Tomogram Segmentation

Availability: EMAN2 daily build after 2016-10

Programs in the tomogram segmentation requires Theano, which is not distributed with EMAN2. To use the protocol, one needs to build EMAN2 from source and install Theano manually.

Getting Started

First, make an empty directory and get into that directory in command line. Then run from the command line. While a GUI window will show up, it is still a good idea to keep the command line window open to view the messages.

Click the Workflow Mode drop-down menu next to navigate to the TomoSeg panel. TomoSeg Panel

Import Tomograms

Click "Import Tomogram Files" on the left panel. On the panel showed up on the right, click "Browse" next to import_files, and select the tomogram you would like to segment in the browser window, and click "Ok". If you want to bin the tomogram before processing, write the shrinking factor in the text box next to "shrink". Import Tomogram

Select Positive Samples

Manually Annotate Samples

Select Negative Samples

Build Training Set

Train Neural Network

Apply to Tomograms


Darius Jonasch, the first user of the tomogram segmentation protocol, provided many useful advices to make the workflow user-friendly. He also wrote a tutorial of the earlier version of the protocol, on which this tutorial is based.