Automatic 3D Synapse Analyzer
“Automatic Analysis of 3D Subcellular Distribution of Synapses in Complex Dendritic Arbors”
Jonathan Sanders, Edward Hottendorf , Gabriella Sterne, Hanchuan Peng, Bing Ye, and Jie Zhou
This project contains codes for a 3D synapse quantifier. It is to analyze 3D subcellular synapse distribution using multi-channel microscopic images.
The system consists of 3 components: Synapse Counter, Neuron Reconstructor and Distribution Quantifier. The 3rd component, Distribution Quantifier, takes the outputs of the first two components to produce the subcellular synapse distribution. Example outputs of synapse counter and neuron reconstructor are provided for testing out the Distribution Quantifier directly.
Code:
./ThreeDSynapseCounter
Usage:
Synapse Counter is an ImageJ Plugin. Follow ./ThreeDSynapseCounter/readme.txt
Input: 3D image of synapses. Preprocessing steps are described in ./ThreeDSynapseCounter/readme_long.txt Section (2), if needed.
Output: marker files of detected synapses.
Note: If the image has a pre-synaptic channel, run Colocal_filer.java for co-localization of post- and pre- synaptic makers.
Code/Usage:
It is deployed as a Vaa3D plugin. Vaa3D can be downloaded from vaa3d.org Vaa3d -> plug-in -> simple axis analyzer
Input: 3D image of the neurite
Output: a swc file that describes the structure of neurite.
Code:
./Analyzer
Usage:
The distribution quantifier is a standalone Java program. Follow the readme ./Analyzer/readme.txt
Input: a) a marker file from the Synapse Counter and b) a (sorted) swc file from Neuron Reconstructor.
Output: Statistics of synapse distribution on screen; a space-separated file and its bins based on radius of associated branches.
Note: Example synapse marker file (ExampleDetectedSynapse.marker) and example reconstructed neuron file (ExampleReconstructed.swc) are provided in the folder.