Datasets:
File size: 3,144 Bytes
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"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."
} |