| Organelle,Source,Role,Train tiles,Val tiles,Test tiles,Total tiles,% of organelle tiles,Annotated crops,Dataset DOI / URL | |
| Mitochondria,CEM-MitoLab,Train/val,12868,0,0,12868,51.19,12868,https://doi.org/10.6019/EMPIAR-11037 | |
| Mitochondria,MitoEM 2.0,Train/val + benchmark,1736,155,55,1946,7.74,890,https://doi.org/10.5281/zenodo.17635006 | |
| Mitochondria,OrgSegNet / Plantorgan Hunter,Train/val + benchmark,1474,182,198,1854,7.38,993,https://doi.org/10.57760/sciencedb.01335 | |
| Mitochondria,DeepContact,Train/val + benchmark,1644,35,67,1746,6.95,244,https://doi.org/10.6084/m9.figshare.19898404 | |
| Mitochondria,In-house segmentations,Train/val,1029,31,0,1060,4.22,161, | |
| Mitochondria,Zenodo 15602048 (breast TEM),Train/val,1000,30,0,1030,4.1,142,https://doi.org/10.5281/zenodo.15602048 | |
| Mitochondria,Zenodo 17068504 (cardiomyocyte),Train/val,1000,6,0,1006,4,35,https://doi.org/10.5281/zenodo.17068504 | |
| Mitochondria,OpenOrganelle / CellMap (COSEM),Train/val,810,149,0,959,3.82,253,"https://doi.org/10.1038/s41586-021-03977-3, https://doi.org/10.1038/s41586-021-03992-4, https://openorganelle.janelia.org" | |
| Mitochondria,EMPIAR-13420 (macrophage / A431),Train/val,670,29,0,699,2.78,164,https://doi.org/10.6019/EMPIAR-13420 | |
| Mitochondria,EMPIAR-10994 (HeLa SBF-SEM),Train/val,566,18,0,584,2.32,72,https://doi.org/10.6019/EMPIAR-10994 | |
| Mitochondria,EMPIAR-13156 (HeLa STARD3),Train/val,353,17,0,370,1.47,84,https://doi.org/10.6019/EMPIAR-13156 | |
| Mitochondria,FAST-EM (TU Delft),Train/val,279,21,0,300,1.19,141,"https://doi.org/10.4121/bf3f2b23-2328-4d81-a0f4-05fdb33117d7, https://webknossos.tnw.tudelft.nl" | |
| Mitochondria,DeepPI-EM (skeletal muscle),Train/val + benchmark,186,2,6,194,0.77,27,"https://doi.org/10.1038/s41598-025-03311-1, https://github.com/LAIT-CVLab/DeepPI-EM" | |
| Mitochondria,EMPIAR-10982 (MitoNet benchmark),Benchmark (held-out test),0,0,192,192,0.76,192,https://doi.org/10.6019/EMPIAR-10982 | |
| Mitochondria,EMPIAR-12885 (AIVE),Train/val,155,12,0,167,0.66,65,https://doi.org/10.6019/EMPIAR-12885 | |
| Mitochondria,ASEM / incasem,Train/val,94,20,0,114,0.45,78,"https://doi.org/10.1083/jcb.202208005, s3://asem-project" | |
| Mitochondria,Guay et al. (platelet),Train/val,30,7,0,37,0.15,37,"https://doi.org/10.1038/s41598-021-81590-0, https://leapmanlab.github.io/dense-cell/" | |
| Mitochondria,EMPIAR-11746 (U-2 OS FIB-SEM),Train/val,10,1,0,11,0.04,11,"https://doi.org/10.6019/EMPIAR-11746, https://doi.org/10.5281/zenodo.10043461" | |
| Mitochondria,TOTAL,,23904,715,518,25137,100,16457, | |
| Endoplasmic reticulum,OpenOrganelle / CellMap (COSEM),Train/val,586,123,0,709,45.51,238,"https://doi.org/10.1038/s41586-021-03977-3, https://doi.org/10.1038/s41586-021-03992-4, https://openorganelle.janelia.org" | |
| Endoplasmic reticulum,EMPIAR-10791 (mouse liver ER),Train/val,152,28,0,180,11.55,180,https://doi.org/10.6019/EMPIAR-10791 | |
