| { |
| "name": "MitoEM (publicly-labeled half)", |
| "challenge": "MitoEM \u2014 MICCAI 2020 / ISBI 2021", |
| "papers": [ |
| "10.1007/978-3-030-59722-1_7", |
| "10.1109/TMI.2023.3320497" |
| ], |
| "source": { |
| "images": "https://huggingface.co/datasets/pytc/EM30", |
| "labels": "https://huggingface.co/datasets/pytc/MitoEM", |
| "challenge": "https://mitoem.grand-challenge.org/" |
| }, |
| "license": "CC BY 4.0", |
| "modality": "serial-section multi-beam SEM (ssSEM)", |
| "resolution_nm_xyz": [ |
| 8, |
| 8, |
| 30 |
| ], |
| "body_part": "brain cortex (rat V1 L2/3; human L2)", |
| "task": "mitochondria instance segmentation", |
| "splits": { |
| "train": 800, |
| "val": 200 |
| }, |
| "ground_truth": "v2 instance labels (corrected release used by the IEEE TMI 2023 challenge report); uint16, 0=background, non-zero=instance ID; single tier, no competing raters", |
| "excluded": [ |
| "z 500-999 of both volumes (challenge test half; GT withheld by organizers)" |
| ], |
| "subsets": { |
| "MitoEM-H": { |
| "organism": "human", |
| "tissue": "cortex, Layer II", |
| "resolution_nm_xyz": [ |
| 8, |
| 8, |
| 30 |
| ], |
| "n_instances_labeled": 10552, |
| "source_images": "pytc/EM30 :: EM30-H-im-pad.zip", |
| "source_labels": "pytc/MitoEM :: EM30-H-mito-train-val-v2.zip", |
| "preprocessing": "cropped [0:4096, 0:4096] from the 5120x5120 padded slices" |
| }, |
| "MitoEM-R": { |
| "organism": "rat", |
| "tissue": "primary visual cortex (V1), Layer II/III", |
| "resolution_nm_xyz": [ |
| 8, |
| 8, |
| 30 |
| ], |
| "n_instances_labeled": 5446, |
| "source_images": "pytc/EM30 :: EM30-R-im.zip", |
| "source_labels": "pytc/MitoEM :: EM30-R-mito-train-val-v2.zip", |
| "preprocessing": "none (already 4096x4096)" |
| } |
| }, |
| "loader_notes": [ |
| "binary semantic mitochondria = mask > 0", |
| "instance IDs are volume-global and sparse; not contiguous within a slice", |
| "both subsets are pre-aligned at 4096x4096; no crop/offset needed on read", |
| "MitoEM-H upstream is 5120x5120 padded at the FAR edges -- the label frame is [0:4096, 0:4096], NOT the [512:4608] implied by 'pad-20-512-512'", |
| "annotated instances have a minimum size of 2000 voxels", |
| "MOAS and small/medium/large bins are evaluation strata, not label classes" |
| ], |
| "overlap_warning": "MitoEM-H and AxonEM-Human are the SAME image volume (EM30-H); AxonEM is already mirrored at MedOtter/AxonEM. 5 of its 9 human crops intersect MitoEM's labeled range. Targets differ (axons vs mitochondria) so this is benchmark non-independence, not label leakage. MitoEM-R is clean.", |
| "license_note": "Upstream pytc/EM30 + pytc/MitoEM declare MIT, which covers the ANNOTATIONS. MitoEM-H is the EM30-H human volume whose governing imagery layer is the H01 release (Shapson-Coe et al.) under CC BY 4.0, so the mirror is tagged with the most restrictive governing layer -- matching MedOtter/AxonEM, served from the same pytc/EM30 archive. Both licences permit redistribution; only the attribution obligation differs. MitoEM-R's rat volume has no separately adjudicated upstream; CC BY 4.0 applied uniformly as the conservative choice." |
| } |
