[{"dataset_id":"kichuk-2024-058","title":"Saccharomyces cerevisiae whole-cell dataset (Fluorescence)","paper_title":"Using MitER for 3D analysis of mitochondrial morphology and ER contacts.","year":2024,"source":"Cell Reports Methods","source_type":"paper","public_data_status":"none","species":"Saccharomyces cerevisiae","cell_type":"Saccharomyces cerevisiae","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State","modality":"Fluorescence","modality_family":"optical","lateral_resolution_nm":141.0,"axial_resolution_nm":373.0,"isotropic":false,"organelles":["nucleus","er","mitochondria"],"organelle_pairs":["er:mitochondria","er:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","surface_area","distance","contacts"],"sample_size":90,"sample_size_bucket":"51+","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Kichuk 2024","publication_pmid":"38232737","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/38232737/","public_locator_urls":[],"included_status":"included"},{"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":"cho-2023-118","title":"HeLa whole-cell dataset (Optical tomography (diffraction))","paper_title":"Influence of Chemical and Genetic Manipulations on Cellular Organelles Quantified by Label-Free Optical Diffraction Tomography.","year":2023,"source":"Analytical Chemistry","source_type":"paper","public_data_status":"none","species":"Human (cancer)","cell_type":"HeLa","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"Optical tomography (diffraction)","modality_family":"optical","lateral_resolution_nm":110.0,"axial_resolution_nm":365.0,"isotropic":false,"organelles":["nucleus","autophagosome"],"organelle_pairs":["autophagosome:nucleus"],"metric_families":["other"],"sample_size":2,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"(nucleus + autophagosome, Fig 5C, originally thought we'd include Fig 7 but cells appear to be cut off)","source_study_id":"Cho 2023","publication_pmid":"37523497","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37523497/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"koutsogiannis-2023-017","title":"Toxoplasma gondii whole-cell dataset (Optical tomography (diffraction))","paper_title":"Assessment of Toxoplasma gondii lytic cycle and the impact of a gene deletion using 3D label-free optical diffraction holotomography.","year":2023,"source":"Frontiers in Cellular and Infection Microbiology","source_type":"paper","public_data_status":"none","species":"Toxoplasma gondii","cell_type":"Toxoplasma gondii","tissue_or_system":null,"comparator_class":"cell type","comparator_detail":"Cell Type/Species","modality":"Optical tomography (diffraction)","modality_family":"optical","lateral_resolution_nm":null,"axial_resolution_nm":null,"isotropic":null,"organelles":["nucleus"],"organelle_pairs":[],"metric_families":["volume","surface_area","other"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":0.85,"whole_cell_boundary_confirmed":"yes","notes":"1 WT, 2 cerS1 mutant","source_study_id":"Koutsogiannis 2023","publication_pmid":"37600951","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37600951/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"mirasole-2023-050","title":"Arabidopsis thaliana, guard cell whole-cell dataset (Fluorescence)","paper_title":"Vacuolar control of stomatal opening revealed by 3D imaging of the guard cells.","year":2023,"source":"Scientific Reports","source_type":"paper","public_data_status":"none","species":"Arabidopsis thaliana","cell_type":"Arabidopsis thaliana, guard cell","tissue_or_system":null,"comparator_class":"treatment","comparator_detail":"Stressors; Other: osmo/ion flux","modality":"Fluorescence","modality_family":"optical","lateral_resolution_nm":120.0,"axial_resolution_nm":285.0,"isotropic":false,"organelles":["nucleus","vacuole/lysosome","chloroplast/plastid"],"organelle_pairs":["chloroplast/plastid:nucleus","chloroplast/plastid:vacuole/lysosome","nucleus:vacuole/lysosome"],"metric_families":["volume","volume_fraction","shape"],"sample_size":10,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Mirasole 2023","publication_pmid":"37169939","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37169939/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wang-2023-103","title":"MCF10A (breast epithelia) whole-cell dataset (Fluorescence)","paper_title":"Spatial topology of organelle is a new breast cancer cell classifier.","year":2023,"source":"iScience","source_type":"paper","public_data_status":"none","species":"Human (differentiated)","cell_type":"MCF10A (breast epithelia)","tissue_or_system":null,"comparator_class":"methodology","comparator_detail":"Cell Type/Species; Methodology","modality":"Fluorescence","modality_family":"optical","lateral_resolution_nm":40.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","mitochondria","early endosome"],"organelle_pairs":["early endosome:mitochondria","early endosome:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area","distance","contacts","shape"],"sample_size":20,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Wang 2023","publication_pmid":"37519903","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37519903/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wang-2023-112","title":"MDA231 (breast cancer) whole-cell dataset (Fluorescence)","paper_title":"Spatial topology of organelle is a new breast cancer cell classifier.","year":2023,"source":"iScience","source_type":"paper","public_data_status":"none","species":"Human (cancer)","cell_type":"MDA231 (breast cancer)","tissue_or_system":null,"comparator_class":"methodology","comparator_detail":"Cell Type/Species; Methodology","modality":"Fluorescence","modality_family":"optical","lateral_resolution_nm":40.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","mitochondria","early endosome"],"organelle_pairs":["early endosome:mitochondria","early endosome:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area","distance","contacts","shape"],"sample_size":20,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"10 cells per 4 cell lines per 2 culture conditions","source_study_id":"Wang 2023","publication_pmid":"37519903","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37519903/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wang-2023-113","title":"T47D (breast cancer) whole-cell dataset (Fluorescence)","paper_title":"Spatial topology of organelle is a new breast cancer cell classifier.","year":2023,"source":"iScience","source_type":"paper","public_data_status":"none","species":"Human (cancer)","cell_type":"T47D (breast cancer)","tissue_or_system":null,"comparator_class":"methodology","comparator_detail":"Cell Type/Species; Methodology","modality":"Fluorescence","modality_family":"optical","lateral_resolution_nm":40.