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SPIDER
(System for
Processing Image
Data from
Electron microscopy and
Related fields) is an
image processing system for electron microscopy.
SPIDER has been in use since 1978 and contains over 210,000 lines of Fortran code and 7400 files. SPIDER is currently an open source project maintained by volunteers.
The code release from July 2020 (which will probably be the final code release)
contains new support for reading/writing MRC files.
Releases are available on Github at:
github.com/spider-em/SPIDER/releases
Uses:
Features:
- Interactive command line interface.
- Hierarchical modular design for scripting.
- Graphical User Interface,
Web ,
for visualizing and interacting with images.
- SPIDER Reconstruction Engine,
Spire
for common Reconstruction tasks.
- File format
interchangeable with other scientific imaging software.
- 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, 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.
-
SPIDER is often used in conjunction with other software e.g.
the iterative helical real space reconstruction methods developed
by Edward Egelman.
- 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, Kishchenko, and Kennedy.
- In 2025 we are happy to see that
citations for use of SPIDER continue
in the methodology sections of significant new research publications.
Spotlight:
Citation for SPIDER system:
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)
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