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Four-dimensional cryo-electron microscopy at quasi-atomic resolution: IMAGIC 4D
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, ch. 19.9, pp. 624-628 [ doi:10.1107/97809553602060000875 ]
... the 3Ds reach stability (Harauz & van Heel, 1986; van Heel & Schatz, 2005). 19.9.8. MSA and its parallelization | | Multivariate statistical analysis ... coherent with contributors operating from three different continents. References Adrian, M., Dubochet, J., Lepault, J. & McDowall, A. W. (1984). Cryo ... 32-36. Boekema, E. J., Berden, J. A. & van Heel, M. G. (1986). Structure of mitochondrial F1-ATPase studied ...

Angular reconstitution 4D refinements
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.10, p. 627 [ doi:10.1107/97809553602060000875 ]
... the case with the MRA program in IMAGIC. References Heel, M. van (1987). Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy, 21, 111-124. Heel, M. van, Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. (2000). Single-particle electron cryo- ...

Handling multiple 3D reconstructions in parallel
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.9, pp. 626-627 [ doi:10.1107/97809553602060000875 ]
... Harauz & van Heel, 1986). References Harauz, G. & van Heel, M. (1986). Exact filters for general geometry three dimensional reconstruction. ...

MSA and its parallelization
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.8, p. 626 [ doi:10.1107/97809553602060000875 ]
... of the normal IMAGIC distribution. References Borland, L. & van Heel, M. (1990). Classification of image data in conjugate representation spaces. ... Dimensional Electron Microscopy of Macromolecular Assemblies. Oxford University Press. Heel, M. van (1984). Multivariate statistical classification of noisy images (randomly oriented biological macromolecules). Ultramicroscopy, 13, 165-183. Heel, M. van & Frank, J. (1981). Use of multivariate statistics ...

Parallel multi-reference alignments and reference bias
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.7, p. 626 [ doi:10.1107/97809553602060000875 ]
... the 3Ds reach stability (Harauz & van Heel, 1986; van Heel & Schatz, 2005). References Boekema, E. J., Berden, J. A. & van Heel, M. G. (1986). Structure of mitochondrial F1-ATPase studied by ... 353-360. Dube, P., Tavares, P., Lurz, R. & van Heel, M. (1993). The portal protein of bacteriophage SPP1: a ...

Parallel automatic particle picking
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.6, p. 625 [ doi:10.1107/97809553602060000875 ]
... . References Boekema, E. J., Berden, J. A. & van Heel, M. G. (1986). Structure of mitochondrial F1-ATPase studied by ... and image processing. Biochim. Biophys. Acta, 851, 353-360. Heel, M. van (1982). Detection of objects in quantum noise-limited ...

Full 2D (parallel) astigmatic contrast transfer function correction
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.5, p. 625 [ doi:10.1107/97809553602060000875 ]
... References Grant, T., van Duinen, G., Patwardhan, A. & van Heel, M. (2011). Exploiting astigmatism in single particle cryo electron microscopy. Submitted. Heel, M. van, Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. (2000). Single-particle electron cryo- ...

Software parallelization
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.4, p. 625 [ doi:10.1107/97809553602060000875 ]
... Scientific and Engineering Computation Series. Cambridge, MA: MIT Press. Heel, M. van, Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, M. & Patwardhan, A. (2000). Single-particle electron cryo-microscopy: ...

IMAGIC `4D' processing/data format
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.3, pp. 624-625 [ doi:10.1107/97809553602060000875 ]
IMAGIC `4D' processing/data format 19.9.3. IMAGIC `4D' processing/data format Recently, another major overhaul of the system was undertaken in order to better handle three-dimensional structural heterogeneity. The relevant IMAGIC programs can now loop over entire three-dimensional volumes (and not just two-dimensional images) allowing programs to tackle ...

The IMAGIC software system
van Heel, M., Portugal, R., Rohou, A., Linnemayr, C., Bebeacua, C., Schmidt, R., Grant, T. and Schatz, M.  International Tables for Crystallography (2012). Vol. F, Section 19.9.2, p. 624 [ doi:10.1107/97809553602060000875 ]
... Windows XP/Vista/7 and Mac OS-X. References Heel, M. van, Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. (1996). A new generation of the IMAGIC image ...

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