[{"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":"johkura-2022-090","title":"R. norvegicus, hepatocyte whole-cell dataset (SBF-SEM)","paper_title":"Whole-cell observation of ZIO-stained Golgi apparatus in rat hepatocytes with serial block-face scanning electron microscope, SBF-SEM.","year":2022,"source":"Microscopy","source_type":"paper","public_data_status":"none","species":"R. norvegicus","cell_type":"R. norvegicus, hepatocyte","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species; Other","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":10.0,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","golgi"],"organelle_pairs":["golgi:nucleus"],"metric_families":["volume","volume_fraction","count","surface_area"],"sample_size":8,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"4 single-nuc, 4 binuc","source_study_id":"Johkura 2022","publication_pmid":"35535544","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35535544/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"muller-2021-094","title":"M. musculus, beta cell whole-cell dataset (FIB-SEM)","paper_title":"3D FIB-SEM reconstruction of microtubule-organelle interaction in whole primary mouse Î² 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":"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"}]