Dataset stringlengths 13 214 | Experiment stringlengths 14 76 | Dataset DOI / URL stringlengths 32 128 | Grouping stringclasses 3
values | 2D images int64 0 5.2k | 3D acquisitions int64 0 358 | Training tiles int64 0 17.6k |
|---|---|---|---|---|---|---|
Subcellular connectomic analyses of energy networks in striated muscle | Mouse Striated Muscle Mitochondrial Network FIB-SEM | https://zenodo.org/records/3936061 | Public | 0 | 3 | 118 |
HuaLab Mouse Testis Tissue | Mouse Testis SBF-SEM | https://doi.org/10.6019/EMPIAR-12535 | Public | 0 | 1 | 33 |
Mouse thymus FIB-SEM volume (jrc_mus-thymus-2a) | Mouse Thymus FIB-SEM | https://openorganelle.janelia.org/datasets/jrc_mus-thymus-2a | Public | 0 | 1 | 0 |
ATUM-Tomo: A multi-scale approach to cellular ultrastructure by combined volume scanning electron microscopy and electron tomography | Mouse Traumatic Brain Injury Cortex Correlative ATUM-Tomo | https://doi.org/10.6019/S-BIAD1274 | Public | 0 | 6 | 1,259 |
Venous puncture wound thrombi, 1, 5, 20 min post-puncture, 100 nm XY raw images, 20 nm XY pixels every 20 micons, 3 nm wide area TEM montages at selected depth | Mouse Venous Puncture Thrombus SBF-SEM | https://doi.org/10.6019/EMPIAR-10785 | Public | 0 | 18 | 3,820 |
Mouse V1 ssTEM Volume | Mouse Visual Cortex Connectomics TEM | https://webknossos.org/datasets/lee16-5c61b71c0100003f3b177de3/view | Public | 0 | 1 | 400 |
Mouse dLGN ATUM-SEM Volume - WEBKNOSSOS | Mouse Visual Thalamus (dLGN) Serial-Section SEM | https://webknossos.org/datasets/morgan2020-6373490b01000026011a53f7/view | Public | 0 | 1 | 400 |
Mouse dLGN Serial-Section EM Volume - BossDB | Mouse Visual Thalamus (dLGN) Serial-Section SEM | https://doi.org/10.60533/BOSS-2020-OMCN | Public | 0 | 1 | 400 |
NIH-3T3 Control & OPA1-KD FIB-SEM Volumes | NIH-3T3 Mitochondrial Cristae Control & OPA1 Knockdown FIB-SEM | https://doi.org/10.6019/EMPIAR-11449 | Public | 0 | 3 | 226 |
Nematode pharyngeal connectome ssTEM (BossDB) | Nematode Pharyngeal Connectome TEM | https://doi.org/10.60533/BOSS-2013-XKV2 | Public | 0 | 2 | 593 |
P. pacificus pharynx ssTEM volume (webKnossos) | Nematode Pharyngeal Connectome TEM | https://webknossos.org/datasets/bumbarger13-5ca4dd07010000a02931d708/view | Public | 0 | 1 | 611 |
Focused Ion Beam - Scanning Electron Microscopy volume of the aboral pole of a Nematostella Vectensis polyp | Nematostella vectensis Aboral Pole FIB-SEM | https://doi.org/10.6019/EMPIAR-13099 | Public | 0 | 1 | 72 |
Nocodazole-Treated HeLa Cell FIB-SEM Volume (jrc_hela-nz-1) | Nocodazole-Treated HeLa Cell FIB-SEM | https://doi.org/10.25378/janelia.24944784 | Public | 0 | 1 | 400 |
Nocodazole-Treated HeLa Cell FIB-SEM Volume (jrc_hela-nz-2) | Nocodazole-Treated HeLa Cell FIB-SEM (jrc_hela-nz-2) | https://openorganelle.janelia.org/datasets/jrc_hela-nz-2 | Public | 0 | 1 | 400 |
3D reconstruction of structures of hatched larva and young juvenile of the larvacean Oikopleura dioica using SBF-SEM. - Juvenile | Oikopleura dioica SBF-SEM | https://doi.org/10.5061/dryad.d51c5b012 | Public | 0 | 1 | 400 |
