AutoSynapse technology is now included in Neurolucida 360.
Please go to the Neurolucida 360 webpage to learn about automatic spine detection.
If you own AutoSynapse, contact us to upgrade.

Automatic synapse detection and quantification

AutoSynapse, an extension module for Neurolucida, automatically detects and analyzes pre-synaptic markers such as synaptophysin and post-synaptic markers such as PSD95, then uses nearby dendrites traced with AutoNeuron or Neurolucida to analyze which of those synaptic markers are associated with particular dendrites.

  • Quantifies location and volume of fluorescent markers.
  • Limits detection to within a user-prescribed radius of the dendritic branch surface.
  • Interactively chooses dendritic branch(es) for synapse detection.
  • Uses a Workflow approach to walk you through the detection step by step.
  • Includes a tool to test detection parameters on small branch segments.
  • Fast execution - runs in under a minute on multiple dendritic branches.
  • Features built-in thickness re-estimation of pre-traced branches.
  • Saves results in standard Neurolucida data format (.ASC, .DAT, or .XML).
  • Includes synapse analysis via Neurolucida Explorer application.
  • Enables results exports to Microsoft Excel.

Up until now, this method for analyzing synapses could only be done manually with Neurolucida, but AutoSynapse provides a new type of automatic analysis based on distance from the dendritic surface that is not available with any other software.


AutoSynapse has been developed with support from SBIR grants awarded by the NIMH.