"Everything should be made as SIMPLE as possible, but no simpler"

(A. Einstein)

About SIMPLE 2.5

Single-particle IMage Processing Linux Engine is a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles. The SIMPLE back-end consists of an object-oriented numerical library written in modern Fortran. The SIMPLE front-end consists of a few standalone, interoperable components developed according to the "Unix toolkit philosophy".

SIMPLE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the license, or (at your option) any later version. SIMPLE is distributed with the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

   What is new in SIMPLE release 2.5

– A new DDD movie pre-processing program unblur that implements motion correction based the same principal strategy as Grigorieff’s program (hence the name). There are two important differences: automatic weighting of the frames using a correlation-based M-estimator and stochastic continuous optimisation of the shift parameters. This enables analysis of movies with severe pathologies due to radiation damage or extreme drift.

– A new program unblur_tomo for movie processing of tomographic tilt-series.

– Improved simultaneous 2D alignment and clustering with prime2D using a hybrid extremal/stochastic hill-climbing search approach, Wiener restoration-based CTF correction and acceleration of the search using Hadamard projection matching. It is now possible to generate a sub-nanometer resolution ab initio 3D reconstruction from class averages obtained with prime2D in a about 10 minutes on a laptop (MacBook Pro mid 2015, 2.8 GHz Intel i7, four physical cores).

– Improved ab initio 3D reconstruction from class averages using stochastic neighbourhood hill-climbing for initialisation of the 3D orientation search, improving the success rate from around 40% to 90-100% for more challenging starting model generation problems, executed with program ini3D_from_cavgs

– Serial CPU code optimisation through data re-organisation and pipelining.

– Improved parallel CPU performance through load balancing as well as data and algorithm re-organisation. It is now possible to process data sets of realistic size on laptops or lightweight workstations that cost less than 2,000 USD.

– High-level workflows for 2D analysis and initial 3D model generation that automate initialisation, update of search parameters and dynamic down-scaling of the images for improved performance.

 SIMPLE 1.0 can be found here.

 SIMPLE 2.0 can be found here.

 SIMPLE 2.1 can be found here.