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.




ndex allows exchange of large image volumes with NeuroData


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


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


ndwebtools is a web application that provides NeuroData tools for managing and viewing data on NeuroData's spatial database store.


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

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

A. K. Simhal et al. Probabilistic fluorescence-based synapse detection. PLoS Computational Biology, 2017.

A. Burette et al. Knowing a synapse when you see one. Frontiers in Neuroanatomy, 2015.

F. Collman et al. Mapping Synapses by Conjugate Light-Electron Array Tomography. Journal of Neuroscience, 2015.

People on project

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