Visualizing Tomograms

Tom Goddard
November 3, 2022
CZI Imaging Institute workshop

What are the needs for visualization tools for tomography?

Tomograms and segmentations

   Chikungunya virus assembly and budding visualized in situ using cryogenic electron tomography.
   Chmielewski D, Schmid MF, Simmons G, Jin J, Chiu W.
   Nat Microbiol. 2022 Aug;7(8):1270-1279.

  • Tomogram of budding Chikungunya virus particles and segmentation.
  • Subtomogram averaging on partially budded viruses, 12 states.
  • 185 tomograms, 1900 budding viruses, 545 nucleocapsid-like particles, 7700 trimer spikes.

Large EM data: Connectomics

   Dense connectomic reconstruction in layer 4 of the somatosensory cortex.
   Motta A, Berning M, Boergens KM, Staffler B, Beining M, Loomba S, Hennig P, Wissler H, Helmstaedter M.
   Science. 2019 Nov 29;366(6469)

Software for visualizing segmentations

Segmentations at the EMDB

Prototype EMDB segmentation web viewer

Mock-up of what a volume browser for 3D cellular imaging data could look like, using HIV and simian immunodeficiency virus (SIV) as an example, by integrating data from different imaging modalities. Figure 2 from 2012 workshop "A 3D Cellular Context for the Macromolecular World".

Prototype EMDB segmentation annotation tool

Mock-up of a possible Segmentation-Annotation Tool (SAT).
Figure 3 from 2015 workshop "Building bridges between cellular and molecular structural biology."

EMDB Segmentation File Format

Research community adoption

How CZI Imaging Institute can help EMDB segmentation effort

I asked Paul Korir how the CZI Imaging Institue could help. Here are his suggestions


Seeing what is hard to see in 3D images

Virtual Reality

Trying to place molecular complexes involved in photosynthesis in a tomogram in the Chlamydomonas thylakoid membrane.


Mitochondrial ATP synthase dimer atomic model and single-particle map
Shadows from all directions. No shadows.

AGAVE 3D microscopy viewer with lighting controls.
3D light microscopy of cells rendered with and without lighting.

Machine learning segmentation methods

Animating cell processes

Chikungunya segmentation. Phage T4 sheath contraction. Kinesin motor rotation.