Serial section images of Oikopleura dioica larva using SBF-SEM - Larva | Oikopleura dioica SBF-SEM | https://doi.org/10.5061/dryad.dbrv15dzh | Public | 0 | 1 | 400 |
P7 Mouse Heart FIB-SEM Volume | P7 Mouse Heart FIB-SEM | https://doi.org/10.25378/janelia.24020919 | Public | 0 | 1 | 399 |
P7 Mouse Hippocampus FIB-SEM Volume | P7 Mouse Hippocampus FIB-SEM | https://doi.org/10.25378/janelia.24085176 | Public | 0 | 1 | 400 |
P7 Mouse Kidney | P7 Mouse Kidney FIB-SEM | https://doi.org/10.25378/janelia.24020799 | Public | 0 | 1 | 400 |
P7 Mouse Liver | P7 Mouse Liver FIB-SEM | https://doi.org/10.25378/janelia.24051189 | Public | 0 | 1 | 400 |
P7 Mouse Pancreas | P7 Mouse Pancreas FIB-SEM | https://doi.org/10.25378/janelia.23411843 | Public | 0 | 1 | 400 |
P7 Mouse Skin | P7 Mouse Skin FIB-SEM | https://doi.org/10.25378/janelia.24085269 | Public | 0 | 1 | 400 |
P7 Mouse Thymus | P7 Mouse Thymus FIB-SEM | https://doi.org/10.25378/janelia.24085287 | Public | 0 | 1 | 400 |
Paramecium Macronucleus TEM | Paramecium Macronucleus TEM | https://doi.org/10.6075/j0nz86k4 | Public | 1 | 0 | 4 |
Cytoklepty in the plankton: a host strategy to optimize the bioenergetic machinery of endosymbiotic algae | Phaeocystis-Acantharia Photosymbiosis FIB-SEM | https://doi.org/10.6019/EMPIAR-10672 | Public | 0 | 8 | 48 |
Data from: Phylogenetic distribution and expression pattern analyses identified a divergent basal body assembly protein involved in land plant spermatogenesis | Physcomitrium patens Spermatid TEM | https://doi.org/10.5281/zenodo.6546077 | Public | 0 | 3 | 6 |
FIB-SEM of Gemmata obscuriglobus - a species of the Planctomycetes phylum | Planctomycetes Bacteria FIB-SEM | https://doi.org/10.6019/EMPIAR-10553 | Public | 0 | 1 | 0 |
Tuwongella immobilis FIB-SEM Volume | Planctomycetes Bacteria FIB-SEM | https://doi.org/10.6019/EMPIAR-10554 | Public | 0 | 1 | 100 |
Plantorganelle Hunter EM images | Plant Leaf Organelle TEM | https://doi.org/10.57760/sciencedb.01335 | Public | 929 | 0 | 2,459 |
Potato virus Y coat protein involvement in viral movement | Plant Leaf Potato Virus Y Movement TEM | https://doi.org/10.5281/zenodo.17643798 | Public | 100 | 0 | 385 |
Plasmodium berghei Male Gamete SBF-SEM | Plasmodium berghei Male Gamete Formation SBF-SEM | https://doi.org/10.6019/EMPIAR-11710 | Public | 0 | 2 | 800 |
Plasmodium berghei ookinete | Plasmodium berghei Ookinete FIB-SEM | https://doi.org/10.6019/EMPIAR-12956 | Public | 0 | 1 | 24 |
Cellular Hallmarks from Volume Electron Microscopy reveals Developmental Progression of Plasmodium Ookinetes | Plasmodium berghei Ookinete SBF-SEM | https://doi.org/10.6019/EMPIAR-12951 | Public | 0 | 23 | 146 |
Comparative 3D ultrastructure of Plasmodium falciparum gametocytes | Plasmodium falciparum Gametocyte 3D Ultrastructure FIB-SEM | https://doi.org/10.6019/EMPIAR-12160 | Public | 0 | 24 | 2,868 |
