SPARX protocols

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SPARX specifications

Information


Unique identifier OMICS_15602
Name SPARX
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Source code URL http://sparx-em.org/sparxwiki/Downloads?action=AttachFile&do=view&target=eman2.sparx.2016.09.07.linux64.tar.gz
Maintained Yes

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Maintainer


  • person_outline Steven Ludtke <>

Publication for SPARX

SPARX in pipelines

 (12)
2018
PMCID: 5847486
PMID: 29191673
DOI: 10.1016/j.jsb.2017.11.013

[…] a python software program for micrograph-based helix tracing (michelixtrace) that is part of the spring software suite (). scientific computation steps are performed by numpy (), scipy () and eman2/sparx () libraries. the required input parameters are summarized in and listed for three different test cases. finally, michelixtrace outputs either a text file containing coordinate traces […]

2017
PMCID: 5572924
PMID: 28659339
DOI: 10.1074/jbc.M117.787671

[…] at a nominal magnification of ×67,000 and a pixel size of 1.57 å employing the em-menu software (tvips gmbh). data processing was done using the spring suite employing ctffind, ctftilt, eman2, and sparx (). straight regions of the pilus filaments were extracted, segmented, and averaged to determine outer dimensions and helical parameters. averaged intensity width profiles were plotted, […]

2017
PMCID: 5607996
PMID: 28570515
DOI: 10.3791/55448

[…] scipion , that provide a single processing pipeline which integrates approaches and protocols from the different software packages listed above., to contribute to the current development of cryo-em, sparx was re-developed into a new stand-alone and complete platform for single particle analysis, called sphire (sparx for high-resolution electron microscopy). in order to increase accessibility […]

2017
PMCID: 5666345
PMID: 28937604
DOI: 10.3390/toxins9100298

[…] bio-beads, and constant rotation during formation yielded smaller nanodiscs within the expected diameter range (100–150 å) containing a single pa pore (b)., initial classification analysis using sparx [] revealed heterogeneity in the dataset with one, two, or three lfn bound to pa pores (a–c). the release of lfn-pa-nanodisc complexes from the bead surface into solution also resulted […]

2016
PMCID: 4880445
PMID: 27223329
DOI: 10.7554/eLife.14313.022

[…] 66,033 particles using e2boxer () from 4x binned images (pixel size on the specimen: 5.6 å). we carried out 2d classification using the isac procedure () implemented in the image processing package sparx (). image defocus was determined with ctffind3 (). we selected 52 good class averages to calculate initial maps with eman2 (e2initialmodel.py, []). the highest scoring map was used […]


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SPARX in publications

 (80)
PMCID: 5940312
PMID: 29453311
DOI: 10.1083/jcb.201711047

[…] normalization and particle centering, the particle images were classified into 200 groups using k-means classification procedures implemented in spider (). for the isac algorithm () implemented in sparx software (), the particle images were reduced to 76 × 76 pixels and subjected to several isac generations specifying 50 images per group and a pixel error threshold of 0.7 (the number of isac […]

PMCID: 5847486
PMID: 29191673
DOI: 10.1016/j.jsb.2017.11.013

[…] a python software program for micrograph-based helix tracing (michelixtrace) that is part of the spring software suite (). scientific computation steps are performed by numpy (), scipy () and eman2/sparx () libraries. the required input parameters are summarized in and listed for three different test cases. finally, michelixtrace outputs either a text file containing coordinate traces […]

PMCID: 5861120
PMID: 29559617
DOI: 10.1038/s41467-018-03504-5

[…] iterative alternating rounds of supervised multi-reference alignment and classification as well as reference-free alignment were run to improve the homogeneity of the image classes with spider and sparx., the nua4 complex was diluted to final concentration 20–50 μg/ml (20 mm hepes [ph 8.0], 40 mm koac, 5 mm mgcl2, 0.1% trehalose, 2 mm dtt, 0.01% np-40) and 3 μl of aliquots were applied […]

PMCID: 5801516
PMID: 29362208
DOI: 10.2196/mental.9041

[…] to extend service delivery and improve treatment engagement and outcomes [,,]. one study has developed monitoring within a self-directed online cognitive behavioral therapy (cbt) intervention (sparx: smart, positive, active, realistic, x-factor thoughts) [] for young people with depression, showing this to be acceptable to users. we have developed and tested an online monitoring tool, […]

PMCID: 5819950
PMID: 29460780
DOI: 10.7554/eLife.31502.023

[…] selected automatically, clustered using iterative stable alignment and clustering (isac) (), and an initial 3d map was generated de novo using stochastic hill climbing refinement () implemented in sparx (). the initial map was used as reference for refinement of image alignment parameters using sparx, to obtain a final map that has an overall resolution of approximately 3.3 å, and a maximum […]


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SPARX funding source(s)
This research has been supported by NIH Grant P01GM064692 and by the US Department of Energy under Contract No. DE-AC02-05CH11231.

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