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  • Visiting Scientist
  • Deputy Director of Center
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  • Deputy Head of Facility
  • Director of Center
  • Director of Department
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Scientific Fields
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Technique
Starting Date
11
May 2020
Status
Ongoing
Members
5
Structures
1

About

 

Tomographic reconstruction

In electron tomography, the tilt series acquired, by tilting the sample to different angles under the electron beam (usually every 1 or 2 degrees from about −60° to +60°), can then be computationally reconstructed into a 3D volume.

Typically, reconstruction of electron tomograms consists of five steps; pre-processing, estimation of initial image shifts, preparation of the fiducial model and tilt-series alignment, post-processing, and reconstruction. In case of dual axis tomography the tomographic volumes from each axis are build separately and combined in a final step.

UBI users are encouraged to reconstruct their own tomograms with IMOD, using either their own computing resources or the ones provided by UBI.  IMOD is installed in all UBI’s workstations.

 

Segmentation

For volume data (either coming from electron tomography or FIB-SEM acquisitions) containing more complex structures, a direct 3D volume rendering is often difficult to analyze. Especially in CryoET where the signal to noise ratio is quite low. Their interpretation is therefore simplified by creating 3D surface models by locating objects of interest and boundaries using segmentation tools.

UBI offers three workstations for manual segmentation with Amira.  One of which is equipped with a Wacom interactive pen display. Academic solutions are also available from all UBI’s workstations through IMOD segmentation tools coupled to the UCSF Chimera for further 3D modeling and surface rendering.

UBI is further encouraging the use of semi-automated segmentation methods through ilastik and/or eman2.3

Quemin ER, Corroyer-Dulmont S, Baskaran A, Penard E, Gazi AD, Christo-Foroux E, Walther P, Abergel C, Krijnse-Locker J, (2019). Complex Membrane Remodeling during Virion Assembly of the 30,000-year-old Mollivirus Sibericum. J Virol. 2019 Jul 1; 93(13): e00388-19. 
Lemos M, Mallet A, Bertiaux E, Impert A, Rotureau B, Bastin P, (2020). Timing and original features of flagellum assembly in trypanosomes during development in the tsetse fly. Parasit Vectors.  13:169. 

 

Subtomogram analysis

 

-under construction-