SBF-SEM of early schizont-stage malaria parasite infected red blood cell | Plasmodium falciparum-Infected Red Blood Cell SBF-SEM | https://doi.org/10.6019/EMPIAR-10054 | Public | 0 | 1 | 14 |
SBF-SEM of late schizont-stage malaria parasite infected red blood cell | Plasmodium falciparum-Infected Red Blood Cell SBF-SEM | https://doi.org/10.6019/EMPIAR-10055 | Public | 0 | 1 | 15 |
SBF-SEM of ring-stage malaria parasite infected red blood cell | Plasmodium falciparum-Infected Red Blood Cell SBF-SEM | https://doi.org/10.6019/EMPIAR-10052 | Public | 0 | 1 | 20 |
SBF-SEM of trophozoite-stage malaria parasite infected red blood cell | Plasmodium falciparum-Infected Red Blood Cell SBF-SEM | https://doi.org/10.6019/EMPIAR-10053 | Public | 0 | 1 | 19 |
SBF-SEM datasets of chaetoblasts constructing bristles in Platynereis dumerilii | Platynereis dumerilii Chaetoblast SBF-SEM | https://doi.org/10.6019/EMPIAR-11851 | Public | 0 | 3 | 734 |
Data from: A serial multiplex immunogold labeling method for identifying peptidergic neurons in connectomes | Platynereis dumerilii Nerve Cord siGOLD Immunogold TEM | https://doi.org/10.5061/dryad.c7366 | Public | 12 | 0 | 258 |
FIB-SEM of parapodia from Platynereis dumerilii | Platynereis dumerilii Parapodia FIB-SEM | https://doi.org/10.6019/EMPIAR-10310 | Public | 0 | 1 | 0 |
Whole-body integration of gene expression and single-cell morphology | Platynereis dumerilii Whole-Body Larva SBF-SEM | https://doi.org/10.6019/EMPIAR-10365 | Public | 0 | 1 | 0 |
Fib-SEM stacks for Prey (Phaeocystis antarctica) and Host (Ross Sea Dinoflagellate; RSD) | Polar Plankton Organelle Hijacking FIB-SEM | https://doi.org/10.6019/EMPIAR-12627 | Public | 0 | 18 | 1,189 |
RAEM random-access electron microscopy for revisitable 3D imaging | RAEM Revisitable 3D Imaging SEM | https://doi.org/10.60533/boss-2026-mw96 | Public | 2 | 2 | 354 |
Rabbit Retina e1088 SBEM Volume | Rabbit Retina SBF-SEM | https://webknossos.org/datasets/e1088_large-5c010a3c010000f6145257c8/view | Public | 0 | 1 | 211 |
Denk and Horstmann 2004 rat cortex SBF-SEM | Rat Cerebral Cortex SBF-SEM | https://webknossos.org/datasets/denk2004-5bfd0b1c0100003f3574cc8e | Public | 0 | 1 | 24 |
Data for: Axonal Structure-Function relationships across experimental modalities | Rat Corpus Callosum Axon TEM | https://doi.org/10.5281/zenodo.17476529 | Public | 1 | 0 | 58 |
Harris 2015 Hippocampal Neuropil 3DEM - Apical Dendrite | Rat Hippocampal CA1 Neuropil TEM | https://webknossos.org/datasets/kharris15_apical-5c7e907c010000160cc8d8d0/view | Public | 0 | 1 | 185 |
Harris 2015 Hippocampal Neuropil 3DEM - Oblique Dendrite | Rat Hippocampal CA1 Neuropil TEM | https://webknossos.org/datasets/kharris15_oblique-5c7e907c010000790cc8d8cf/view | Public | 0 | 1 | 85 |
Harris 2015 Hippocampal Neuropil 3DEM - Spine | Rat Hippocampal CA1 Neuropil TEM | https://webknossos.org/datasets/kharris15_spine-5c7e907c010000c60bc8d8ce/view | Public | 0 | 1 | 21 |
Harris 2015 Rat Hippocampal CA1 Neuropil | Rat Hippocampal CA1 Neuropil TEM | https://doi.org/10.60533/BOSS-2015-GYEN | Public | 0 | 3 | 185 |
