Using the Batch Reconstruction Interface with Dual-axis
Tutorial Data Sets
University of Colorado,
This document will take you through the steps required to reconstruct the IMOD
dual-axis tutorial data sets in Etomo's interface for batch reconstruction with
It explains some of the most important points as they arise. For more details,
consult Batch Tomography Guide, which you
should read through before trying to process your own data sets in this
interface. In this document, labels in the interface
are shown in Bold, and entries in fields are shown in Italics.
- Download both the
and the unbinned tutorial data sets from the IMOD web site;
this allows more features to be illustrated than doing just one data set.
- Move both files, "tutorialData.tar.gz" and "tutorialData-1K.tar.gz", to the
directory where you want to do batch processing.
- In a terminal, cd to that directory.
- Unpack the unbinned set, rename its directory, and unpack the binned set:
mv tutorialData BB-unbinned (Use ren instead of mv on Windows without Cygwin)
You can use code>tar -xzf instead of
imoduntar except on Windows without Cygwin.
Go to the batch interface and set up the batch parameters:
- Start Etomo with
- Press Batch Tomograms on the Front Page. The interface opens
with the Batch Setup tab.
- Select plasticSection.adoc as the System Template.
This template turns on Sobel filtering when tracking beads to give improved
centering of the points.
- The initial radio buttons allow stacks to be moved
from elsewhere into automatically created data set directories. Your
stacks are already in their own data set directories, so there is no need to
change the default selection.
- At the bottom, two fields allow one to change the root name that will be used as a
prefix for all the batch processing files, and to select a different Location in which various batch project files will be kept. Again,
there is no need to change the defaults here.
Add the two stacks, unbinned then binned, and set their properties: