A critical problem in electron tomography is the deformation of the specimen due to radiation, or ‘‘shrinkage,’’ which interferes with image alignment and thereby limits resolution. Here, we describe a general strategy for refining preliminary reconstructions which allows the damage due to the shrinkage of plastic-embedded thin sectioned specimens (50–80 nm) to be corrected. The basic steps of the strategy involve: (a) the partition of the preliminary reconstruction into sub-volumes; (b) the extraction of corresponding sub-areas for each subvolume from the micrographs of the tilt series; (c) the re-projection of each sub-volume according to the orientation parameters; and (d) the refinement of these parameters by correlating each sub-area to the corresponding computed projection. We tested the strategy by refining chemical synapses reconstructed from series imaged with conical, double and single tilt geometries. The results gathered with local refinement were evaluated by visually inspecting the structure of biological membranes in the maps. In an effort to quantify these improvements, we studied the refined maps using correlation criteria and mapped the corrections applied to the orientation parameters in each sub-volume of the reconstruction. Simulation experiments complemented the data gathered by correlation analysis. Based on these criteria, we concluded that local refinement significantly improves the overall quality of the reconstructions of chemical synapses calculated from series imaged with conical and double tilt geometries.

Local refinement : an attempt to correct for shrinkage and distortion in electron tomography / Francesca Cantele, Lorenzo Zampighi, Michael Radermacher, Guido Zampighi, Salvatore Lanzavecchia. - In: JOURNAL OF STRUCTURAL BIOLOGY. - ISSN 1047-8477. - 158:1(2007), pp. 59-70.

Local refinement : an attempt to correct for shrinkage and distortion in electron tomography

Francesca Cantele;Salvatore Lanzavecchia
2007

Abstract

A critical problem in electron tomography is the deformation of the specimen due to radiation, or ‘‘shrinkage,’’ which interferes with image alignment and thereby limits resolution. Here, we describe a general strategy for refining preliminary reconstructions which allows the damage due to the shrinkage of plastic-embedded thin sectioned specimens (50–80 nm) to be corrected. The basic steps of the strategy involve: (a) the partition of the preliminary reconstruction into sub-volumes; (b) the extraction of corresponding sub-areas for each subvolume from the micrographs of the tilt series; (c) the re-projection of each sub-volume according to the orientation parameters; and (d) the refinement of these parameters by correlating each sub-area to the corresponding computed projection. We tested the strategy by refining chemical synapses reconstructed from series imaged with conical, double and single tilt geometries. The results gathered with local refinement were evaluated by visually inspecting the structure of biological membranes in the maps. In an effort to quantify these improvements, we studied the refined maps using correlation criteria and mapped the corrections applied to the orientation parameters in each sub-volume of the reconstruction. Simulation experiments complemented the data gathered by correlation analysis. Based on these criteria, we concluded that local refinement significantly improves the overall quality of the reconstructions of chemical synapses calculated from series imaged with conical and double tilt geometries.
3D reconstruction; Conical geometry; Electron tomography; Local refinement; Shrinkage correction
Settore INF/01 - Informatica
2007
Article (author)
File in questo prodotto:
Non ci sono file associati a questo prodotto.
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/44089
Citazioni
  • ???jsp.display-item.citation.pmc??? 13
  • Scopus 22
  • ???jsp.display-item.citation.isi??? 21
social impact