Datasets:
license: other
task_categories:
- image-segmentation
tags:
- electron-microscopy
- connectomics
- mitochondria
- 3d-segmentation
- instance-segmentation
pretty_name: MitoVerse
size_categories:
- 10B<n<100B
MitoVerse
A generalist 3D-EM mitochondria segmentation benchmark: many domains (modality, species, tissue, resolution) in one consistent format, with instance labels.
Code, loaders, ingestion, and PyTorchConnectomics usage: 👉 https://github.com/PytorchConnectomics/mitoverse
Each volume is one zarr store data/<dataset>/<volume>.zarr with arrays img (uint8, ZYX) and
mito (instance, 0=background); per-volume metadata (voxel size, modality, species, tissue) lives in
its .zattrs and in catalog.json. Semantic masks are mito > 0 — derive as needed.
3D EM Datasets with Mitochondria Annotation
* = instance labels we converted from binary segmentation. † = redistribution caveat.
Shape is the average (x,y,z) per volume, ×N = number of volumes.
| Microscope | Dataset | Species | Region | Avg Shape (xyz) | Resolution (nm) | # Mitos |
|---|---|---|---|---|---|---|
| FIB-SEM | OpenOrganelle (Xu'21), CellMap annot. | mixed | various cells/tissues | (213,204,203)×147 | 8×8×8 | 1580 |
| FIB-SEM | └ + MitoEM2.0 chunks (Liu et al. '26) | mixed | jurkat/macro/kidney/liver/cardiac | (1024,1024,256)×10 | 8×8×8 | 2910 |
| FIB-SEM | Müller'21 (BetaSeg)* | Mouse | Pancreas (β-cells) | (874,669,979)×7 | 16×16×16 | 1852 |
| FIB-SEM | Mekuč'20 (UroCell) | Mouse | Urinary bladder | (256,256,256)×5 | 16×16×15 | 287 |
| FIB-SEM | Kunduri'22 | Drosophila | Gonad (spermatocyte) | (1024,1024,341)×3 | 16×16×16 | 621 |
| FIB-SEM | Conrad'23 (MitoNet) | mixed | fly brain / C. elegans / HeLa / muscle / salivary | (546,446,466)×5 | 12–24 (iso) | 635 |
| ssSEM | Wei'20 (MitoEM) | Human | Temporal lobe (L2) | (4096,4096,500) | 8×8×30 | 10552 |
| ssSEM | Wei'20 (MitoEM) | Rat | V1 (L2/3) | (4096,4096,500) | 8×8×30 | 5446 |
| ssSEM | Casser'20 (Kasthuri++)* | Mouse | Somatosensory (L4/5) | (700,791,80)×2 | 12×12×30 | 265 |
| FIB-SEM | └ Lucchi++ (Lucchi'13)* | Mouse | Hippocampus | (512,768,82) | 10×10×10 | 70 |
| ssSEM | Xiao'18 | Mouse | Auditory cortex | (2156,2104,31) | 8×8×50 | 468 |
| ssSEM | Han'24 | Mouse | Cerebellum (mossy fiber) | (1357,1411,331)×5 | 8×8×30 | 1144 |
| ssTEM | Turner'22 (MICrONS, Pinky)† | Mouse | V1 (Pinky + MICrONS1) | (1203,1282,83)×16 | 8×8×40 | 1420 |
| SBF-SEM | Jiang'25 | Mouse | Brainstem | (1000,1000,100)×3 | 15×15×40 | 2057 |
| SBF-SEM | Guay'21* | Human | Platelet | (667,736,65)×3 | 10×10×50 | 279 |
| SBF-SEM | Haberl'18 (CDeep3M)* | Mouse | Cerebellum (brain) | (256,256,15)×2 | 10×10×24 | 247 |
Total: 212 volumes, 29,833 mitochondria. Volumes are organized by imaging source; benchmarks are
split overlays in splits/: cellmap.json (CellMap challenge over OpenOrganelle crops) and
mitoem2.0.json (MitoEM2.0 generalization suite). The OpenOrganelle *_test0/_test1 volumes are
lab-annotated and belong to mitoem2.0.
MitoEM2.0 benchmark
MitoEM2.0 (Liu et al., 2026) is a multi-domain generalization benchmark of 8 sub-datasets. Official
nnU-Net release: Zenodo 10.5281/zenodo.20417683. Within
MitoVerse it is not duplicated — it is the split overlay splits/mitoem2.0.json
over the source volumes below (muller21, openorganelle, han24, wei20, jiang25, kunduri22). EFI/DCI are
per-dataset difficulty metrics from the MitoEM2.0 paper; † redistribution caveat, * converted to instances.
| Name | Organism | Tissue | Cell type | Modality | Avg Shape (xyz) | Voxels | Split (tr/val/te) | # Mito | EFI/DCI | Source |
|---|---|---|---|---|---|---|---|---|---|---|
| ME2-Beta | Mouse | Pancreas | β-cell | FIB-SEM | (874,669,979) | 3961M | 3/1/3 | 1935 | 0.02/2.68 | Müller'21 † |
| ME2-Jurkat | Human | Cell line | Jurkat | FIB-SEM | (1024,1024,256) | 805M | 1/1/1 | 372 | 0.00/1.62 | Xu'21 * |
| ME2-Macro | Human | Cell line | Macrophages | FIB-SEM | (1024,1024,256) | 805M | 1/1/1 | 497 | 0.01/1.38 | Xu'21 * |
| ME2-Mossy | Mouse | Cerebellum | Mossy Fiber | ssSEM | (1024,1024,500) | 3333M | 3/1/3 | 1099 | 0.10/4.13 | Han'24 |
| ME2-Pyra | Human | Cerebrum | Pyramidal | ssSEM | (4096,4096,500) | 8388M | 3/1/11 | 45 | 0.96/0.53 | Wei'20 |
| ME2-Podo | Mouse | Kidney | Podocyte | FIB-SEM | (1024,1024,256) | 805M | 1/1/1 | 1333 | 0.00/2.43 | CellMap'24 † |
| ME2-Sperm | Drosophila | Gonad | Spermatocyte | FIB-SEM | (1024,1024,341) | 1073M | 3/1/4 | 775 | 0.01/0.96 | Kunduri'22 † |
| ME2-Stem | Mouse | Brainstem | Mix | SBF-SEM | (1024,1024,100) | 300M | 1/1/1 | 2058 | 0.09/0.80 | Jiang'25 |
License
Per-volume; see each volume's source in catalog.json. Some sources (MICrONS †, CellMap) carry
attribution or redistribution caveats — check before reuse.