Skip to content


Tomviz supports two types of data; volumes and tilt series. Volumes are from tomographic reconstructions or sectioning, and tilt series are projection images with associated angles. Specialized tools are provided for each type of data, more specifically, Data Transforms and Segmentation menu have tools for volumes, while Tomography menu provides tools for tilt series. Users can also add their own tools to Custom Transforms menu.

Tilt Series

The Tomviz installer bundles a sample tilt series and the corresponding reconstruction. The tilt series sample will automatically set the tilt angles.

Loading sample tilt series

To load the sample tilt series select Star Nanoparticle (Tilt Series) from the Sample Data menu.

Open sample tilt series

Once loaded you will see a default view of the data showing the outline and a slice through the center of the tilt series.

Sample tilt series

Creating a tilt series

Data can be marked as a tilt series by selecting Mark Data As Tilt Series from the Tomography menu as shown below.

Create tilt series

The angles can be specified in a number of ways, such as specifying the start and end image number with the start and end angles. It is important to enter accurate angles in order to obtain a good reconstruction.

Create tilt series by range

You can also set the angle for each image by choosing Set Individually from the dialog. That mode supports loading a list of angles from a file too.

Create tilt series custom

Aligning Data

The key to a good reconstruction is well aligned data. The Tomography menu offers a number of automated and manual alignment options.

Image data alignment

Image alignment can be achieved with automated algorithms, we currently offer cross-correlation and center-of-mass based alignments.

Tomography menu

It is often necessary to use manual alignment methods as a final step to achieve the best alignment of projection images. The alignment offsets can be saved to a state file and adjusted in future sessions.

Manual align

The manual alignment procedure uses two main interaction modes: toggling between images or showing a difference between two images. Ideally your sample will have a fiducial marker that can be used across all images for alignment. The current image can be aligned to the previous, next or a fixed image. The tool supports keyboard shortcuts to move between frames, introduce offsets, etc.

Alignment dialog

The image above shows the standard toggle mode, and below shows a typical image difference. Both modes can benefit from zooming, adjusting the brightness or the contract. Alignment offsets can be saved to a file, or loaded from a file.

Manual align difference

Tilt axis alignment

Once the images are aligned it is important to assure the tilt axis is aligned. The tilt axis can be shifted and tilted, with reconstruction previews showing the impact of these adjustments. There are automated routines, and the manual tilt axis alignment tool.

Tilt axis menu

You can choose three slices to show a preview of the reconstruction, these should be positioned one on a fiducial particle ideally, with the other two positioned on features that have contrast spread along the volume.

Tilt axis dialog

If the tilt axis is well aligned a fiducial marker will appear to be circular in the reconstruction preview. If they are crescent shaped this is normally an indication that the tilt axis is not well aligned.

Tilt axis dialog

It is possible to select independent color maps for the reconstruction previews.

Tilt axis dialog

Additionally, it is possible to align a tilt series that uses a vertical axis of rotation rather than a horizontal one. This can be done by selecting "Vertical" from the "Orientation" combo box. The lines will then be rotated, and the tilt series may be manually aligned as before.

Tilt axis dialog