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 www.wadsworth.org/spider_doc/spider/docs/master.html
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.
The provided M-files are:
readSPIDERfile |
reads SPIDER binary files |
writeSPIDERfile |
writes SPIDER binary files |
readSPIDERheader |
reads the header of SPIDER binary files |
readSPIDERdoc |
reads SPIDER document files |
writeSPIDERdoc |
writes SPIDER document files |
example.m |
Example usage |
NB: there is no specific data extension for SPIDER files.
readSPIDERfile
Read a SPIDER image, volume, or stack file into an array.
Usage
m = readSPIDERfile(filename)
If filename is a SPIDER image, readSPIDERfile
reads it into a 2D array, m
. If filename is a SPIDER volume, or image stack, it is read into a 3D array. readSPIDERfile
calls readSPIDERheader
.
writeSPIDERfile
Write a 2D or 3D array out to a SPIDER file.
Usage
writeSPIDERfile(filename, array)
writeSPIDERfile(filename, array, 'stack')
writeSPIDERfile(filename, array)
will write data to a SPIDER image or volume, depending on whether the array is 2D or 3D.
writeSPIDERfile(filename, array, 'stack')
writes a 3D array out as a stack file of images.
readSPIDERheader
Read the header of a SPIDER file.
Usage
v = readSPIDERheader(filename)
Reads the header of a SPIDER binary file into a vector (1D array). All the entries are floating point values. E.g., the width, height and depth are in v(12), v(2), v(1), respectively. For the meaning of other values, see www.wadsworth.org/spider_doc/spider/docs/image_doc.html
readSPIDERdoc
Read data from a SPIDER document file.
Usage
m = readSPIDERdoc(filename)
m = readSPIDERdoc(filename, column)
m = readSPIDERdoc(filename, [column1, column2, ...])
m = readSPIDERdoc(filename)
reads all the columns of the document file into a 2D array, a matrix of [nrows ncolumns]. The array is accessed by m(row,column)
.
m(:,i)
returns the ith column
m(j,:)
returns the jth row
m(j,i)
returns a single element
m = readSPIDERdoc(filename, i)
returns a single column of data.
m = readSPIDERdoc(filename, [i j k])
returns a set of columns. Column=1 refers to the first SPIDER data column (textually, column 3). To retrieve the key column, use column=0.
writeSPIDERdoc
Write an array out to a SPIDER document file.
Usage
writeSPIDERdoc(filename, array)
writeSPIDERdoc(filename, array, column_headers)
writeSPIDERdoc(filename, array)
writes a 2D array to a SPIDER document file.
writeSPIDERfile(filename, array, column_headers)
writes the 2D array to a doc file with text headings over each column. The column_headers
are a cell array of strings, created by e.g., hdrs = { 'column1'; 'column2'; 'column3'}
.
Created: 02/04/09 Bill Baxter
Enquiries: spider@wadsworth.org