Awesome
Awesome vEM Datasets
Contents
- Overview of Connectomics
- Distinguish Connectome
- Accessible Ground Truth
- Background
- Reference
- Materials
- Group
- Contribution
Overview of Connectomics
(we are focusing synapse-level connectomics datasets generated by the volume electron microscopy)
Online Challenge
| Year | Name | Conference | Link |
|---|---|---|---|
| SNEMI3D | |||
| CREMI | |||
| ISBI 2012 |
Distinguish Connectome
| Full set | Subset | Connectome | Link |
|---|---|---|---|
| FAFB | CREMI-A/B/C | FlyWire | FlyWire |
| Kasthuri15 | SNEMI3D/AC3/AC4 | two fully manually reconstructed cylinders | VAST |
| Hemi-brain | Hemi-brain training set | LSD | |
| FIB-25 | FIB-25 training set | LSD | |
| J0126 | J0126 training set | LSD/FFN |
Towards Whole Mouse Brain
- Mouse Visual Cortex ~ 1 mm<sup>3</sup>, Auto TEM
- Human Cerebral Cortex ~ 1 mm<sup>3</sup>, MultiBeam SEM
- Mouse Cortical-Basal-Ganglia-Thalamic Loop ~ 10 mm<sup>3</sup>, Tilt TEM Tomography
- Mouse Hippocampus ~ 10 mm<sup>3</sup>, MultiBeam SEM with Ion Beam Milling
Accessible Ground Truth
<table> <tr> <th>Name<br><i>for short</i></th> <th>Size<br><i>μm<sup>3</sup></i></th> <th>Resolution<br><i>nm<sup>3</sup></i></th> <th>GT Size<br><i>μm<sup>3</sup></i></th> <th>GT Resolution<br><i>nm<sup>3</sup></i></th> <th>GT Size<br><i>voxel</i></th> <th>Link</th> <th> Note </th> </tr> <tr> <td rowspan="2">AxonEM</td> <td rowspan="2">30x30x30</td> <td>7x7x40</td> <td rowspan="2"></td> <td>7x7x40</td> <td rowspan="2"></td> <td rowspan="2"><a href="https://axonem.grand-challenge.org/">grand-challenge</a></td> <td rowspan="2">subsets of MICrONS and H01</td> </tr> <tr> <td>8x8x30</td> <td>8x8x30</td> </tr> <tr> <td>H01</td> <td>2,000x3,000x175</td> <td>4x4x30</td> <td></td> <td>8x8x30</td> <td></td> <td><a href="https://h01-release.storage.googleapis.com/landing.html">google</a></td> <td></td> </tr> </table>Open-access Resource
Related Review
- Kornfeld <i>and</i> Denk. Progress and Remaining Challenges in High-throughput Volume Electron Microscopy. 2018
- Kievits <i>et al.</i> How Innovations in Methodology Offer New Prospects for Volume Electron Microscopy. 2022
- Beyer <i>et al.</i> A Survey of Visualization and Analysis in High-Resolution Connectomics. 2022
- Jefferis <i>et al.</i> Scaling up Connectomics: The Road to a Whole Mouse Brain Connectome. 2023
Related Survey
- connectomics-vis-survey.github.io
- braincircuits.io/resources
- tianyan.gitlab.io/braindata/connectomics-survey
- github.com/subeeshvasu/Awesome-Neuron-Segmentation-in-EM-Images
- github.com/Levishery/connectomic-paper-datasets
Related Code
Contribution
(including the private communication)
- Hao Zhai
- Liuyun Jiang
- Xinghui Zhao
- Yanchao Zhang
- Jinyue Guo
Please contribute <sup>Pull Request & Issue</sup> if you think a new dataset or a relevant paper is missing.
Let's enjoy the beauty of EM data and the awesome micro-connectomes!