Training Subset — Unannotated
A total of around 35,050 patches of size 300×300×300 voxels, cropped from whole organs or organisms. These patches encompass a wide range of structural densities. Information on the original volume corresponding to each patch will also be provided.
Isolated Structures (~17,400 patches)
| Structure Type | Patches | Source Volumes |
|---|---|---|
| c-Fos+ cells [1] | ~5,300 | 18 3D images |
| Cell nuclei [2] | ~3,400 | 4 3D images |
| Amyloid-beta plaques [3] | ~1,600 | 4 3D images |
| Chondrocytes [4] | ~1,100 | 1 3D image |
| Chondrogenic cells [4] | ~1,100 | 1 3D image |
| Dopaminergic neurons [5] | ~2,500 | 1 3D image |
| Astrocytes [5] | ~2,400 | 1 3D image |
Contiguous Structures (~17,650 patches)
| Structure Type | Patches | Source Volumes |
|---|---|---|
| Blood vessels [6] | ~2,600 | 9 3D images |
| Arteries [7] | ~800 | 4 3D images |
| Sympathetic nerves [7] | ~2,000 | 4 3D images |
| Peripheral nerves (PGP9.5) [4, 5, 7, 8] | ~4,600 | 5 3D images |
| Lymphatic vessels [7] | ~650 | 4 3D images |
| Cranial nerves [4, 5] | ~4,500 | 2 3D images |
| Axonal markers [9] | ~2,500 | 8 3D images |
Training Subset — Annotated
A total of 82 patches of size 200×200×200 voxels with precise manual annotations.
Dense Isolated Structures (18 patches)
| Structure Type | Patches |
|---|---|
| c-Fos+ cells [1] | 9 |
| Cell nuclei [2] | 9 |
Sparse Isolated Structures (20 patches)
| Structure Type | Patches |
|---|---|
| Amyloid-beta plaques [3] | 20 |
Dense Contiguous Structures (16 patches)
| Structure Type | Patches |
|---|---|
| Blood vessels [6] | 16 |
Sparse Contiguous Structures (28 patches)
| Structure Type | Patches |
|---|---|
| Peripheral nerves [8] | 16 |
| Axonal markers [9] | 12 |
Preliminary Test Set
A total of 26 patches of size 200×200×200 voxels. Ground truth annotations are withheld from participants for evaluation purposes.
Dense Isolated Structures (5 patches)
| Structure Type | Patches |
|---|---|
| c-Fos+ cells [1] | 1 |
| Cell nuclei [2] | 1 |
| Microglia [10] | 3 |
Sparse Isolated Structures (7 patches)
| Structure Type | Patches |
|---|---|
| Amyloid-beta plaques [3] | 3 |
| Fluorescent protein (EGFP) [11] | 4 |
Dense Contiguous Structures (6 patches)
| Structure Type | Patches |
|---|---|
| Blood vessels [6] | 2 |
| Gut lymphatic vessels [7] | 4 |
Sparse Contiguous Structures (8 patches)
| Structure Type | Patches |
|---|---|
| Peripheral nerves [8] | 2 |
| Axonal markers [9] | 2 |
| Gut nerves [7] | 4 |
Final Test Set
A total of 96 patches of size 200×200×200 voxels. Ground truth annotations are withheld from participants for evaluation purposes.
Dense Isolated Structures (22 patches)
| Structure Type | Patches |
|---|---|
| c-Fos+ cells [1] | 5 |
| Cell nuclei [2] | 4 |
| Microglia [10] | 13 |
Sparse Isolated Structures (24 patches)
| Structure Type | Patches |
|---|---|
| Amyloid-beta plaques [3] | 11 |
| Fluorescent protein (EGFP) [11] | 13 |
Dense Contiguous Structures (22 patches)
| Structure Type | Patches |
|---|---|
| Blood vessels [6] | 8 |
| Gut lymphatic vessels [7] | 14 |
Sparse Contiguous Structures (28 patches)
| Structure Type | Patches |
|---|---|
| Peripheral nerves [8] | 8 |
| Axonal markers [9] | 6 |
| Gut nerves [7] | 14 |
References
[1] D. Kaltenecker, R. Al-Maskari, M. Negwer, et al. Virtual reality empowered deep learning analysis of brain activity. Nature Methods 21: 1306–1315, 2024 April.
