Removing contamination-induced reconstruction artefacts
in cryo electron tomograms from FIB-milled samples
JJ Fernandez (1), U Laugks (2), M Schaffer (2) (2), FJB Bauerlein (2), M Khoshouei (2),
W Baumeister (2), V Lucic (2)
(1) Spanish National Research Council (CSIC). Oviedo. Spain.
(2) Max-Planck-Institute of Biochemistry, Martinsried, Germany.
Contact: jjfernandez.software @ gmail.com
Description
MaskTomRec is a software program for tomographic reconstruction that removes artefacts caused by contamination present in samples during imaging by electron microscopy. Those artefacts in tomograms may be induced by different types of contamination, for instance surface contamination associated with thinning by focused ion beam (FIB). The layer of platinum usually sputtered on FIB-milled lamellas to improve the conductivity can also induce artefacts in the tomograms, and thus can also be subjected to removing. Even gold fiducial markers typically added to the sample to facilitate tilt-series alignment can be considered contamination that, indeed, generates streak artefacts in tomograms.
The procedure implemented in MaskTomRec makes use of a mask enclosing the contamination in the tomogram. As the procedure evolves, the contamination, and as a result, the reconstruction artefacts induced by the contamination are gradually removed, while the valuable structural information is preserved. As an output, the program provides the cleaned tomogram. Optionally, it may also give the restored tilt-series, where the contamination is removed. The tomographic reconstruction method within the cleaning procedure in MaskTomRec is Weighted Backprojection (WBP). SIRT might be used as well, later on the output restored tiltseries using other packages, for instance our program tomo3d.
A detailed description of the procedure implemented in the package can be found in the following article:
Removing contamination-induced reconstruction artefacts from cryo electron tomograms.
J.J. Fernandez, U. Laugks, M. Schaffer, F.J.B. Bauerlein, M. Khoshouei, W. Baumeister, V. Lucic
Biophysical Journal 110:850-859, 2016.
Please, cite this article if you use MaskTomRec in your works.
Download
Current version: April 2018
Available material:
Documentation in PDF: masktomrec.pdf
Binaries for x86-based platforms under Linux (64 bits).
Binaries for Intel-based Macs under OSX (built on OSX 10.6).