[{"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":"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":"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":"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":"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":"sakaguchi-2016-024","title":"Plasmodium falciparum whole-cell dataset (SBF-SEM)","paper_title":"Three-dimensional analysis of morphological changes in the malaria parasite infected red blood cell by serial block-face scanning electron microscopy.","year":2016,"source":"Journal of Structural Biology","source_type":"paper","public_data_status":"partial","species":"Plasmodium falciparum","cell_type":"Plasmodium falciparum","tissue_or_system":null,"comparator_class":"developmental stage","comparator_detail":"Other: developmental/life cycle stages","modality":"SBF-SEM","modality_family":"EM","lateral_resolution_nm":8.22,"axial_resolution_nm":70.0,"isotropic":false,"organelles":["nucleus","mitochondria","vacuole/lysosome","vesicles"],"organelle_pairs":["mitochondria:nucleus","mitochondria:vacuole/lysosome","mitochondria:vesicles","nucleus:vacuole/lysosome","nucleus:vesicles","vacuole/lysosome:vesicles"],"metric_families":["volume","volume_fraction","surface_area"],"sample_size":22,"sample_size_bucket":"11-50","metadata_completeness_score":1.0,"whole_cell_boundary_confirmed":"yes","notes":"Some public data available. 22 iRBCs, as well as 10 non-iRBCs which don't count becase they don't have organelles","source_study_id":"Sakaguchi 2016","publication_pmid":"26772147","source_publication_url":"https://pubmed.ncbi.nlm.nih.gov/26772147/","public_locator_urls":["https://www.ebi.ac.uk/empiar/EMPIAR-10052/","https://www.ebi.ac.uk/empiar/EMPIAR-10053/","https://www.ebi.ac.uk/empiar/EMPIAR-10054/","https://www.ebi.ac.uk/empiar/EMPIAR-10055/"],"included_status":"included"}]