[3dem] RELEASE NOTE SIMPLE 2.5

[Hans Elmlund]

Dear All:

We announce the release of a new version of our program package SIMPLE
(v2.5) for single-particle cryo-EM *ab initio* 3D reconstruction (web:
simplecryoem.com)

New features include:

* A new DDD movie pre-processing program that implements motion correction
based the same principal strategy as Grigorieff's Unblur. 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 for DDD movie pre-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 the
new 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
automates initialisation, updates search parameters automatically and
dynamically down-scales the images for improved performance.

If you need help installing SIMPLE, optimising its execution for your
computer architecture or experience any problems or bugs please use the
contact form on the webpage (www.simplecryoem.com/contact.html) to file a
help ticket. We will endeavour to respond within two days.

Happy image processing!

The SIMPLE team:

Cyril F Reboul
Michael Eager
Dominika & Hans Elmlund

-- 
*HANS ELMLUND PhD *
Associate Professor

*ARC Centre of Excellence for Advanced Molecular Imaging*
*Dept. of Biochemistry and Molecular Biology*
Monash University
Room 228, Level 2, Building 77, Clayton Campus
23 Innovation Walk
Clayton VIC 3800
Australia

T: +61 399029310
M: +61 (0)45271213
E: hans.elmlund at monash.edu
simplecryoem.com
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