[{"dataset_id":"bianco-2023-055","title":"Saccharomyces cerevisiae whole-cell dataset (Optical tomography (phase contrast))","paper_title":"Label-Free Intracellular Multi-Specificity in Yeast Cells by Phase-Contrast Tomographic Flow Cytometry.","year":2023,"source":"Small Methods","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":"Optical tomography (phase contrast)","modality_family":"optical","lateral_resolution_nm":0.5,"axial_resolution_nm":null,"isotropic":null,"organelles":["nucleus","vacuole/lysosome"],"organelle_pairs":["nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","dimensions","surface_area","distance","contacts","density","shape","other"],"sample_size":4,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Bianco 2023","publication_pmid":"37670547","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37670547/","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":"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":"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":"umemura-2020-034","title":"Cylindrotheca sp. whole-cell dataset (Optical tomography (diffraction))","paper_title":"Label-free imaging and analysis of subcellular parts of a living diatom cylindrotheca sp. using optical diffraction tomography.","year":2020,"source":"MethodsX","source_type":"paper","public_data_status":"none","species":"Cylindrotheca sp.","cell_type":"Cylindrotheca sp.","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"Optical tomography (diffraction)","modality_family":"optical","lateral_resolution_nm":100.0,"axial_resolution_nm":360.0,"isotropic":false,"organelles":["vacuole/lysosome","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:vacuole/lysosome"],"metric_families":["volume","surface_area","density","shape","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Umemura 2020","publication_pmid":"32382522","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/32382522/","public_locator_urls":[],"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":"liu-2018-070","title":"Candida utilis whole-cell dataset (SXT)","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Candida utilis","cell_type":"Candida utilis","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"SXT","modality_family":"X-ray","lateral_resolution_nm":30.0,"axial_resolution_nm":30.0,"isotropic":true,"organelles":["nucleus","mitochondria","vacuole/lysosome","lipid droplets"],"organelle_pairs":["lipid droplets:mitochondria","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","mitochondria:nucleus","mitochondria:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","other"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 G1 and 1 budding","source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"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-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":"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"}]