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

(A. Einstein)

**S**ingle-particle **IM**age **P**rocessing **L**inux **E**ngine 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.

Our **PRIME** (for **PR**obabilistic **I**nitial **M**odel generation for single-particle cryo-**E**lectron microscopy) code has undergone major revisions. First, we re-cast the original PRIME algorithm into an approach for solving the problem of Simultaneous 2D Alignment and Clustering (SAC). The PRIME SAC solver, implemented in the program simple_prime2D

- generates improved 2D class averages from large single-particle cryo-EM datasets
- can be used in conjunction with simple_prime3D to obtain a reliable 3D starting model in a rapid and unbiased fashion
- overcomes inherent limitations in widely used clustering approaches, such as initialisation bias and local optimality
- is many times faster than other widely used approaches

Secondly, the program simple_prime3D implements a revised version of our *ab initio* 3D reconstruction code that is about 150 times faster than the previously released version. This speedup was accomplished using new theory for fast rotational matching of polar Fourier transforms based on Hadamard products calculated using a re-organised and highly parallelizable data structure. The paper describing this is not yet published, but we have released the code since we anticipate that the massive speedup will have major impacts for our users. For example, less than 10,0000 particles downscaled to about 100x100 pixels can feasibly be processed on a modern laptop equipped with an Intel i5 or i7 processor. We executed an *ab initio* 3D reconstruction run using simple_prime3D on half a million images downscaled to 64x64 pixels in less than 5 hours on a cluster with 224 CPU cores (Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz).

**SIMPLE 2.0 can be found here.**

**SIMPLE 1.0 can be found here.**