/synapse-unet

A three dimensional U-net for synaptic cleft detection.

Primary LanguagePythonMIT LicenseMIT

Synapse-unet

A three dimensional U-net for synaptic cleft detection from electron microscopy (EM) images.

Network Architecture

image

Loss Function

We try to solve the extreme class imbalance by using an energy function:

where V is the total number of voxels in each training block, α is a weight index, Ω and Ω' denote synaptic cleft voxels and non-synaptic voxels respectively.

Dataset

Training and testing data comes from MICCAI Challenge on Circuit Reconstruction from Electron Microscopy Images (CREMI challenge). Three training volumes of adult Drosophila melanogaster brain imaged with serial section Transmission Electron Microscopy (ssTEM) are provided.