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Read SPIDER files

version (1.68 MB) by Bill Baxter
Read and write files in SPIDER format

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Updated 19 May 2009

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SPIDER is a free image processing system for electron microscopy. It is used for three-dimensional reconstruction of single particle macromolecules, multivariate statistical classification, and electron tomography. See the extensive documentation and many available techniques at

SPIDER has its own binary format for images and volumes. The SPIDER M-file collection lets users read SPIDER images, volumes, image stacks, and textual document files directly into Matlab data types for processing and visualization.

Cite As

Bill Baxter (2021). Read SPIDER files (, MATLAB Central File Exchange. Retrieved .

Comments and Ratings (2)

Charles Sindelar

Thank you Bill for a very useful set of routines.
I have discovered a problem with writeSPIDERfile.m when it is used with Octave, an open-source matlab equivalent, so I thought I would share the fix. The problem is that the header length is computed wrong by the line:

labrec = uint32(1024 / lenbyt);

In Octave, at least, "uint32" seems to perform a rounding operation, whereas the correct operation is a "floor". So, the following fix appears to work just fine:

labrec = uint32(floor(1024 / lenbyt));

MATLAB Release Compatibility
Created with R2008a
Compatible with any release
Platform Compatibility
Windows macOS Linux

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