Dl-3-n-butylphthalide alleviates cognitive impairment induced by chronic cerebral hypoperfusion via inhibiting the mitochondrial permeability transition pore opening and excessive mitophagy | Rat Hippocampus Chronic Cerebral Hypoperfusion TEM | https://doi.org/10.5281/zenodo.14253010 | Public | 9 | 0 | 36 |
GLAM Rat Hippocampus Demo Bundle | Rat Hippocampus FIB-SEM | https://doi.org/10.5061/dryad.808k4r0 | Public | 0 | 1 | 0 |
Rat Medial Entorhinal Cortex P25 Motortile 1 | Rat Medial Entorhinal Cortex SBF-SEM | https://webknossos.org/datasets/HS_st218_MT1-5a7c738a48d7a73cea3c83c2/view | Public | 0 | 1 | 318 |
FAST-EM array tomography data of rat pancreas prepared with rOTO protocol and stained with neodymium acetate - EMPIAR-12174 (4x4 mosaics) | Rat Pancreas FAST-EM Array Tomography | https://doi.org/10.6019/EMPIAR-12174 | Public | 0 | 43 | 2,601 |
FAST-EM array tomography data of rat pancreas prepared with rOTO protocol and stained with neodymium acetate - EMPIAR-12193 (10x10 mosaics) | Rat Pancreas FAST-EM Array Tomography | https://doi.org/10.6019/EMPIAR-12193 | Public | 0 | 72 | 16,889 |
3D serial block-face scanning electron microscopy (SBF-SEM) imaging of a rat pelvic nerve - Volume 1 (Version 2) | Rat Pelvic Nerve SBF-SEM | https://doi.org/10.26275/8bbl-fzip | Public | 0 | 1 | 400 |
SARS-CoV-2-infected Vero Cell FIB-SEM Volume | SARS-CoV-2-Infected Vero Cell FIB-SEM | https://doi.org/10.25378/janelia.16638316 | Public | 0 | 1 | 318 |
Serial Block Face Scanning Electron Micrscopy dataset of fetal day 64 guinea pig psoas muscle in transverse | SBF-SEM Reconstruction Guide Example Volumes | https://doi.org/10.6019/EMPIAR-10092 | Public | 0 | 1 | 93 |
Serial Block Face Scanning Electron Micrscopy dataset of the optic lobe from an adult locust | SBF-SEM Reconstruction Guide Example Volumes | https://doi.org/10.6019/EMPIAR-10152 | Public | 0 | 1 | 240 |
SM WT1 8 nm Lysosome Combined FIB-SEM Volume | SM WT1 Lysosome FIB-SEM | https://webknossos.org/datasets/SM_WT1_8nm_lysosome_combined-661d83c20100008c0298c110/view | Public | 0 | 1 | 30 |
Mouse Brown Adipose Tissue WT & Smc5 K371/K371 SBF-SEM | SMC5 Mutant Mouse Brown Adipose Tissue SBF-SEM | https://doi.org/10.6019/EMPIAR-13505 | Public | 0 | 2 | 800 |
Immortalized breast cancer cell (SUM159) - jrc_sum159-1 | SUM159 Breast Cancer Cell FIB-SEM (jrc_sum159-1) | https://doi.org/10.25378/janelia.13114352 | Public | 0 | 1 | 187 |
Immortalized breast cancer cell (SUM159) - jrc_sum159-4 | SUM159 Breast Cancer Cell FIB-SEM (jrc_sum159-4) | https://doi.org/10.25378/janelia.20134103 | Public | 0 | 1 | 400 |
Adaptive traits of cysts of the snow alga Sanguina nivaloides unveiled by 3D subcellular imaging | Sanguina nivaloides Snow Alga Cyst FIB-SEM | https://doi.org/10.6019/EMPIAR-11694 | Public | 0 | 2 | 7 |
FIB/SEM sample dataset MCB-CLEM IV Weiner | Shigella flexneri HeLa Cell Invasion FIB-SEM | https://doi.org/10.6019/EMPIAR-10479 | Public | 0 | 1 | 12 |