[2] S. Zhao, M.I. Todorov, R. Cai, et al. Cellular and molecular probing of intact human organs. Cell 180(4): 796-812, 2020 Feb.
[3] H.S. Bhatia, A. Brunner, F. Öztürk, et al. Spatial proteomics in three-dimensional intact specimens. Cell 185(26): 5040-5058, 2022 Dec.
[4] R. Blain, G. Couly, E. Shotar, et al. A tridimensional atlas of the developing human head. Cell 186(26): 5910-5924, 2023 Dec.
[5] https://mab3d-atlas.com/validated-antibody-database
[6] M.I. Todorov, J.C. Paetzold, O. Schoppe, et al. Machine learning analysis of whole mouse brain vasculature. Nature Methods 17: 442-449, 2020 Mar.
[7] H. Mai, J. Luo, L. Hoeher, et al. Whole-body cellular mapping in mouse using standard IgG antibodies. Nature Biotechnology 42: 617–627, 2023 July.
[8] R. Cai, C. Pan, A. Ghasemigharagoz, et al. Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull-meninges connections. Nature Neuroscience 22: 317-327, 2019 Dec.
[9] E. Özen, et al. Multicolor High Resolution SCAPE microscopy for Understanding Neural Connectivity. Optics and the Brain, Optica Publishing Group, 2025.
[10] H. Mai, Z. Rong, S. Zhao, et al. Scalable tissue labeling and clearing of intact human organs. Nature Protocols 17: 2188-2215, 2022 July.
[11] J. Luo, M. Molbay, Y. Chen, et al. Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning. Nature Biotechnology, 2025 Jan.
[1] D. Kaltenecker, R. Al-Maskari, M. Negwer, et al. Virtual reality empowered deep learning analysis of brain activity. Nature Methods 21: 1306–1315, 2024 April.
[2] S. Zhao, M.I. Todorov, R. Cai, et al. Cellular and molecular probing of intact human organs. Cell 180(4): 796-812, 2020 Feb.
[3] H.S. Bhatia, A. Brunner, F. Öztürk, et al. Spatial proteomics in three-dimensional intact specimens. Cell 185(26): 5040-5058, 2022 Dec.
[4] R. Blain, G. Couly, E. Shotar, et al. A tridimensional atlas of the developing human head. Cell 186(26): 5910-5924, 2023 Dec.
[5] https://mab3d-atlas.com/validated-antibody-database
[6] M.I. Todorov, J.C. Paetzold, O. Schoppe, et al. Machine learning analysis of whole mouse brain vasculature. Nature Methods 17: 442-449, 2020 Mar.
[7] H. Mai, J. Luo, L. Hoeher, et al. Whole-body cellular mapping in mouse using standard IgG antibodies. Nature Biotechnology 42: 617–627, 2023 July.
[8] R. Cai, C. Pan, A. Ghasemigharagoz, et al. Panoptic imaging of transparent mice reveals whole-body neuronal projections and skull-meninges connections. Nature Neuroscience 22: 317-327, 2019 Dec.
[9] E. Özen, et al. Multicolor High Resolution SCAPE microscopy for Understanding Neural Connectivity. Optics and the Brain, Optica Publishing Group, 2025.
[10] H. Mai, Z. Rong, S. Zhao, et al. Scalable tissue labeling and clearing of intact human organs. Nature Protocols 17: 2188-2215, 2022 July.
[11] J. Luo, M. Molbay, Y. Chen, et al. Nanocarrier imaging at single-cell resolution across entire mouse bodies with deep learning. Nature Biotechnology, 2025 Jan.