Awesome vEM Datasets

Contents

• Overview
• Background
• Reference
• Materials
  • Elaborate Review
  • Open-access Resource
  • Related Work
• Group
• Contribution

Overview

We are mainly focusing connectomics datasets generated by the volume electron microscopy.

Challenge-level Datasets (size ~10μm³)

Name for short	Species	Sample	Microscopy	Size μm3	Resolution nm3	Number	Link	Reference	Note
AxonEM	mouse	primary visual cortex	ssTEM	30x30x30	7x7x40	18,000 axons	grand-challenge	Wei et al., 2021	subsets of MICrONS and H01
	human	temporal cortex	ATUM-mSEM		8x8x30
ISBI	drosophila	ventral nerve line	ssTEM	2x2x1.5	4x4x50				Segmentation of neuronal structures in EM stacks
SNEMI3D	mouse	cortex	ATUM-SEM	6x6x3	6x6x30				SNEMI3D: 3D Segmentation of neurites in EM images
AC3/AC4	mouse	cortex	ATUM-SEM	6x6x3	6x6x30				different membrane labeling at myelin
CREMI	drosophila	melanogaster brain	ssTEM	5x5x5	4x4x40		CREMI		MICCAI Challenge on Circuit Reconstruction from Electron Microscopy Images
VNC	drosophila	ventral nerve cord	ssTEM	4.7x4.7x1	4.6x4.6x45		github	Gerhard et al., 2013
SegEM								et al., 2015
FIB-25 (training)							https://github.com/janelia-flyem/neuroproof_examples	et al., 2013
MICRONS (training from 3 stacks)								et al., 2013

Name for short	Species	Sample	Microscopy	Size μm3	Resolution nm3	Number	Link	Reference	Note
AxonEM	mouse	primary visual cortex	ssTEM	30x30x30	7x7x40	18,000 axons	grand-challenge	Wei et al., 2021	subsets of MICrONS and H01
	human	temporal cortex	ATUM-mSEM		8x8x30
H01	human	temporal lobe	ATUM-mSEM	2,000x3,000x175	4x4x30	50,000 cells 133,700,000 synapses	google	Shapson-Coe et al., 2021
J0126	finch	area X	SBF-SEM	96x98x114	9x9x20	33 blocks 12+50 skels	cloudvolume-raw cloudvolume-seg	Januszewski et al., 2018	testing for FFN
Kasthuri	mouse	neocortex	ATUM-SEM	40x40x50	3x3x30	1,700 synapses	vast	Kasthuri et al., 2015	superset of SNEMI
MICrONS Cortical mm3	mouse	primary visual cortex and three higher visual areas	autoTEM	1,300x870x820	4x4x40	200,000 cells 524,000,000 synapses	microns zenodo bossdb	MICrONS Consortium et al., 2021
MICrONS Layer 2/3	mouse	primary visual cortex	ssTEM	250x140x90	3.58x3.58x40	451 neurons (417 PyCs) 169 non-neuronal cells	microns	Turner et al., 2022	pilot dataset of MICrONS Cortical mm3
ISBI	drosophila	ventral nerve line	ssTEM	2x2x1.5	4x4x50				Segmentation of neuronal structures in EM stacks
SNEMI3D	mouse	cortex	ATUM-SEM	6x6x3	6x6x30				SNEMI3D: 3D Segmentation of neurites in EM images
CREMI	drosophila	melanogaster brain	ssTEM	5x5x5	4x4x40		CREMI		MICCAI Challenge on Circuit Reconstruction from Electron Microscopy Images
Images of mouse piriform cortex	mouse	piriform cortex	ssTEM	3.5x3.5x6.8	7x7x40			Kisuk Lee et al., 2015
VNC	drosophila	ventral nerve cord	ssTEM	4.7x4.7x1	4.6x4.6x45		github	Gerhard et al., 2013

Elaborate 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

Open-access Resource

• Open Connectome Project
• BossDB
• webKnossos
• Neuroglancer
• Local Shape Descriptors
• PyTorch Connectomics
• EMPIAR
• Zenodo

Related Work

• connectomics-vis-survey.github.io

Group

• Lichtman Lab, Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University
• Seung Lab, Computer Science Department, Princeton Neuroscience Institute
• Helmstaedter Lab, Department of Connectomics, Max Planck Institute for Brain Research
• Pfister Lab, Visual Computing Group, School of Engineering and Applied Sciences, Harvard University
• Funke Lab, Janelia Research Campus, Howard Hughes Medical Institute
• Lee Lab, Boston Children's Hospital, Harvard Medical School

Contribution

• Hao Zhai
• Liuyun Jiang

Please contribute 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!