Automated Synapse Detection Method for Cerebellar Connectomics.

The connectomic analyses of large-scale volumetric electron microscope (EM) images enable the discovery of hidden neural connectivity. While the technologies for neuronal reconstruction of EM images are under rapid progress, the technologies for synapse detection are lagging behind. Here, we propose a method that automatically detects the synapses in the 3D EM images, specifically for the mouse cerebellar molecular layer (CML). The method aims to accurately detect the synapses between the reconstructed neuronal fragments whose types can be identified. It extracts the contacts between the reconstructed neuronal fragments and classifies them as synaptic or non-synaptic with the help of type information and two deep learning artificial intelligences (AIs). The method can also assign the pre- and postsynaptic sides of a synapse and determine excitatory and inhibitory synapse types. The accuracy of this method is estimated to be 0.955 in F1-score for a test volume of CML containing 508 synapses. To demonstrate the usability, we measured the size and number of the synapses in the volume and investigated the subcellular connectivity between the CML neuronal fragments. The basic idea of the method to exploit tissue-specific properties can be extended to other brain regions.

Automatic white blood cell segmentation using stepwise merging rules and gradient vector flow snake.

This study aims at proposing a new stained WBC (white blood cell) image segmentation method using stepwise merging rules based on mean-shift clustering and boundary removal rules with a GVF (gradient vector flow) snake. This paper proposes two different schemes for segmenting the nuclei and cytoplasm of WBCs, respectively. For nuclei segmentation, a probability map is created using a probability density function estimated from samples of WBC's nuclei and sub-images cropped to include a nucleus based on the fact that nuclei have a salient color against the background and red blood cells. Mean-shift clustering is then performed for region segmentation, and a stepwise merging scheme applied to merge particle clusters with a nucleus. Meanwhile, for cytoplasm segmentation, morphological opening is applied to a green image to boost the intensity of the granules and canny edges detected within the sub-image. The boundary edges and noise edges are then removed using removal rules, while a GVF snake is forced to deform to the cytoplasm boundary edges. When evaluated using five different types of stained WBC, the proposed algorithm produced accurate segmentation results for most WBC types.