Macrophage cell | THP-1 Macrophage FIB-SEM | https://doi.org/10.25378/janelia.13114343 | Public | 0 | 1 | 447 |
TEM Image Dataset for Mitochondrial Morphology Analysis in Chemotherapy Response and Cancer Metastasis Studies | TNBC Mitochondrial Chemotherapy-Response TEM | https://doi.org/10.5281/zenodo.15608455 | Public | 1,742 | 0 | 13,196 |
TEM Mitochondria Segmentation Dataset for Triple Negative Breast Cancer Chemotherapy Analysis | TNBC Mitochondrial Chemotherapy-Response TEM | https://doi.org/10.5281/zenodo.15602048 | Public | 209 | 0 | 1,442 |
Plant SBF-SEM - Tobacco Leaf Chloroplast | Tobacco Leaf Chloroplast SBF-SEM | https://doi.org/10.6019/EMPIAR-11831 | Public | 0 | 1 | 26 |
Processed FIB SEM images of a parasitophorous vacuole containing Toxoplasma gondii ΔCAP parasites | Toxoplasma gondii CAP Parasitophorous Vacuole FIB-SEM | https://doi.org/10.6019/EMPIAR-10324 | Public | 0 | 1 | 3 |
Processed FIB SEM images of a parasitophorous vacuole containing Toxoplasma gondii ΔCAP parasites, complemented with CAP | Toxoplasma gondii CAP Parasitophorous Vacuole FIB-SEM | https://doi.org/10.6019/EMPIAR-10327 | Public | 0 | 1 | 4 |
SBF-SEM of the Trichuris muris Stichosome | Trichuris muris Stichosome SBF-SEM | https://doi.org/10.5281/zenodo.3601280 | Public | 0 | 2 | 800 |
FIB-SEM dataset of a human bone osteosarcoma epithelial cell (U2-OS) | U2-OS Cell FIB-SEM | https://doi.org/10.6019/EMPIAR-11746 | Public | 0 | 1 | 48 |
FIB-SEM of U2OS cell at leading edge of a wound assay, LPA stimulated, polarized | U2-OS Cell Wound Assay Leading Edge FIB-SEM | https://doi.org/10.6019/EMPIAR-11002 | Public | 0 | 1 | 1 |
FIB-SEM of U2OS cell at leading edge of a wound assay, non-LPA stimulated, non-polarized | U2-OS Cell Wound-Assay Leading Edge FIB-SEM | https://doi.org/10.6019/EMPIAR-11003 | Public | 0 | 1 | 30 |
Cryo-FIB-SEM volume (ROI6) | U2OS Cell Mitochondrial Pearling Cryo-FIB-SEM | https://doi.org/10.5281/zenodo.17769238 | Public | 0 | 1 | 400 |
FIBSEM Run2 Feb 2026 pt1 | Unprovenanced FIB-SEM Volume (Run2 Feb 2026 pt1) | https://webknossos.org/datasets/FIBSEM_Run2_Feb2026_pt1-69814e310100009701047c11 | Public | 0 | 1 | 19 |
Vero Cell Culture Image Dataset | Vero E6 Cell Culture FBS Variation TEM | https://doi.org/10.5281/zenodo.17928456 | Public | 117 | 0 | 1,340 |
Electron tomography of endosymbiotic bacteria inside a bacteriocyte of the cereal weevil Sitophilus oryzae - EMPIAR-12198 | Weevil Bacteriocyte Endosymbiont Tubular Networks ET | https://doi.org/10.6019/EMPIAR-12198 | Public | 0 | 1 | 10 |
Electron tomography of endosymbiotic bacteria inside a bacteriocyte of the cereal weevil Sitophilus oryzae - EMPIAR-12602 | Weevil Bacteriocyte Endosymbiont Tubular Networks ET | https://doi.org/10.6019/EMPIAR-12602 | Public | 0 | 1 | 15 |
Zebra Finch Brain MagC Correlative Volumes | Zebra Finch Brain MagC Correlative SEM | https://doi.org/10.60533/BOSS-2019-B9NV | Public | 0 | 2 | 800 |
Zebra Finch HVC j0256 | Zebra Finch HVC SBF-SEM | https://webknossos.org/datasets/j0256-5c051f59010000b538527270/view | Public | 0 | 1 | 400 |
