fidoptSELMA3D c-Fos-positive cells, light-sheet microscopy
A 100 x 100 x 100 voxel patch of a light-sheet volume of a cleared mouse brain, its c-Fos-positive cells drawn by experts (SELMA3D 2024).
10 test casesmouse brainimage FLUORESCENCE
Read before comparing (6)
- Truth. One binary mask a patch, the c-Fos-positive cells drawn by hand; separate c-Fos-positive cells that touch are one region, and no instance is scored.
- Ranked apart. Four blocks of one or more brains, each cut into octants, and the deposit names no animal: the eight test octants of block 695 are parts of one block.
- 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 6 µm without saying whether the patches keep it.
- Contact. Across the split the best face correlation is 0.82 and the best overlap of 1 to 15 slices scores 0.61, where octants of one block score up to 1.00; both come from the borders of zeroed regions, and inside the tissue fall to 0.20, as unrelated patches score.
- Start. The whole patch named c-Fos-positive scores a median Dice of 0.002 on the test patches, its bright voxels (Otsu) 0.007.
- 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 name each patch an octant of one of four 200-voxel blocks: patchvolume_695 (patch_000 to 007), 969 (008 to 015), 1147 (016) and 1230 (017, 018). The 10 test patches are blocks 695 and 1230, the 9 development patches blocks 969 and 1147, so no block crosses the split.
- Truth
- contours by experts the deposit's pixel-wise masks of the c-Fos-positive cells, 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/s41592-024-02245-2 - Licence
- CC BY 4.0 (BioImage Archive deposit S-BIAD1196)
9 cases for tuning, never tested
patch_008, patch_009, patch_010, patch_011, patch_012, patch_013, patch_014, patch_015, patch_016