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","mitochondria","early endosome"],"organelle_pairs":["early endosome:mitochondria","early endosome:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area","distance","contacts","shape"],"sample_size":20,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Wang 2023","publication_pmid":"37519903","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37519903/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"wang-2023-114","title":"AU565 (breast cancer) whole-cell dataset (Fluorescence)","paper_title":"Spatial topology of organelle is a new breast cancer cell classifier.","year":2023,"source":"iScience","source_type":"paper","public_data_status":"none","species":"Human (cancer)","cell_type":"AU565 (breast cancer)","tissue_or_system":null,"comparator_class":"methodology","comparator_detail":"Cell Type/Species; Methodology","modality":"Fluorescence","modality_family":"optical","lateral_resolution_nm":40.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","mitochondria","early endosome"],"organelle_pairs":["early endosome:mitochondria","early endosome:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","dimensions","count","surface_area","distance","contacts","shape"],"sample_size":20,"sample_size_bucket":"11-50","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Wang 2023","publication_pmid":"37519903","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/37519903/","public_locator_urls":[],"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":"liu-2018-078","title":"Danio rerio, neural progenitor cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, neural progenitor cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":"1 of each cell type (see below); 3 time points for zebrafish neural progenitor","source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"liu-2018-079","title":"Danio rerio, lens cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, lens cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"liu-2018-080","title":"Danio rerio, skin cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, skin cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"liu-2018-083","title":"Danio rerio, retinal neuroepithelial cell whole-cell dataset (Fluorescence (AO-LLSM))","paper_title":"Quantitative imaging of Candida utilis and its organelles by soft X-ray Nano-CT.","year":2018,"source":"Journal of Microscopy","source_type":"paper","public_data_status":"none","species":"Danio rerio","cell_type":"Danio rerio, retinal neuroepithelial cell","tissue_or_system":null,"comparator_class":"cell cycle","comparator_detail":"Cell Cycle","modality":"Fluorescence (AO-LLSM)","modality_family":"optical","lateral_resolution_nm":97.0,"axial_resolution_nm":200.0,"isotropic":false,"organelles":["nucleus","er","mitochondria","golgi"],"organelle_pairs":["er:golgi","er:mitochondria","er:nucleus","golgi:mitochondria","golgi:nucleus","mitochondria:nucleus"],"metric_families":["volume","volume_fraction","other"],"sample_size":3,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Liu 2018","publication_pmid":"28960304","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28960304/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"kelbauskas-2017-096","title":"J774A.1 (M. musculus) whole-cell dataset (Optical tomography (LCCT))","paper_title":"Optical computed tomography for spatially isotropic four-dimensional imaging of live single cells.","year":2017,"source":"Science Advances","source_type":"paper","public_data_status":"none","species":"Rodent","cell_type":"J774A.1 (M. musculus)","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"Optical tomography (LCCT)","modality_family":"optical","lateral_resolution_nm":311.0,"axial_resolution_nm":266.0,"isotropic":true,"organelles":["nucleus","mitochondria"],"organelle_pairs":["mitochondria:nucleus"],"metric_families":["volume"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Kelbauskas 2017","publication_pmid":"29226240","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/29226240/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"kelbauskas-2017-115","title":"K562 (leukemia) whole-cell dataset (Optical tomography (LCCT))","paper_title":"Optical computed tomography for spatially isotropic four-dimensional imaging of live single cells.","year":2017,"source":"Science Advances","source_type":"paper","public_data_status":"none","species":"Human (cancer)","cell_type":"K562 (leukemia)","tissue_or_system":null,"comparator_class":null,"comparator_detail":null,"modality":"Optical tomography (LCCT)","modality_family":"optical","lateral_resolution_nm":311.0,"axial_resolution_nm":266.0,"isotropic":true,"organelles":["nucleus","mitochondria"],"organelle_pairs":["mitochondria:nucleus"],"metric_families":["volume"],"sample_size":1,"sample_size_bucket":"1","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Kelbauskas 2017","publication_pmid":"29226240","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/29226240/","public_locator_urls":[],"included_status":"included"},{"dataset_id":"valm-2017-100","title":"COS-7 (Cercopithecus aethiops) whole-cell dataset (Fluorescence (LLS))","paper_title":"Applying systems-level spectral imaging and analysis to reveal the organelle interactome","year":2017,"source":"Nature","source_type":"paper","public_data_status":"none","species":"NHP","cell_type":"COS-7 (Cercopithecus aethiops)","tissue_or_system":null,"comparator_class":"metabolic condition","comparator_detail":"Metabolic State; Stressors; Methodology","modality":"Fluorescence (LLS)","modality_family":"optical","lateral_resolution_nm":334.5,"axial_resolution_nm":798.0,"isotropic":false,"organelles":["er","mitochondria","vacuole/lysosome","lipid droplets","peroxisome","golgi"],"organelle_pairs":["er:golgi","er:lipid droplets","er:mitochondria","er:peroxisome","er:vacuole/lysosome","golgi:lipid droplets","golgi:mitochondria","golgi:peroxisome","golgi:vacuole/lysosome","lipid droplets:mitochondria","lipid droplets:peroxisome","lipid droplets:vacuole/lysosome","mitochondria:peroxisome","mitochondria:vacuole/lysosome","peroxisome:vacuole/lysosome"],"metric_families":["volume","volume_fraction","count","distance","contacts"],"sample_size":10,"sample_size_bucket":"2-10","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Valm 2017","publication_pmid":"28538724","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/28538724/","public_locator_urls":[],"included_status":"included"}]