Package: emspring
AboutSPRING(SingleParticleReconstruction fromImages of kNownGeometry) 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:ClassificationHelical symmetry determination and refinement toolsHigh-resolution structure refinementMulti-symmetry structure refinementSpring is still maintained in theSachselab at theErnst-Ruska Centreof theResearch Centre Juelichfor the Unix operating systems of MacOSX and Linux.ReferenceIf 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-relatedpublications.InstallationWe provide binary downloads that include all required components and build recipes for all dependencies.
Followinstallinstructions for more details.AcknowledgementsSpring is released under the modified BSD lisence and integrates several different electron-microscopy specific and other open-source packages. Spring is entirely written inPythonand is based on the EM functions and libraries of:EMAN2.91SPARXCTFFIND/CTFTILTDependenciesSpring makes use of a number of scientific computing packages:Numpy and ScipyMpi4pyMatplotlibVispySQLAlchemyChangelog0.87.1723 (2021-03-08)Internal upgrade to EMAN2 (v2.91 March 2021) and python3.Moved home site tohttps://spring.fz-juelich.de.0.86.1661 (2017-12-12)MICHELIXTRACE: release of algorithm as published in Huber et al. 2017 including statistical thresholding, search for optimal parameter combination and persistence length pruningWeb-based Helical Diffraction Simulator onhttp://spring.embl.debased on SEGLAYER2LATTICE.0.85.1617 (2017-07-12)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 cluster0.84.1470 (2016-01-04)General bugfixes and improvement in stability.  Addition of explanatory tool tips.SEGCLASSEXAMMultiple bugfixes including wrong computation of pixelsize.SEGMENTREFINE3DAddition of new parameter “Choose out-of-plane tilt for amplitude correlation.”Installation proceduresUpdated dependencies GCC, matplotlib, libpng including build procedures.0.83.1449 (2015-1-26)Fixes in SEGMENTREFINE3D procedure, now also works for non-zero out-of-plane tilts.0.83.1432 (2014-12-30)Fixes and improvementsInstallation proceduresUpdated dependencies GCC, Numpy, Scipy, Openmpi including build procedures.SEGMENTREFINE3DComputation 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 clusterAdded support for SLURM.SEGMENTCLASS, SEGLAYERLATTICEMany 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'-inpgrid.db-outgrid_upd.db%spring-udb=refinement.db-inp=refinement024.db-out=refinement024_up.db0.82.1339 (2014-09-15)Improved installation procedures including build and binary install scripts.0.82.1339 (2014-04-25)General fixes, optimizations and enhancementsSEGMENTREFINE3DFixes for data sets with large number of asymmetric unitsFix/workaround for occasional database lock problems on cluster mounted nodesFix 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 filamentImplementation 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.dbSEGREFINE3DINSPECTAdditional option of signal-to-noise weighting using FSC file.SEGLAYER2LATTICESimulation of layer-line pattern takes rotational symmetry into account0.81.1282 (2014-01-26)Fixes, enhancements and optimizationSEGMENTREFINE3DDisk 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.SEGMENTFix in frame processing.Rotated stack only written if requested.SEGMENTEXAMAddition of selection options from spring.db.SEGCLASSEXAMAddition of mpi option.SEGLAYER2LATTICEAddition of tooltips of predicted Bessel orders.SEGCLASSLAYERAccepts also power spectra as input.Added tooltips on Bessel look up table.GeneralParameter input from prompt now works using Tab auto completion including file search.LicenseSpring is subject to the (new) BSD license:Copyright (c) 2010 - 2021, Carsten Sachse
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