fidoptSELMA3D blood vessels (VesSAP), light-sheet microscopy
A 500 x 500 x 50 voxel patch of a light-sheet volume of a cleared mouse brain, its blood vessels drawn by experts (SELMA3D 2024, patches from VesSAP).
10 test casesmouse brainimage FLUORESCENCE
Read before comparing (8)
- Truth. One binary mask a patch, the blood vessels drawn by hand; separate blood vessels that touch are one region, and no instance is scored.
- Ranked apart. The deposit gives no animal or brain for a patch, and VesSAP drew its 17 annotated volumes of this size from 5 brains: several patches come from one brain, and test and development may share one.
- 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 1.625 x 1.625 x 3 µm without saying whether the patches keep it.
- Channels. A patch has two channels, the two vessel dyes (Evans blue and WGA); only the first file (_0000), the one whose vessels stand out more, is given, so that single-image methods run. The deposit does not say which file is which dye.
- Values. Four of the masks used (patch_000, 001, 003 and 004) hold 255 for vessel where the others hold 1, and patch_000 also 95 on 886 voxels; every nonzero value is vessel.
- Contact. The deposit keeps no tile names for these patches; no test patch touches or overlaps a development one: across the split the best face correlation is 0.48 and the best overlap of 1 to 15 slices 0.13, where the halves of one patch score 0.96 and 1.00.
- Start. The whole patch named vessel scores a median Dice of 0.23 on the test patches, its bright voxels (Otsu) 0.15 (0.07 to 0.58).
- 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
- 10 test patches drawn with seed 2026 among the deposit's 24 and 10 development patches from the other end of the seeded order; 4 are unused. The deposit names no animal for a patch, so test and development may share one.
- Truth
- contours by experts the deposit's pixel-wise masks of the blood vessels, 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
doi.org/10.1038/s41592-020-0792-1
github.com/vessap/vessap - Licence
- CC BY 4.0 (BioImage Archive deposit S-BIAD1196)
10 cases for tuning, never tested
patch_003, patch_022, patch_012, patch_015, patch_013, patch_010, patch_011, patch_017, patch_004, patch_006