README.md

Awesome vEM Datasets

Contents

• Overview of Connectomics
  • Distinguish Connectome
  • Accessible Ground Truth
• Background
• Reference
• Materials
  • Open-access Resource
  • Related Review
  • Related Survey
• 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 (mm3)	~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

Name for short	Size μm3	Resolution nm3	GT Size μm3	GT Resolution nm3	GT Size voxel	Link	Note
AxonEM	30x30x30	7x7x40		7x7x40		grand-challenge	subsets of MICrONS and H01
		8x8x30		8x8x30
H01	2,000x3,000x175	4x4x30		8x8x30		google

TODO: Other Accessible Ground Truth

Open-access Resource

• Open Connectome Project
• BossDB
• EMPIAR
• Zenodo
• webKnossos
• Neuroglancer

Related Review

• Kornfeld and Denk. Progress and Remaining Challenges in High-throughput Volume Electron Microscopy. 2018
• Kievits et al. How Innovations in Methodology Offer New Prospects for Volume Electron Microscopy. 2022
• Beyer et al. A Survey of Visualization and Analysis in High-Resolution Connectomics. 2022
• Jefferis et al. 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

• Local Shape Descriptors
• PyTorch Connectomics

Contribution

(including the private communication)

• Hao Zhai
• Liuyun Jiang
• Xinghui Zhao
• Yanchao Zhang
• Jinyue Guo

Please contribute ^{Pull Request & Issue} 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!