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SPIDER (System for Processing Image Data from Electron microscopy and Related fields) is an image processing system for electron microscopy, especially usefull for single-particle reconstruction. SPIDER has been in use since 1978 and contains over 210,000 lines of Fortran code and 7400 files. The 2020 release, which will probably be the final code update, contains new support for reading/writing MRC files.
See the SPIDER Github Website for complete details.

• Uses:

  1. Toolkit for algorithm development.
  2. Averaging of single particles.
  3. 3D reconstruction from projections.
  4. Multivariate data analysis.
  5. Electron tomography.
  6. Object segmentation from volumes.
  7. Learning techniques in cryo-em image processing.

• Features:

  1. Interactive command line interface.
  2. Hierarchical modular design for scripting.
  3. Graphical user interface, Web
     for visualizing and interacting with images.
  4. Data file format interchangeable with other electron microscopy imaging systems.
  5. Extensive documentation of operations and techniques.
  6. Includes source code and executables for use on Linux.

• History:

  1. 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.

  2. Contributors (in chronological order): J. Frank, B. Shimkin, H. Dowse, D. Parsons, A. Verschoor, L. Miranda, W. Goldfarb, S. Basu, R. Banerjee, C. Mannella, J.P. Bretaudiere, M.V. Heel, M. Radermacher, A. Leith, J.M. Carazo, P. Penczek, S. Sibal, L. Odesanya, Y.H. Li, M. Ladjadj, Y.W. 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.

  3. SPIDER has often been used in conjunction with other software e.g. the iterative helical real space reconstruction methods developed by Edward H. Egelman.

  4. Maintained since 2007 by: ArDean Leith & Tanvir (Tapu) Shaikh. During these 18 years they have added numerous operations, procedures, parallelizations, and over 500 pages of documentation. No significant contributors since 2007 other than Leith, Shaikh, Kischenko, and Kennedy.

  5. Please use following citation when you use SPIDER:
     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)

  6. In 2025 we are happy to see that citations for use of SPIDER continue in the methodology sections of significant new research publications.

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[Copyright under GPL].