The synapse is the principle active signaling component of the brain's circuitry. As such, tools to visualize, detect, and label synapses would be a useful resource for the neuroscience community. The Open Synaptome Project, a collaboration between NeuroData and the Allen Institute for Brain Science, provides a synaptic analysis toolbox open to the scientific community as well as open access to the array tomography data generated by the Allen Institute.



meda implements the top 10 analyses/visualizations we recommend for any matrix valued data.

The deployment of tools which support the Open Connectome Project

SynapseAnalysis (PSD) is a framework to evaluate synaptic antibodies for fluorescence array tomography (AT)



S. J. Smith. Q & A: Array tomography. BMC Biology, (1)16:98, 2018.

C. Ounkomol, S. Seshamani, M. M. Maleckar, and F. Collman. Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy. bioRxiv:289504, 2018.

A. K. Simhal, B. Gong, J. S. Trimmer, R. J. Weinberg, S. J. Smith, G. Sapiro, and K. D. Micheva. A Computational Synaptic Antibody Characterization and Screening Framework for Array Tomography. bioRxiv, 2018.

G. Fran├ža and J. T. Vogelstein. Energy Clustering. arXiv, 2017.

A. K. Simhal, C. Aguerrebere, F. Collman, J. T. Vogelstein, K. D. Micheva, R. J. Weinberg, S. J. Smith, and G. Sapiro. Probabilistic fluorescence-based synapse detection. PLoS Computational Biology, 2017.

A. Burette, F. Collman, K. D. Micheva, S. J. Smith, and R. J. Weinberg. Knowing a synapse when you see one. Frontiers in Neuroanatomy, 2015.

F. Collman, J. Buchanan, K. D. Phend, K. D. Micheva, R. J. Weinberg, and S. J. Smith. Mapping Synapses by Conjugate Light-Electron Array Tomography. Journal of Neuroscience, 2015.

People on project

Randal Burns
Stephen Smith
Joshua Vogelstein
Jesse Leigh Patsolic
Ben Falk
Eric Perlman
James Trimmer
Bill Seeley
Daniel V. Madison
Kristina Micheva
Richard Weinberg
Guillermo Sapiro
Ed Lein
Anish Simhal
Jonathan Ting
Michelle Naugle
Forrest Collman
Sharmishtaa Seshamani
Alex Baden


Synaptomes of Mouse and Man