[{"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":"xu-2024-043","title":"Chlamydomonas reinhartdii whole-cell dataset (SXT)","paper_title":"Near-Native Imaging of Label-Free Silver Nanoparticles-Triggered 3D Subcellular Ultrastructural Reorganization in Microalgae.","year":2024,"source":"ACS Nano","source_type":"paper","public_data_status":"none","species":"Chlamydomonas reinhartdii","cell_type":"Chlamydomonas reinhartdii","tissue_or_system":null,"comparator_class":"treatment","comparator_detail":"Stressors","modality":"SXT","modality_family":"X-ray","lateral_resolution_nm":30.0,"axial_resolution_nm":30.0,"isotropic":true,"organelles":["nucleus","er","vacuole/lysosome","lipid droplets","flagella/cilia"],"organelle_pairs":["er:flagella/cilia","er:lipid droplets","er:nucleus","er:vacuole/lysosome","flagella/cilia:lipid droplets","flagella/cilia:nucleus","flagella/cilia:vacuole/lysosome","lipid droplets:nucleus","lipid droplets:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction"],"sample_size":12,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"6 ctrl + 6 AgNP-treated","source_study_id":"Xu 2024","publication_pmid":"38198284","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/38198284/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"dang-2023-069","title":"Candida utilis whole-cell dataset (SXT)","paper_title":"Direct Visualization and Restoration of Metallic Ion-Induced Subcellular Ultrastructural Remodeling.","year":2023,"source":"ACS Nano","source_type":"paper","public_data_status":"none","species":"Candida utilis","cell_type":"Candida utilis","tissue_or_system":null,"comparator_class":"treatment","comparator_detail":"Stressors","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","count","density","shape"],"sample_size":40,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Dang 2023","publication_pmid":"37156644","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37156644/","public_locator_urls":[],"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":"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":"chen-2022-107","title":"B lymphocyte whole-cell dataset (SXT)","paper_title":"Soft X-ray Tomography Reveals HSV-1-Induced Remodeling of Human B Cells.","year":2022,"source":"Viruses","source_type":"paper","public_data_status":"none","species":"B lymphocyte","cell_type":"B lymphocyte","tissue_or_system":null,"comparator_class":"other","comparator_detail":"Other: N/A","modality":"SXT","modality_family":"X-ray","lateral_resolution_nm":60.0,"axial_resolution_nm":60.0,"isotropic":true,"organelles":["nucleus","mitochondria","lipid droplets"],"organelle_pairs":["lipid droplets:mitochondria","lipid droplets:nucleus","mitochondria:nucleus"],"metric_families":["other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"true whole-cell reconstruction","source_study_id":"Chen 2022","publication_pmid":"36560654","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/36560654/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"white-2020-089","title":"INS-1E (R. norvegicus) whole-cell dataset (SXT)","paper_title":"Visualizing subcellular rearrangements in intact Î² cells using soft x-ray tomography.","year":2020,"source":"Science Advances","source_type":"paper","public_data_status":"none","species":"Rodent","cell_type":"INS-1E (R. norvegicus)","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State","modality":"SXT","modality_family":"X-ray","lateral_resolution_nm":60.0,"axial_resolution_nm":60.0,"isotropic":true,"organelles":["nucleus","mitochondria","lipid droplets","vesicles"],"organelle_pairs":["lipid droplets:mitochondria","lipid droplets:nucleus","lipid droplets:vesicles","mitochondria:nucleus","mitochondria:vesicles","nucleus:vesicles"],"metric_families":["volume","volume_fraction","dimensions","count","distance","density"],"sample_size":40,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"8 x 5 conditions","source_study_id":"White 2020","publication_pmid":"33298443","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/33298443/","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":"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":"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":"diaz-2015-041","title":"Chlamydomonas reinhartdii whole-cell dataset (HXT (ptychography))","paper_title":"Three-dimensional mass density mapping of cellular ultrastructure by ptychographic X-ray nanotomography.","year":2015,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"none","species":"Chlamydomonas reinhartdii","cell_type":"Chlamydomonas reinhartdii","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"HXT (ptychography)","modality_family":"X-ray","lateral_resolution_nm":180.0,"axial_resolution_nm":180.0,"isotropic":true,"organelles":["nucleus","vacuole/lysosome","lipid droplets"],"organelle_pairs":["lipid droplets:nucleus","lipid droplets:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["density"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Diaz 2015","publication_pmid":"26470812","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/26470812/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"hummel-2012-042","title":"Chlamydomonas reinhartdii whole-cell dataset (SXT)","paper_title":"3D Ultrastructural Organization of Whole Chlamydomonas reinhardtii Cells Studied by Nanoscale Soft X-Ray Tomography","year":2012,"source":"PLoS One","source_type":"paper","public_data_status":"none","species":"Chlamydomonas reinhartdii","cell_type":"Chlamydomonas reinhartdii","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species; Other: 2 strains: WT CC125 & cw15+","modality":"SXT","modality_family":"X-ray","lateral_resolution_nm":40.0,"axial_resolution_nm":40.0,"isotropic":true,"organelles":["nucleus","mitochondria","vacuole/lysosome","lipid droplets","chloroplast/plastid","flagella/cilia"],"organelle_pairs":["chloroplast/plastid:flagella/cilia","chloroplast/plastid:lipid droplets","chloroplast/plastid:mitochondria","chloroplast/plastid:nucleus","chloroplast/plastid:vacuole/lysosome","flagella/cilia:lipid droplets","flagella/cilia:mitochondria","flagella/cilia:nucleus","flagella/cilia: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":14,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"(6 wt; 8 mutant)","source_study_id":"Hummel 2012","publication_pmid":"23300909","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/23300909/","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":"uchida-2011-062","title":"Saccharomyces cerevisiae whole-cell dataset (SXT)","paper_title":"Quantitative analysis of yeast internal architecture using soft X-ray tomography.","year":2011,"source":"Yeast","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; Cell Type/Species; Other: haploid/diploid, cell cycle stages, daughter/mother, WT strains (supp)","modality":"SXT","modality_family":"X-ray","lateral_resolution_nm":50.0,"axial_resolution_nm":50.0,"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","count","surface_area","density"],"sample_size":200,"sample_size_bucket":"51+","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Uchida 2011","publication_pmid":"21360734","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/21360734/","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":"uchida-2009-071","title":"Candida albicans whole-cell dataset (SXT)","paper_title":"Soft X-ray tomography of phenotypic switching and the cellular response to antifungal peptoids in Candida albicans.","year":2009,"source":"Proc Natl Acad Sci USA","source_type":"paper","public_data_status":"none","species":"Candida albicans","cell_type":"Candida albicans","tissue_or_system":null,"comparator_class":"treatment","comparator_detail":"Stressors; Other: stressor - peptoid. 3 cell morphologies - triggers unclear, could be caused by multiple conditions but M&M only states \"The phenotype was switched by modifying the growth conditions, as described in ref. 1.\" where ref 1 is a review article that describes a range of things.","modality":"SXT","modality_family":"X-ray","lateral_resolution_nm":50.0,"axial_resolution_nm":50.0,"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","density"],"sample_size":42,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"split between yeast-like and germ tube (life cycle)","source_study_id":"Uchida 2009","publication_pmid":"19880740","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/19880740/","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"}]