Code for synapse detection via neurite interface classification (Staffler et al.)
- SynEM: Code package for neurite interface classification
- SynapseAnnotationGUI: Graphical User Interface for manual neurite interface annotation (Figure 3 - figure supplement 1 in Staffler et al.)
- data: Data for examples and prediction
MATLAB R2015b or higher is required. The Matlab-mex compiler has to be configured. This can be done by typing “mex -setup” in command line or the Matlab command prompt. In case your system does not have a compiler installed please follow the instructions by Mathworks. This is required to compile some of the routine for the user’s computer.
Before using SynEM for the first time run the setup.m file from the SynEM main folder (the same folder that this readme file is located in) with the SynEM main folder set to the working directory.
Code was tested with MATLAB R2015b.
The package SynEM.Examples contains examples for running SynEM:
- synEMWorkflow.m: Direct test application of SynEM using only a volume segmentation and raw data array
- neuron2neuronErrorEstimates.m: How to use the connectome error estimation (Fig. 5 in Staffler et al.)
To test run SynEM, execute the following Matlab command
>> SynEM.Examples.synEMWorkflow
or
>> run('SynEM.Examples.synEMWorkflow.m')