Walkthrough on GUI based tilt series alignment

Dynamo includes a package for automated aligned and reconstruction of tilt series. This walkthrough guides you through the steps on how to use it with a GUI. A different page in this wiki

Data

We have prepared version a tilt series from the EMPIAR entry [XXXX]

/html/w/doc/data/hiv/align/b001ts001.mrc

In this binned version, the pixel size is 2'7 Angstrom (original was 1.35, this is bin level 1 in Dynamo)

Creating an alignment workflow

The basic function for invoking the GUI is dtsa (short form of dynamo_tilt_series_alignment;

 dtsa('folder','firstAlign);

The data for the workflow (tilt series, angles) could have been introduced directly when creating the workflow, we however will introduce each item explicitly in this walkthrough.

GUI description

Execution Areas

The GUI is divided in five areas, which are sets of steps that can be executed sequentially. Sequential execution is the natural way of proceeding; but steps can be visited in any order, i.e., a step can be reexecuted in a later moment after updating its information.

Steps

Steps needs to be open (letters in grey) in order to be executed. They become open when the input they require gets computed and stored during execution of the workflow. When a step is under execution, its pushbutton becomes green.

Toolbox

The tool icon can be secondary clicked and will provide a

The areas in the alignment task

Detection

Visualization matrix

This step just creates a binned version of the tilt series stack to accelerate visualizations that will be invoked in a later point.

CTF

In this GUI CTF estimation and correction are delegated to CTFFIND4 and Imod's ctfphaseflip programs respectively.