Synapse Detection in EM Stacks

Learning Context Cues for Synapse Segmentation in EM Volumes

We present a new approach for the automated segmentation of excitatory synapses in image stacks acquired by electron microscopy. We rely on a large set of image features specifically designed to take spatial context into account and train a classifier that can effectively utilize cues such as the presence of a nearby post-synaptic region. As a result, our algorithm successfully distinguishes synapses from the numerous other organelles that appear within an EM volume, including those whose local textural properties are relatively similar. This enables us to achieve very high detection rates with very few false positives.

C. Becker, K. Ali, G. Knott, P. Fua


Automatic segmentation of synapses. Comparison between our method and [1].

This video shows 2D cuts at different Z-planes. Voxels detected as synapses labeled in red.

[1] Kreshuk, A., Straehle, C., Sommer, C., Koethe, U., Knott, G., Hamprecht, F.: Automated segmentation of synapses in 3D EM data. ISBI 2012

3D reconstruction of the detected synaptic voxels after removing connected regions with less than 2000 voxels on a somatosensory cortex EM cube.


C. J. Becker; K. Ali; G. Knott; P. Fua : Learning Context Cues for Synapse Segmentation; IEEE Transactions on Medical Imaging. 2013. DOI : 10.1109/Tmi.2013.2267747.