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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.

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README.md


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 lastest release from July 2020 (which will probably be the final release) contains support for reading/writing MRC files.

This latest release is available here or can be downloaded from the Wadsworth Center.

  • Uses:

    1. Averaging of single particle objects

    2. Multivariate statistical analysis

    3. 3D reconstruction

    4. Electron tomography

    5. Object segmentation from volumes

  • Features:

    1. Interactive command line interface.

    2. Hierarchical modular design for scripting.

    3. Graphical user interface, Web, for visualizing and interacting with images.

    4. Uses a 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, L. Miranda, W. Goldfarb, S. Basu, R. Banerjee, 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. 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. Maintained since 2007 by: ArDean Leith & Tanvir Shaikh. During these 13 years they added numerous operations, procedures, parallelizations, and over 500 pages of documentation. There have been no significant contributors other than Leith, Shaikh, Kischenko, and Kennedy since 2007.


Copyright under GPL.

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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.

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