Orientation of Synapse

Apart from predicting the location of the synapse we will also predict the orientation of the synapse. We will be trying out the following methods to determine the orientation:

1. Fitting an ellipse
   
2. Image moments
3. Gradient image analysis
   
4. Image processing toolbox

As per previous months meeting discussions apart from determining the orientation of the synapse the direction of the synapse also has to be Synapse also has to be determined. The clue that we have is the pre-synaptic densities bend the membrane to a concave shape (from the receptor neuron). One visual clue that we have is that the pre-synaptic density if vesicles makes the transmitter part of the Synapses appear blobbier.

The easiest one to try quickly is the one in image processing toolbox. The algorithm for determining the angle that is the following.

1. For the circular patch, threshold values below the gray value that is at 50 percentile point.
2. For the resulting binary image choose the largest patch and determine the orientation of the match from the "regionprops" command.
3. The orientation of the synapse is perpendicular to the orientation of the region.

The results for this method are shown below. The input image is shown to the left. THe input image is an image downsampled 25% and smoothened by perona-malik smoothening for 25 iterations. Then the grey values of this image have be ordered and the 50 percentile grey value is calculated and all grey value above it are set as "1" and the rest are set as "0".

The result of the above thresholding is shown to the left here. The region property of orientation is determined which is likely to the orientation of the membrane. The orientation of the synapse is perpendicular to the synapse. Hence the orientation of the synapse is +15.7 degrees to the positive X-axis.