Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.
train command accepts radius as an optional argument, and in most places it's set to either 1, 2, or 3 (default), regardless of what actual radius in pix is. For example, this is the radius description in train script:
training.add_argument('-r', '--radius', default=3, type=int, help='pixel radius around particle centers to consider positive (default: 3)')
However, the actual positive area particle center is usually larger (8 and more, even with downscaling). Even extract command reflects radius boundaries (for tuning) between 5 and 100.
When I tried to increase the radius for training, I got worse results than with a smaller radius. Why the radius for training don't seem to correspond to an actual radius of particles?
traincommand accepts radius as an optional argument, and in most places it's set to either 1, 2, or 3 (default), regardless of what actual radius in pix is. For example, this is the radius description intrainscript:However, the actual positive area particle center is usually larger (8 and more, even with downscaling). Even
extractcommand reflects radius boundaries (for tuning) between 5 and 100.When I tried to increase the radius for training, I got worse results than with a smaller radius. Why the radius for training don't seem to correspond to an actual radius of particles?