[{"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":"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":"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":"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":"loconte-2022-088","title":"INS-1E (R. norvegicus) whole-cell dataset (SXT)","paper_title":"Soft X-ray tomography to map and quantify organelle interactions at the mesoscale.","year":2022,"source":"Structure","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","vesicles"],"organelle_pairs":["mitochondria:nucleus","mitochondria:vesicles","nucleus:vesicles"],"metric_families":["volume","volume_fraction","count","distance","contacts","density","other"],"sample_size":56,"sample_size_bucket":"51+","metadata_completeness_score":0.95,"whole_cell_boundary_confirmed":"yes","notes":null,"source_study_id":"Loconte 2022","publication_pmid":"35148829","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/35148829/","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":"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":"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/ Â 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":"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":"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"},{"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":"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":"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"}]