| Endoplasmic reticulum,EMPIAR-13420 (macrophage / A431),Train/val,130,40,0,170,10.91,170,https://doi.org/10.6019/EMPIAR-13420 | |
| Endoplasmic reticulum,In-house segmentations,Train/val + benchmark,8,1,135,144,9.24,144, | |
| Endoplasmic reticulum,DeepContact,Train/val + benchmark,59,24,11,94,6.03,94,https://doi.org/10.6084/m9.figshare.19898404 | |
| Endoplasmic reticulum,EMPIAR-13156 (HeLa STARD3),Benchmark (held-out test),0,0,84,84,5.39,84,https://doi.org/10.6019/EMPIAR-13156 | |
| Endoplasmic reticulum,EMPIAR-10994 (HeLa SBF-SEM),Benchmark (held-out test),0,0,74,74,4.75,74,https://doi.org/10.6019/EMPIAR-10994 | |
| Endoplasmic reticulum,EMPIAR-12885 (AIVE),Benchmark (held-out test),0,0,57,57,3.66,57,https://doi.org/10.6019/EMPIAR-12885 | |
| Endoplasmic reticulum,ASEM / incasem,Train/val,27,8,0,35,2.25,35,"https://doi.org/10.1083/jcb.202208005, s3://asem-project" | |
| Endoplasmic reticulum,EMPIAR-11746 (U-2 OS FIB-SEM),Train/val,7,4,0,11,0.71,11,"https://doi.org/10.6019/EMPIAR-11746, https://doi.org/10.5281/zenodo.10043461" | |
| Endoplasmic reticulum,TOTAL,,969,228,361,1558,100,1087, | |
| Nucleus,OrgSegNet / Plantorgan Hunter,Train/val + benchmark,216,58,65,339,26.51,339,https://doi.org/10.57760/sciencedb.01335 | |
| Nucleus,Platynereis atlas (Zenodo 3675220),Benchmark (held-out test),0,0,300,300,23.46,300,https://doi.org/10.5281/zenodo.3675220 | |
| Nucleus,S-BIAD2822 (NucleoNet),Benchmark (held-out test),0,0,219,219,17.12,219,"https://doi.org/10.64898/2026.04.02.713930, https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2822" | |
| Nucleus,EMPIAR-13420 (macrophage / A431),Train/val,166,39,0,205,16.03,205,https://doi.org/10.6019/EMPIAR-13420 | |
| Nucleus,In-house segmentations,Benchmark (held-out test),0,0,154,154,12.04,154, | |
| Nucleus,EMPIAR-12885 (AIVE),Train/val,30,10,0,40,3.13,40,https://doi.org/10.6019/EMPIAR-12885 | |
| Nucleus,Zenodo 17068504 (cardiomyocyte),Train/val,20,2,0,22,1.72,22,https://doi.org/10.5281/zenodo.17068504 | |
| Nucleus,TOTAL,,432,109,738,1279,100,1279, | |
| Lipid droplet,OpenOrganelle / CellMap (COSEM),Train/val,918,329,0,1247,72.58,256,"https://doi.org/10.1038/s41586-021-03977-3, https://doi.org/10.1038/s41586-021-03992-4, https://openorganelle.janelia.org" | |
| Lipid droplet,EMPIAR-13420 (macrophage / A431),Benchmark (held-out test),0,0,370,370,21.54,370,https://doi.org/10.6019/EMPIAR-13420 | |
| Lipid droplet,DeepContact,Benchmark (held-out test),0,0,41,41,2.39,41,https://doi.org/10.6084/m9.figshare.19898404 | |
| Lipid droplet,EMPIAR-12885 (AIVE),Benchmark (held-out test),0,0,35,35,2.04,35,https://doi.org/10.6019/EMPIAR-12885 | |
| Lipid droplet,EMPIAR-10994 (HeLa SBF-SEM),Train/val,11,5,0,16,0.93,16,https://doi.org/10.6019/EMPIAR-10994 | |
| Lipid droplet,EMPIAR-11746 (U-2 OS FIB-SEM),Train/val,6,3,0,9,0.52,9,"https://doi.org/10.6019/EMPIAR-11746, https://doi.org/10.5281/zenodo.10043461" | |
| Lipid droplet,TOTAL,,935,337,446,1718,100,727, | |