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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 ]
... Opt. Soc. Am. A, 7, 601-610. Brenner, S. & Horne, R. W. (1959). A negative staining method for high resolution ... Biochim. Biophys. Acta, 34, 103-110. Carragher, B. & Smith, P. R. (1996). Advances in computational image processing for microscopy. J. ... Nature (London), 217 130-134. Dube, P., Tavares, P., Lurz, R. & van Heel, M. (1993). The portal protein of ...

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 ]
... 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 ...

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 ]
Handling multiple 3D reconstructions in parallel 19.9.9. Handling multiple 3D reconstructions in parallel A new parallel 3D reconstruction program was created based on the earlier ex-core program implementing the `exact filter' algorithm (Harauz & van Heel, 1986). With all 3D reconstructions now organized in in-core subroutines, the new program ...

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 ]
... 7, 601-610. Elad, N., Clare, D. K., Saibil, H. R. & Orlova, E. V. (2008). Detection and separation of heterogeneity ... Ultramicroscopy, 6, 187-194. Heel, M. van, Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, ...

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 ]
... Biophys. Acta, 851, 353-360. Dube, P., Tavares, P., Lurz, R. & van Heel, M. (1993). The portal protein of bacteriophage ... J. 12, 1303-1309. Heel, M. van, Gowen, B., Matadeen, R., Orlova, E. V., Finn, R., Pape, T., Cohen, D., Stark, H., Schmidt, R., Schatz, ...

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 ]
Parallel automatic particle picking 19.9.6. Parallel automatic particle picking Parallel processing is of increasing importance for collecting the large raw data sets required for 4D cryo-EM. If we are interested in a structure that represents 1% of all molecular complexes, we need to increase the size of the data set ...

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 ]
... 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 ...

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 ]
... 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 ...

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 ]
... References Heel, M. van, Harauz, G., Orlova, E. V., Schmidt, R. & Schatz, M. (1996). A new generation of the IMAGIC ...

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