Software:

The Environment for Modular Image Reconstruction Algorithms and Data Analysis (EMIRA).  EMIRA Primer,  Release notes, Manual, Download (last update December 19, 2016).

Short description: This package contains a universal user interface for modular image processing using a plugin type mechanism for accessing standalone image processing programs. Image format conversion from and too standard EM image formats is provided through the implementation of bconvert (BSOFT). It is very easy to add your own operations to the system, which then are available in an interactive and scripting environment. This not only makes it an excellent environment for highly flexible image processing task, but also provides an ideal environment to test new algorithms. Highlights of the algorithms currently implemented are:

3D and 2D Radon transforms and inversions, 3D projection alignment, 3D classification of volumes with missing data including estimation of missing data, nonlinear mapping with variable distance weights. Standard operations include: Fourier transform, rotation, shift, cross-correlation, Fourier ring correlation, correspondence and principal component analysis, classification with moving centers and many more.

If you have created your own modules for EMIRA we gladly add them to the distribution. Please contact us for details. (Note, all code provided for distribution must be open source, compatible with the GPL license.)

(see also: M. Radermacher, A New Environment for Modular Image Reconstruction and Data Analysis, Microscopy and Microanalysis 19, S2, 2013, 762 – 763)

Gadgets:

Grid preparation, a device for obtaining deep stain embedding by fast drying. For more sample preparation instructions see also: Ruiz T, Radermacher M.Three-dimensional analysis of single particles by electron microscopy: sample preparation and data acquisition. Methods Mol Biol. 2006;319:403-25.