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.
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.
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
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