The software package protomo was originally developed at Florida State University by Hanspeter Winkler. It is distributed for the Linux operating system and consists of standalone programs for general image manipulation, tilt series alignment, and subvolume processing. Shell scripts are provided that call the command line programs to automate the alignment, so that multiple datasets can be processed in parallel.

References for tilt series alignment

Winkler Hanspeter and Taylor Kenneth A. (2006). Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography. Ultramicroscopy 106, 240-254.

Winkler Hanspeter and Taylor Kenneth A. (2013). Marker-free dual-axis tilt series alignment. J. Struct. Biol. 182, 117-124.

References for subvolume processing

Winkler Hanspeter (2007). 3D reconstruction and processing of volumetric data in cryo-electron tomography. J. Struct. Biol. 157, 126-137.

Winkler Hanspeter and Taylor Kenneth A. (1999). Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle. Ultramicroscopy 77, 141-152.

Winkler Hanspeter, Zhu Ping, Liu Jun, Ye Feng, Roux Kenneth H., and Taylor Kenneth A. (2009). Tomographic subvolume alignment and subvolume classification applied to myosin V and SIV envelope spikes. J. Struct. Biol. 165, 64-77.

Wu Shenping, Liu Jun, Reedy Mary C., Winkler Hanspeter, Reedy Michael K., and Taylor Kenneth A. (2009). Methods for identifying and averaging variable molecular conformations in tomograms of actively contracting insect flight muscle. J. Struct. Biol. 168, 485-502.