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Ultrastructural Connectomics

Data Collections

MICRONS Layer 2/3 of V1 Electron Microscopy Connectomics Reconstructions

Electron Microscopy |  Mouse  |  301 Cells  |  3D Reconstructions

BIL Data Directory*  |   Download File Manifest and Instructions   |  Download Cell Metadata   |  View Data in MiCRONS Explorer

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Project Description

This dataset contains electron microscopy reconstructions obtained from a single 250 x 140 x 90 µm volume from layer 2/3 of a P36 male mouse visual cortex imaged at 3.58 x 3.58 x 40 nm resolution with a dense segmentation and proofreading of the axons and dendrites that are contained within the volume.  The data released here contains reconstructions from 301 neurons whose cell bodies reside within the volume.  The dataset was acquired and analyzed as part of the IARPA MICrONS (Machine Intelligence from Cortical Networks) program, which funded a collaboration between the Allen Institute for Brain Science, Princeton University and Baylor College of Medicine. 

The downloadable reconstruction files are hosted by the Brain Image Library in Pittsburgh. The data directory is subject to their website terms of use. All reconstruction files, as well as the file manifest and cell metadata downloads, are subject to CC 4.0.


Modality: Electron Microscopy

Species: Mouse

Specimen Type: Cell

Techniques: Transmission Electron Microscopy, 3D Reconstruction


Schneider-Mizell et al, 2020,

Dorkenwald et al, 2019,

Yin et al, Nature Communications 2020,

Publishing Information

Contact: Nuno Da Costa, Forrest Collman, Clay Reid

Publisher: Allen Institute for Brain Science

Year: 2020

License: CC 4.0


Functional Imaging: Emmanouil Froudarakis, Jacob Reimer, Andreas Tolias  
Co-registration: Nuno Maçarico da Costa, Adam Bleckert, Marc Takeno
Tissue Preparation: Joann Buchanan, Marc Takeno, Nuno Maçarico da Costa
Sectioning: Agnes Bodor, Adam Bleckert
TEM Design and Maintenance: Derrick Brittain, Clay Reid
TEM Operation: Derrick Brittain, Wenjing Yin, Adam Bleckert, Marc Takeno, Daniel Bumbarger, Nuno Da Costa
EM Stitching and Rough Alignment: Gayathri Mahalingam, Russel Torres, Yang Li, Thomas Macrina, Dodam Ih
EM Fine Alignment: Thomas Macrina, Will Wong
Neuron segmentation: Kisuk Lee, Jingpeng Wu
Agglomeration: Ran Lu 
Synapse Detection: Nicholas Turner, Jingpeng Wu
Neuroglancer Frontend: Nico Kemnitz, Manuel Castro
Proofreading Backend: Sven Dorkenwald, Nico Kemnitz, Chris S. Jordan
Cloud Data Interface: William Silversmith, Ignacio Tartavull
Connectome Versioning System: Forrest Collman, Sven Dorkenwald, Casey Schneider Mizell
Proofreading: Agnes Bodor, Nuno Maçarico da Costa, Szi-Chieh Yu, Alyssa Wilson, Sven Dorkenwald, Casey Schneider-Mizell,  Forrest Collman
Project Management: Lynne Becker, Shelby Suckow
Scientific Management: Clay Reid, Nuno Da Costa, Andreas S. Tolias, Jacob Reimer, H. Sebastian Seung
IARPA MICrONS Program Management: David A. Markowitz, Jacob Vogelstein

Funding Support

IARPA - Machine Intelligence from Cortical Networks

For MiCRONS Explorer