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SPHIRE specifications


Unique identifier OMICS_30849
Alternative name Sparx for High Resolution Electron Microscopy
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes


  • Cter
  • Meridien
  • Sort3D
  • Window




No version available

Additional information


SPHIRE citations


Structural basis for energy transduction by respiratory alternative complex III

Nat Commun
PMCID: 5928083
PMID: 29712914
DOI: 10.1038/s41467-018-04141-8
call_split See protocol

[…] etermined using CTFFIND4 on drift-corrected, non-dose-weighted images. Automatically picked particles were subjected to a first round of reference-free two-dimensional classification with ISAC within Sphire, to exclude false positives. The initial clean data set contained 131,995 particle images (288 pixels × 288 pixels). Dose-weighted particles were subjected to 2D classification in RELION 1.4. V […]


3.3 Å resolution cryo EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound

PMCID: 5819950
PMID: 29460780
DOI: 10.7554/eLife.31502.023
call_split See protocol

[…] Defocus of images was estimated with CTER (). Particles were identified automatically with PARTICLE using three distinct reference projections calculated from the yeast α6 crystal structure (PDB: 3PAW) filtered to 30 Å resolution (). Par […]


Structural basis for tRNA dependent cysteine biosynthesis

Nat Commun
PMCID: 5688128
PMID: 29142195
DOI: 10.1038/s41467-017-01543-y
call_split See protocol

[…] data sets contained 29,266 and 11,972 single particles, respectively. Because of the overall flexibility of the complex, focused reference-free alignment and classification procedures implemented in SPHIRE and EMAN2 were applied. In particular, images were first centered and rotationally aligned, using the reference free approach implemented in SPHIRE. Subsequently, a k-means classification was p […]


High resolution Single Particle Analysis from Electron Cryo microscopy Images Using SPHIRE

PMCID: 5607996
PMID: 28570515
DOI: 10.3791/55448

[…] Calculate the 3D variability map from the particle stack used in the 3D refinement. Click on "SORT3D" icon and then "3D Variability Estimation" button. Set "Input image stack" by selecting the same screened particle stack given to the 3D refinement step 7.1.1. Specify the path for "Output dire […]


On Parallel Streams through the Mouse Dorsal Lateral Geniculate Nucleus

Front Neural Circuits
PMCID: 4811935
PMID: 27065811
DOI: 10.3389/fncir.2016.00020

[…] Spike waveforms from each tetrode were clustered into individual units offline using a mixture of algorithmic and manual sorting (Spike- Sort3D, Neuralynx). Waveforms were initially sorted using KlustaKwik and subsequently manually refined. All clusters with spikes in the 0–1 ms bin of the interspike interval histogram were strictly re […]


The origin of the red emission in n ZnO nanotubes/p GaN white light emitting diodes

PMCID: 3211177
PMID: 21711671
DOI: 10.1186/1556-276X-6-130

[…] O. The post-growth annealing ambient also strongly influences the color-rendering properties of ZnO nanotubes. We have commercially purchased magnesium-doped p-type GaN with film thickness of 4 μm on sphire substrates from TDI Inc. USA. It has hole concentration of approximately 4 × 1017 cm-3.To obtain the ZnO nanotubes, first, the ZnO nanorods were grown on the p-GaN substrates using the low temp […]


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