fidoptSELMA3D amyloid plaques, light-sheet microscopy
A 300 x 300 x 300 voxel patch of a light-sheet volume of a cleared 5xFAD mouse brain, its amyloid plaques drawn by experts (SELMA3D 2024).
10 test casesmouse brainimage FLUORESCENCE
Read before comparing (6)
- Truth. One binary mask a patch, the amyloid plaques drawn by hand; separate amyloid plaques that touch are one region, and no instance is scored.
- Ranked apart. The patches are tiles of a few volumes, neighbouring tiles overlapping by about five slices, and the deposit names no animal: test and development come from different tile groups, but the test patches of one group are correlated.
- Units. The headers give no voxel size, so distances are in voxels and the surface tolerance is one voxel. The deposit gives the acquisition at 1.63 x 1.63 x 4 µm without saying whether the patches keep it.
- Contact. No test patch touches or overlaps a development one: across the split the best face correlation is 0.87 and the best overlap of 1 to 15 slices scores 0.15, where touching tiles of one group score up to 0.99.
- Start. Plaques are under 0.05% of a patch: the whole patch named plaque scores a median Dice of 0.0001, its bright voxels (Otsu) 0.0002.
- Public. These are SELMA3D's public annotated training patches: a network trained on them has seen the test cases.
No method has a result on every case of this dataset yet.
Case by case
Click a score to look at that result: the image, the truth in green and the method's map in red. Underlined scores have their image; for the others you see the case without the result.
About the data
- Test cases
- The deposit's gzip headers keep each patch's tile number, which puts the 34 patches in three groups of touching tiles of one or more volumes: tiles 42 to 138 (patch_000 to 016), tile 303 (patch_017) and tiles 369 to 450 (patch_018 to 033). 10 test patches drawn with seed 2026 from the first two groups, stratified, and 10 development patches from the third in the seeded order, so no group crosses the split; 14 are unused.
- Truth
- contours by experts the deposit's pixel-wise masks of the amyloid plaques, drawn in 3D in virtual reality by four expert annotators, then verified by an expert and reviewed by two organisers; the corpus makes every nonzero value 1
- Source
- www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD1196
doi.org/10.6019/S-BIAD1196
selma3d.grand-challenge.org/data - Licence
- CC BY 4.0 (BioImage Archive deposit S-BIAD1196)
10 cases for tuning, never tested
patch_032, patch_018, patch_020, patch_033, patch_026, patch_025, patch_019, patch_023, patch_024, patch_030