Awesome vEM Datasets

Contents

• Overview of Connectomics
  • Distinguish Connectome
  • Accessible Ground Truth
• Background
• Reference
• Materials
  • Elaborate Review
  • Open-access Resource
  • Related Work
• 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 mm³, Auto TEM
• Human Cerebral Cortex ~ 1 mm³, MultiBeam SEM
• Mouse Cortical-Basal-Ganglia-Thalamic Loop ~ 10 mm³, Tilt TEM Tomography
• Mouse Hippocampus ~ 10 mm³, MultiBeam SEM with Ion Beam Milling

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

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!