","other: secretory organelles (microneme:rhoptry"],"metric_families":["other"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"2 reconstructions stated, 1 full 3D model visualized","source_study_id":"Paredes-Santos 2012","publication_pmid":"22155668","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/22155668/","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":"murphy-2011-109","title":"T cell whole-cell dataset (FIB-SEM)","paper_title":"Correlative 3D imaging of whole mammalian cells with light and electron microscopy.","year":2011,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"none","species":"T cell","cell_type":"T cell","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":21.0,"axial_resolution_nm":21.0,"isotropic":true,"organelles":["nucleus","mitochondria"],"organelle_pairs":["mitochondria:nucleus"],"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":"Murphy 2011","publication_pmid":"21907806","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/21907806/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"ramos-2011-007","title":"Trypanosoma cruzi whole-cell dataset (ssTEM)","paper_title":"Three-dimensional reconstruction of Trypanosoma cruzi epimastigotes and organelle distribution along the cell division cycle.","year":2011,"source":"Cytometry A","source_type":"paper","public_data_status":"none","species":"Trypanosoma cruzi","cell_type":"Trypanosoma cruzi","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":200.0,"axial_resolution_nm":200.0,"isotropic":true,"organelles":["nucleus","mitochondria","vesicles","flagella/cilia"],"organelle_pairs":["flagella/cilia:mitochondria","flagella/cilia:nucleus","flagella/cilia:vesicles","mitochondria:nucleus","mitochondria:vesicles","nucleus:vesicles"],"metric_families":["volume","count"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Ramos 2011","publication_pmid":"21567937","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/21567937/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"yamaguchi-2011-067","title":"Saccharomyces cerevisiae whole-cell dataset (ssTEM)","paper_title":"Structome of Saccharomyces cerevisiae determined by freeze-substitution and serial ultrathin-sectioning electron microscopy.","year":2011,"source":"J Electron Microsc (Tokyo)","source_type":"paper","public_data_status":"none","species":"Saccharomyces cerevisiae","cell_type":"Saccharomyces cerevisiae","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":30.0,"axial_resolution_nm":30.0,"isotropic":true,"organelles":["er","mitochondria","vacuole/lysosome","vesicles"],"organelle_pairs":["er:mitochondria","er:vacuole/lysosome","er:vesicles","mitochondria:vacuole/lysosome","mitochondria:vesicles","vacuole/lysosome:vesicles"],"metric_families":["volume","volume_fraction","dimensions","count","distance","contacts"],"sample_size":6,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"(3 G1, 3 early G1)","source_study_id":"Yamaguchi 2011","publication_pmid":"21908548","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/21908548/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"hanssen-2010-019","title":"Plasmodium falciparum whole-cell dataset (ET (cryo))","paper_title":"Ultrastructure of the asexual blood stages of Plasmodium falciparum.","year":2010,"source":"Methods in Cell Biology","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":"ET (cryo)","modality_family":"EM","lateral_resolution_nm":1.63,"axial_resolution_nm":300.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome"],"organelle_pairs":["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":"Hanssen 2010","publication_pmid":"20869520","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/20869520/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"motta-2010-015","title":"Crithidia deanei whole-cell dataset (FIB-SEM)","paper_title":"The bacterium endosymbiont of Crithidia deanei undergoes coordinated division with the host cell nucleus.","year":2010,"source":"PLoS ONE","source_type":"paper","public_data_status":"none","species":"Crithidia deanei","cell_type":"Crithidia deanei","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":113.5,"isotropic":null,"organelles":["nucleus","flagella/cilia"],"organelle_pairs":["flagella/cilia:nucleus"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"\"The description of events and timings in the C. deanei cell cycle were based on counts of 1000 cells.\"","source_study_id":"Motta 2010","publication_pmid":"20865129","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/20865129/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"heymann-2009-110","title":"MNT-1 (melanoma) whole-cell dataset (FIB-SEM (IA-SEM))","paper_title":"3D imaging of mammalian cells with ion-abrasion scanning electron microscopy.","year":2009,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"none","species":"Human (cancer)","cell_type":"MNT-1 (melanoma)","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"FIB-SEM (IA-SEM)","modality_family":"EM","lateral_resolution_nm":12.0,"axial_resolution_nm":30.0,"isotropic":false,"organelles":["nucleus","er","mitochondria"],"organelle_pairs":["er:mitochondria","er:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","density","shape"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Heymann 2009","publication_pmid":"19116171","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/19116171/","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":"ferreira-2008-005","title":"Trypanosoma cruzi whole-cell dataset (ssTEM)","paper_title":"Active transcription and ultrastructural changes during Trypanosoma cruzi metacyclogenesis.","year":2008,"source":"Annals of the Brazilian Academy of Sciences","source_type":"paper","public_data_status":"none","species":"Trypanosoma cruzi","cell_type":"Trypanosoma cruzi","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":null,"axial_resolution_nm":null,"isotropic":null,"organelles":["nucleus","flagella/cilia"],"organelle_pairs":["flagella/cilia:nucleus"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.85,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Ferreira 2008","publication_pmid":"18345384","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/18345384/","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"},{"dataset_id":"perktold-2007-061","title":"Saccharomyces cerevisiae whole-cell dataset (ssTEM)","paper_title":"Organelle association visualized by three-dimensional ultrastructural imaging of the yeast cell","year":2007,"source":"FEMS Yeast Res","source_type":"paper","public_data_status":"none","species":"Saccharomyces cerevisiae","cell_type":"Saccharomyces cerevisiae","tissue_or_system":null,"comparator_class":"methodology","comparator_detail":"Methodology","modality":"ssTEM","modality_family":"EM","lateral_resolution_nm":30.0,"axial_resolution_nm":80.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","vacuole/lysosome","lipid droplets"],"organelle_pairs":["er:lipid droplets","er:mitochondria","er:nucleus","er:vacuole/lysosome","lipid droplets:mitochondria","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","count","surface_area","distance","contacts"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"at least one chemically fixed and one cryofixed","source_study_id":"Perktold 2007","publication_pmid":"17419771","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/17419771/","public_locator_urls":[],"included_status":"included"}]