Reconstructing a Cryo-Sample with Patch Tracking

(IMOD 4.11)

University of Colorado, Boulder


This tutorial will guide you through processing a cryo tilt series without fiducials, using the patch tracking method of alignment.  The tilt series is from a vitrified section and was acquired by Cedric Bouchet-Marquis.  It is recommended that you do the basic cryo tutorial before this one.


Getting started:

Tomogram setup:


Coarse Alignment

Fiducial Model Generation:

In this step, patches of image will be tracked from one view to the next, and the center positions of the patches will be placed into a model file. This model can be used to solve for the tilt series alignment, much as a model of true fiducial markers can.

Fine Alignment:

For this data set, the fine alignment process will involve cycling back to the patch tracking page.

Tomogram Positioning

This sample can be positioned by viewing X/Z slices in the binned-down tomogram.

Final Aligned Stack Creation:

Tomogram generation:


Clean Up:

Archive the original stack and clean up as usual.