Awesome
Awesome vEM Datasets
Contents
- Overview of Connectomics
- Distinguish Connectome
- Accessible Ground Truth
- Background
- Reference
- Materials
- Research Group
- Contribution
Overview of Connectomics
focus synapse-level connectomics datasets generated by the volume electron microscopy
Petascale Connectome
| Year | Name | Size | Link |
|---|---|---|---|
| 2024 | Si (e.g., Si150L4) | ~1.1 PB | https://wklink.org/7122 |
| 2021 | H01 | ~1.4 PB | https://h01-release.storage.googleapis.com/data.html |
| 2021 | MICrONS (mm<sup>3</sup>) | ~2.0 PB | https://microns-explorer.org/ |
Online Challenge
| Year | Name | Conference | Link |
|---|---|---|---|
| 2024 | NISB | Connectomics Conf | https://structuralneurobiologylab.github.io/nisb/# |
| 2013 | SNEMI3D | ISBI 2013 | https://snemi3d.grand-challenge.org/ |
| 2016 | CREMI | MICCAI 2016 | https://cremi.org/ |
| 2012 | ISBI | ISBI 2012 | https://imagej.net/events/isbi-2012-segmentation-challenge |
Distinguish Connectome
| Full set | Subset | Connectome | Link |
|---|---|---|---|
| FAFB | CREMI-A/B/C | FlyWire | |
| Kasthuri15 | SNEMI3D/AC3/AC4 | two cylinders | |
| Hemi-brain | Hemi-brain training set | ||
| FIB-25 | FIB-25 training set | ||
| J0126 | J0126 training set |
TODO: Other Accessible Ground Truth
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>TODO: Other Accessible Ground Truth
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!