SPIDER

SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy.

• News:  
  • SPIDER is currently an open source project maintained by unpaid volunteers. It has been in use for 42 years and for 2020 it has been modified to accept MRC format files.
• Emphasis on:
  • Toolkit for algorithm development .
  • Averaging of single particle macromolecule specimens
  • 3D reconstruction
  • Multivariate data analysis
  • Object segmentation from volumes
  • Electron tomography .

• Features:
  • Interactive command line interface.
  • Hierarchical modular design for scripting.
  • Graphical User Interface, Web, for visualizing and interacting with images.
  • File format interchangeable with other scientific imaging systems.
  • Extensive documentation of operations and techniques.
  • Includes executables and source code for use on Linux.

• History:
  • Originated in 1978 by Joachim Frank who shared the 2017 Nobel Prize in Chemistry for his pioneering cryo-em research done at the Wadsworth Center in Albany, NY.
  
  
  • Contributors (in chronological order): J. Frank, B. Shimkin, H. Dowse, L. Miranda, C. Mannella, J. P. Bretaudiere, M. V. Heel, A. Verschoor, M. Radermacher, A. Leith, J. M. Carazo, P. Penczek, S. Sibal, L. Odesanya, Y. H. Li, M. Ladjadj, Y. Chen, K. R. Lata, J. Zhu, W. P. Liu, B. Rath, C. Yang, B. Baxter, R. Hegerl, A. Frangakis, L. Joyeux, Z. Huang, R. J. Renka, T. Shaikh, J. Sengupta, J. LeBarron, N. Boisset, H. Gao, G. Kishchenko, J. M. Kennedy, A. GungGong.
    In addition SPIDER is dependent on the Fourier package FFTW by M Frigo and SG Johnson.
  
  
  • Maintained since 2007 by: ArDean Leith & Tanvir Shaikh. During this time they added numerous operations, procedures, parallelizations, and over 500 pages of documentation. There have been no significant contributors other than Leith, Shaikh, Kishchenko, and Kennedy since 2007.
• Spotlight:
  • Spherical Deconvolution Improves Quality of Single Particle Reconstruction.
    Kishchenko GP and Leith A.   J. Struct. Biol., 187, 84-92 (2014).
  • Use of SPIDER and SPIRE in Image Reconstruction .
    Leith A, Baxter AW and Frank J.   International Tables for Crystallography. Vol. F, ch. 19.8, 620-623 (2012)
  • SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs.
    Nature Protocols 3, 1941-1974 (2008)
    Download tar archives of procedures.
  • SPIDER and Web: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields.
    Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, and Leith A.   J. Struct. Biol. 116: 190-199 (1996)