| --- |
| 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](https://openorganelle.janelia.org/) (Xu'21), [CellMap](https://cellmapchallenge.janelia.org/) 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)](https://betaseg.github.io/)* | Mouse | Pancreas (β-cells) | (874,669,979)×7 | 16×16×16 | 1852 | |
| | FIB-SEM | [Mekuč'20 (UroCell)](https://github.com/MancaZerovnikMekuc/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)](https://volume-em.github.io/empanada.html) | mixed | fly brain / C. elegans / HeLa / muscle / salivary | (546,446,466)×5 | 12–24 (iso) | 635 | |
| | ssSEM | [Wei'20 (MitoEM)](https://mitoem.grand-challenge.org/) | Human | Temporal lobe (L2) | (4096,4096,500) | 8×8×30 | 10552 | |
| | ssSEM | [Wei'20 (MitoEM)](https://mitoem.grand-challenge.org/) | Rat | V1 (L2/3) | (4096,4096,500) | 8×8×30 | 5446 | |
| | ssSEM | [Casser'20 (Kasthuri++)](https://sites.google.com/view/connectomics/)* | Mouse | Somatosensory (L4/5) | (700,791,80)×2 | 12×12×30 | 265 | |
| | FIB-SEM | └ Lucchi++ ([Lucchi'13](https://www.epfl.ch/labs/cvlab/data/data-em/))* | Mouse | Hippocampus | (512,768,82) | 10×10×10 | 70 | |
| | ssSEM | [Xiao'18](https://www.frontiersin.org/articles/10.3389/fnana.2018.00092/full) | 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)](https://www.sciencedirect.com/science/article/pii/S0092867422001349)† | Mouse | V1 (Pinky + MICrONS1) | (1203,1282,83)×16 | 8×8×40 | 1420 | |
| | SBF-SEM | [Jiang'25](https://www.sciencedirect.com/science/article/pii/S2667237525000256) | Mouse | Brainstem | (1000,1000,100)×3 | 15×15×40 | 2057 | |
| | SBF-SEM | [Guay'21](https://leapmanlab.github.io/dense-cell/)* | Human | Platelet | (667,736,65)×3 | 10×10×50 | 279 | |
| | SBF-SEM | [Haberl'18 (CDeep3M)](https://doi.org/10.1038/s41592-018-0106-z)* | 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/`](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](https://zenodo.org/records/20417683)**. Within |
| MitoVerse it is **not duplicated** — it is the split overlay [`splits/mitoem2.0.json`](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. |
|
|
| ## Acknowledgement |
|
|
| - [Aswath et al. 2023. Segmentation in large-scale cellular electron microscopy with deep learning: A literature survey](https://arxiv.org/abs/2206.07171) |
|
|
