Organelle stringclasses 4
values | Source stringlengths 5 34 | Role stringclasses 3
values | Train tiles int64 0 23.9k | Val tiles int64 0 715 | Test tiles int64 0 738 | Total tiles int64 9 25.1k | % of organelle tiles float64 0.04 100 | Annotated crops int64 9 16.5k | Dataset DOI / URL stringlengths 36 121 ⌀ |
|---|---|---|---|---|---|---|---|---|---|
Mitochondria | CEM-MitoLab | Train/val | 12,868 | 0 | 0 | 12,868 | 51.19 | 12,868 | https://doi.org/10.6019/EMPIAR-11037 |
Mitochondria | MitoEM 2.0 | Train/val + benchmark | 1,736 | 155 | 55 | 1,946 | 7.74 | 890 | https://doi.org/10.5281/zenodo.17635006 |
Mitochondria | OrgSegNet / Plantorgan Hunter | Train/val + benchmark | 1,474 | 182 | 198 | 1,854 | 7.38 | 993 | https://doi.org/10.57760/sciencedb.01335 |
Mitochondria | DeepContact | Train/val + benchmark | 1,644 | 35 | 67 | 1,746 | 6.95 | 244 | https://doi.org/10.6084/m9.figshare.19898404 |
Mitochondria | In-house segmentations | Train/val | 1,029 | 31 | 0 | 1,060 | 4.22 | 161 | null |
Mitochondria | Zenodo 15602048 (breast TEM) | Train/val | 1,000 | 30 | 0 | 1,030 | 4.1 | 142 | https://doi.org/10.5281/zenodo.15602048 |
Mitochondria | Zenodo 17068504 (cardiomyocyte) | Train/val | 1,000 | 6 | 0 | 1,006 | 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 | null | 23,904 | 715 | 518 | 25,137 | 100 | 16,457 | null |
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 | null |
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 | null | 969 | 228 | 361 | 1,558 | 100 | 1,087 | null |
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 | null |
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 | null | 432 | 109 | 738 | 1,279 | 100 | 1,279 | null |
Lipid droplet | OpenOrganelle / CellMap (COSEM) | Train/val | 918 | 329 | 0 | 1,247 | 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 | null | 935 | 337 | 446 | 1,718 | 100 | 727 | null |
QuantEM — organelle model data sources
Annotated ground-truth sources behind the eight released organelle segmentation models (mitochondria, ER, nucleus, lipid droplet), with train/validation/test tile counts and annotated-crop counts per source.
Emitted verbatim from Supplementary Table 3 of the QuantEM manuscript — 45 rows. Please cite the original sources listed here alongside QuantEM; rows carry a DOI or repository URL where one exists.
Related:
ArrojoeDrigoLab/quantem— the released model weightsArrojoeDrigoLab/quantem-base-model-sources— the other sources table
Sources
| 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 |
Citation
Acree et al., QuantEM: An optimized platform of vision transformer-based models for segmentation and analysis of electron microscopy data. Citation details on publication.
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