Reference

If you find Spring useful for your research, please cite:

Desfosses, A., Ciuffa, R., Gutsche, I., and Sachse, C. (2014). SPRING - an image processing package for single-particle based helical reconstruction from electron cryomicrographs. J Struct Biol 185, 15-26.

For further information find more Spring-related publications.

Installation

We provide binary downloads that include all required components and build recipes for all dependencies. Follow install instructions for more details.

Acknowledgements

Spring is released under the modified BSD lisence and integrates several different electron-microscopy specific and other open-source packages. Spring is entirely written in Python and is based on the EM functions and libraries of:

1. EMAN2

2. SPARX

3. CTFFIND/CTFTILT

Dependencies

Spring makes use of a number of scientific computing packages:

• Numpy and Scipy

• Openmpi

• Mpi4py

• Matplotlib

• VisVis

• SQLAlchemy

• Nosetests

• Sphinx

0.83.1432 (2014-12-30)

• Fixes and improvements

1. Installation procedures

• Updated dependencies GCC, Numpy, Scipy, Openmpi including build procedures.

2. SEGMENTREFINE3D

• Computation of persistence length at the end of each refinement run. Can be used now as a selection criterion for discarding less straight helices in the next refinement run.

• Selection criteria: Straight helices, Layer-line correlation and Projection matching cross-correlation are now selected in percent range of the distribution instead of cutoff values, e.g. upper 20 % –> 80 - 100 %.

• ‘Continue refinement option’ - in case no reference structure is given a 3D reconstruction based on the provided parameters is now created for further refinement.

• Improved segment-based motion correction, now accepts mrcs-stacks.

• Computation of structure-masked FSC with mask deconvolution according to Ultramicroscopy Chen et al. 2013 (Scheres and Henderson) for resolutions better than 12 Angstrom.

• Added error estimates for forward x-shift, forward out-of-plane tilt and in-plane rotation angles according to Sachse et al, 2007 J Mol Biol.

• Overhaul in symmetrization of volumes to make them perfectly even.

• Diagnostic power spectra are now always written out as EMAN2 image files in addition to diagnostic summary.

3. SEGMENTCLASS, SEGLAYERLATTICE

• Many minor fixes.

Note: old grid.dbs need to be upgraded to be readable by SEGGRIDEXPLORE.

% spring -udb='grid.db' -inp grid.db -out grid_upd.db

0.82.1339 (2014-09-15)

• Improved installation procedures including build and binary install scripts.

0.82.1339 (2014-04-25)

• General fixes, optimizations and enhancements

1. SEGMENTREFINE3D

• Fixes for data sets with large number of asymmetric units

• Fix/workaround for occasional database lock problems on cluster mounted nodes

• Fix in ‘Absolute limit of x and y-shifts’ handling. Now properly respects this.

• Declared some options as experimental: support remains limited.

• Occasional over-estimation of FSC fixed due to densities at upper and lower ends of filament

• Implementation of ‘independent half-set’ refinement (a.k.a. gold-standard refinement)

Note: the update will break reading your previous refinement.db files Database files can be updated as follows:

% spring -udb=refinement.db -inp=refinement024.db -out=refinement024_up.db

2. SEGREFINE3DINSPECT

• Additional option of signal-to-noise weighting using FSC file.

3. SEGLAYER2LATTICE

• Simulation of layer-line pattern takes rotational symmetry into account

0.81.1282 (2014-01-26)

• Fixes, enhancements and optimization

1. SEGMENTREFINE3D

• Disk requirements for temporary directories revised.

• Improved handling of selected segments. Spring processes helices as one entity and discards them later for 3D reconstruction.

• FSC only computed with cylinder mask.

• Improved experimental power spectra for high/maximum resolution analysis.

2. SEGMENT

• Fix in frame processing.

• Rotated stack only written if requested.

3. SEGMENTEXAM

• Addition of selection options from spring.db.

4. SEGCLASSEXAM

• Addition of mpi option.

5. SEGLAYER2LATTICE

• Addition of tooltips of predicted Bessel orders.

6. SEGCLASSLAYER

• Accepts also power spectra as input.

• Added tooltips on Bessel look up table.

7. General

• Parameter input from prompt now works using Tab auto completion including file search.