Array Tomography of zebrafish axillary lymphoid organ - an external, experimentally accessible immune organ in the zebrafish | Zebrafish Axillary Lymphoid Organ SEM | https://www.ebi.ac.uk/empiar/EMPIAR-12377/ | Public | 0 | 7 | 597 |
SBF SEM images of a Zebrafish hindbrain containing several Toxoplasma gondii tachizoites at different stages of replication | Zebrafish Hindbrain Toxoplasma Infection | https://doi.org/10.6019/EMPIAR-10463 | Public | 0 | 5 | 1,880 |
SBF SEM images of a Zebrafish hindbrain macrophage containing 2 Toxoplasma gondii tachizoites | Zebrafish Hindbrain Toxoplasma Infection | https://doi.org/10.6019/EMPIAR-10461 | Public | 0 | 3 | 490 |
TEM images of a Zebrafish hindbrain cells containing Toxoplasma gondii tachizoites | Zebrafish Hindbrain Toxoplasma Infection | https://doi.org/10.6019/EMPIAR-10460 | Public | 0 | 3 | 180 |
Zebrafish Hindbrain Macrophage SBF-SEM | Zebrafish Hindbrain Toxoplasma Infection | https://doi.org/10.6019/EMPIAR-10462 | Public | 0 | 2 | 800 |
Zebrafish Hindbrain ROI01 SBF-SEM | Zebrafish Hindbrain Toxoplasma Infection | https://doi.org/10.6019/EMPIAR-10464 | Public | 0 | 11 | 3,516 |
Zebrafish Macrophage FIB-SEM Volume | Zebrafish Hindbrain Toxoplasma Infection | https://doi.org/10.6019/EMPIAR-10459 | Public | 0 | 1 | 160 |
7 day post fertilization larval zebrafish cardiac tissue | Zebrafish Larval Heart FIB-SEM | https://doi.org/10.25378/janelia.22630519 | Public | 0 | 1 | 266 |
Larval Zebrafish Olfactory Bulb SBEM Volume | Zebrafish Larval Olfactory Bulb SBF-SEM | https://doi.org/10.60533/BOSS-2016-U6PR | Public | 0 | 1 | 359 |
Zebrafish lateral-line neuromast SBEM - N1 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_N1-5b4238a61d00004b1d1ab5e2/view | Public | 0 | 1 | 389 |
Zebrafish lateral-line neuromast SBEM - N2 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_N2-5b4238a61d0000c42a1ab5e4/view | Public | 0 | 2 | 658 |
Zebrafish lateral-line neuromast SBEM - T1 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_T1-5b3ce7bb1d0000340240b91b/view | Public | 0 | 1 | 231 |
Zebrafish lateral-line neuromast SBEM - T3 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_T3-5b4238a61d0000c42a1ab5e3/view | Public | 0 | 1 | 216 |
Zebrafish lateral-line neuromast SBEM - T4 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_T4-5b4238a61d0000c42a1ab5e5/view | Public | 0 | 1 | 585 |
Zebrafish lateral-line neuromast SBEM - WT1 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_WT1-5b3ce7bb1d0000340240b921/view | Public | 0 | 1 | 388 |
Zebrafish lateral-line neuromast SBEM - WT2 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_WT2-5b3ce7bb1d0000340240b923/view | Public | 0 | 1 | 366 |
Zebrafish lateral-line neuromast SBEM - WT7 | Zebrafish Lateral-Line Neuromast SBF-SEM | https://webknossos.org/datasets/Neuromast_WT7-5b3ce7bb1d0000340240b91c/view | Public | 0 | 1 | 183 |
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