Electron Microscopy Single-Particle Based Helical Reconstruction
SPRING (S ingle P article R econstruction from I mages of kN own G eometry) is a single-particle based helical reconstruction package for electron cryo-micrographs and has been used to determine 3D structures of a variety of highly ordered and less ordered specimens. Spring provides the entire single-particle based work-flow required for helical reconstruction including:
- Helical symmetry determination and refinement tools
- High-resolution structure refinement
- Multi-symmetry structure refinement
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.
We provide binary downloads that include all required components and build recipes for all dependencies. Follow install instructions for more details.
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:
- MICHELIXTRACE: release of algorithm as published in Huber et al. 2017 including statistical thresholding, search for optimal parameter combination and persistence length pruning
- Web-based Helical Diffraction Simulator on http://spring.embl.de based on SEGLAYER2LATTICE.
- MICCTFDETERMINE: updated to work with ctffind4.
- SEGCLASSRECONSTRUCT: updated to work with binning option.
- SEGMENTCLASS: updates to work with larger datasets for classification to reduce memory issues.
- SEGCLASSLAYER: addition of ‘B-factor’ option to adjust high-resolution layer-line contrast.
- SEGREFINE3DINSPECT: Bfactor/Resolution cutoff option separated from long helix option.
- MICHELIXTRACE: Algorithm update to increase robustness of filament tracing.
- SEGREFINE3DGRID/SEGGRIDEXPLORE: Now with out-of-plane deviation parameter.
- SEGMENTPLOT/SEGREFINE3DPLOT: Now plots quantities on micrograph if subset micrograph chosen.
- Updated to work with SLURM cluster
General bugfixes and improvement in stability. Addition of explanatory tool tips.
- Multiple bugfixes including wrong computation of pixelsize.
- Addition of new parameter “Choose out-of-plane tilt for amplitude correlation.”
- Installation procedures
- Updated dependencies GCC, matplotlib, libpng including build procedures.
- Fixes in SEGMENTREFINE3D procedure, now also works for non-zero out-of-plane tilts.
- Fixes and improvements
- Installation procedures
- Updated dependencies GCC, Numpy, Scipy, Openmpi including build procedures.
- 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.
- High-performance computing cluster
- Added support for SLURM.
- SEGMENTCLASS, SEGLAYERLATTICE
- Many minor fixes.
Note: old refinement.dbs and grid.dbs need to be upgraded to be readable by the latest Spring version.
% spring -udb='grid.db' -inp grid.db -out grid_upd.db % spring -udb=refinement.db -inp=refinement024.db -out=refinement024_up.db
- Improved installation procedures including build and binary install scripts.
- General fixes, optimizations and enhancements
- 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
- Additional option of signal-to-noise weighting using FSC file.
- Simulation of layer-line pattern takes rotational symmetry into account
- Fixes, enhancements and optimization
- 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.
- Fix in frame processing.
- Rotated stack only written if requested.
- Addition of selection options from spring.db.
- Addition of mpi option.
- Addition of tooltips of predicted Bessel orders.
- Accepts also power spectra as input.
- Added tooltips on Bessel look up table.
- Parameter input from prompt now works using Tab auto completion including file search.
Spring is subject to the (new) BSD license:
Copyright (c) 2010 - 2017, Carsten Sachse All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
- Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
- Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
- Neither the name of the European Molecular Biology Laboratory (EMBL) nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL CARSTEN SACHSE BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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