SPIDER statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SPIDER

Tool usage distribution map

This map represents all the scientific publications referring to SPIDER per scientific context
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Associated diseases

This word cloud represents SPIDER usage per disease context

Popular tool citations

chevron_left 3D macromolecule reconstruction Image segmentation 3D image reconstruction Tomogram and subtomogram averaging CTF estimation/correction Single particle analysis Image segmentation chevron_right
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SPIDER specifications


Unique identifier OMICS_15822
Alternative name System for Processing Image Data from Electron microscopy and Related fields
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data The batch file form shows only the default register values, input files and output files that are declared in the header.
Output format HTML
Operating system Unix/Linux, Windows
Programming languages Fortran, Perl, Python, Shell (Bash)
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes




No version available



  • person_outline Joachim Frank

Publications for System for Processing Image Data from Electron microscopy and Related fields

SPIDER citations


Visualization of ligand induced transmembrane signaling in the full length human insulin receptor

PMCID: 5940312
PMID: 29453311
DOI: 10.1083/jcb.201711047
call_split See protocol

[…] and windowed into 180 × 180–pixel images. After image 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 […]


Promotion of virus assembly and organization by the measles virus matrix protein

Nat Commun
PMCID: 5928126
PMID: 29712906
DOI: 10.1038/s41467-018-04058-2

[…] Sub-volume averaging was performed using the PEET software package, . In some cases when the center of the mask was different from the center of the sub-volume, binary masks were generated with SPIDER. All tomograms used for sub-volume averaging were collected at a pixel size of 2.94 Å, then binned by a factor of 2. Tomographic volumes were normalized using e2proc3d.py command (EMAN2) prior […]


Cryo EM reveals the structural basis of microtubule depolymerization by kinesin 13s

Nat Commun
PMCID: 5916938
PMID: 29695795
DOI: 10.1038/s41467-018-04044-8
call_split See protocol

[…] L (right or left handed protofilament twist) were generated, and converted to densities with EMAN1 pdb2mrc with a voxel step size of 4 Å/voxel. The densities were low passed filtered to 15 Å and the Spider operation PJ 3Q was used to generate 200 reference projections per microtubule type. Experimental microtubule image segments were extracted and resampled to 4 Å/pixel. Segments corresponding to […]


TAGLN2 polymerizes G actin in a low ionic state but blocks Arp2/3 nucleated actin branching in physiological conditions

Sci Rep
PMCID: 5883021
PMID: 29615809
DOI: 10.1038/s41598-018-23816-2

[…] , OR, USA) at 120 kV under low-dose conditions. Images of filaments were acquired by a 4 K × 4 K CCD camera (Eagle, FEI). Long, relatively straight filaments were unbent using ImageJ and converted to SPIDER format (EM2EM; Image Science and Imperial College, London, UK). Selected filaments were cut into segments in SPIDER, and iterative helical real space reconstruction (IHRSR) was carried out usin […]


A loop region of BAFF controls B cell survival and regulates recognition by different inhibitors

Nat Commun
PMCID: 5865128
PMID: 29572442
DOI: 10.1038/s41467-018-03323-8

[…] sing, yielding a pixel size of 3.36 Å. Particle picking was performed using a semi-automated procedure. 2D classification of selected particle images was carried out with 'samclasscas.py', which uses SPIDER operations to run 10 cycles of correspondence analysis, K-means classification, and multi-reference alignment. […]


Architecture of the Saccharomyces cerevisiae NuA4/TIP60 complex

Nat Commun
PMCID: 5861120
PMID: 29559617
DOI: 10.1038/s41467-018-03504-5
call_split See protocol

[…] NuA4 complex. 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. […]

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SPIDER funding source(s)
This work was supported by HHMI and NIH grants P41 RR01219 and R37 GM29169.

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