Bsoft: Image Processing for Structural Biology

Background

Bsoft resulted from an effort to deal with the plethora of image formats during a time when we were building a prototype database for microscopic images called BioImage (Carazo et al., 1999). BioImage contributed to the establishment of the Electron Microscopy Databank (EMDB) at the EBI in Hinxton, UK (https://www.ebi.ac.uk/emdb/). Bsoft has been used in many projects, to determine the structures of proteins and assemblies from cryo-electron micrographs, these days called cryoEM.

There are three conceptual domains for using Bsoft: (i) dealing purely with images, (ii) producing and handling the very large number of parameters or metadata required in processing electron micrographs, and (iii) interpreting 3D reconstructions through segmentation and models (Heymann, 2001; Heymann and Belnap, 2007; Heymann et al., 2008; Heymann, 2018a; Heymann, 2020; 2021). This article covers the entry point to image processing in Bsoft, providing the basis for understanding the more complicated processing involved under the last two domains.