Clean up noisy thresholded binary data

Result: before and after

Step 1: de-noise original dataset

usually do a default gaussian, OR median filter

Step 2: threshold and de-noise binary dataset

1. thresholding: I used interactive thresholding, the left side value ( a small number slightly > 0) somehow didn’t show in the property panel, I attach the result as threshold.png, more or less look like that.

   

2. apply majority filter 9x9 in xy plane

   

3. remove small spots 80 pixels, xy plane

   

4. remove small holes, 60 pixels, xy plane