Particle Picking with Convolution Neural Nets

EMAN2 daily build after 2015-11-06

The program can be found in:

This program is developed by Muyuan Chen. Please contact if you have any questions.

Here we train a stack of convolutional neural nets to recognize particles in the micrograph. The basic structure of the convolutional net used in this program is described here:

This program requires Theano, in addition to other EMAN2 dependencies. Guide to install Theano can be found here:

This program runs on GPU if the GPU environment is set up in Theano. If not, it should be able to run on CPU, but the speed may be slower. Also, some functions (not very useful at this point) will be disabled if CPU is used.


We use some IP3R images as a example.

input micrograph

Making Training Set

particles training set

negative training set

Train the convolutional network

convolution training output

Due to some Theano issue, if the program is run on CPU, the second image (output from the first layer) will not display.

convolution training test on image

Box particles



A zoomed in view of the particles:


That's it~

Muyuan 2015-11-05