Overview

This package aims to provide a simple API for aligning tilt-series using IMOD in Python and from the command-line.

Tilt-series alignment models how a 3D specimen is projected into 2D. Reproduced from a paper by David Mastronarde.

Why does this package exist?

IMOD is a powerful software package with a huge API surface. Setting up batchruntomo can be tricky for those unfamiliar with IMOD and taking the results into downstream tools for further processing requires a deep understanding of IMOD's metadata model.

Covering only the use cases of single-axis cryo-TEM tilt-series alignment, this package aims to provide a simple way to align tilt-series and work with IMOD metadata for cryo-ET practitioners more familiar with Python and shell scripting than IMOD.

Usage

I want to...

• align a tilt-series with fiducials in Python
• align a tilt-series with patch-tracking in Python
• align a tilt-series with fiducials from the command-line
• align a tilt-series with patch-tracking from the command-line
• work with IMOD metadata in Python

Further reading

• IMOD tomography guide
• Fiducial Marker and Hybrid Alignment Methods for Single- and Double-axis Tomography