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Electron Tomography Toolbox for Amira

mrcread

Description:

The mrcread module loads an mrc file with default extension .mrc. The file has to be in little endian byte ordering. Mrc files contain typically a 1024 byte header. Alternatively an extended header, followed by the raw data. The extended header contains the information of a maximum of 1000 images. Each section is 128 bytes long. The structure of an mrc header is as follows:

SIZE DATA NAME DESCRIPTION
4 int NX Number of columns (fastest changing in map)
4 int NY Number of rows
4 int NZ Number of sections (slowest changing in map)
4 int MODE Types of pixel in image
      0 = Image unsigned bytes
      1 = Image signed short integer (16 bits)
      2 = Image float
      3 = Complex short*2
      4 = Complex float*2
4 int NXSTART Number of first COLUMN in map (Default = 0)
4 int NYSTART Number of first ROW in map (Default = 0)
4 int NZSTART Number of first SECTION in map (Default = 0)
4 int  MX Number of intervals along X
4 int  MY Number of intervals along Y
4 int  MZ Number of intervals along Z
4 float XLEN Cell Dimensions (Angstroms)
4 float YLEN Cell Dimensions (Angstroms)
4 float ZLEN Cell Dimensions (Angstroms)
4 float ALPHA Cell Angles (Degrees)
4 float BETA Cell Angles (Degrees)
4 float GAMMA Cell Angles (Degrees)
4 int MAPC Which axis corresponds to Columns (1,2,3 for X,Y,Z)
4 int MAPR Which axis corresponds to Rows (1,2,3 for X,Y,Z)
4 int MAPS Which axis corresponds to Sections (1,2,3 for X,Y,Z)
4 float AMIN Minimum density value
4 float AMAX Maximum density value
4 float AMEAN Mean density value
2 short ISPG Space group number (0 for images)
2 short NSYMBT Number of bytes used for storing symmetry operators
4 int NEXT Number of bytes in extended header
2 short CREATID Creator ID
30   EXTRA Not used. All set to zero by default
2 short NINT Number of integer per section
2 short NREAL Number of reals per section
28   EXTRA2 Not used. All set to zero by default
2 short IDTYPE  0=mono, 1=tilt, 2=tilts, 3=lina, 4=lins
2 short LENS  
2 short ND1  
2 short ND2  
2 short VD1  
2 short VD2  
24 float TILTANGLES Used to rotate model to match new rotated image
4 float XORIGIN Origin of image
4 float YORIGIN Origin of image
4 float ZORIGIN Origin of image
4 char CMAP Contains 'MAP '
4 char STAMP  
4 float RMS  
4 int NLABL Number of labels being used
800 char   10 labels of 80 character

The structure of the extended header is as follows:

SIZE DATA NAME DESCRIPTION
4 float a_tilt Alpha tilt (deg)
4 float b_tilt Beta tilt (deg)
4 float x_stage Stage x position (Unit=m. But if value>1, unit=µm)
4 float y_stage Stage y position (Unit=m. But if value>1, unit=µm)
4 float z_stage Stage z position (Unit=m. But if value>1, unit=µm)
4 float x_shift Image shift x (Unit=m. But if value>1, unit=µm)
4 float  y_shift Image shift y (Unit=m. But if value>1, unit=µm)
4 float  z_shift Image shift z (Unit=m. But if value>1, unit=µm)
4 float defocus Defocus Unit=m. But if value>1, unit=µm)
4 float exp_time Exposure time (s)
4 float mean_int Mean value of image
4 float tilt_axis Tilt axis (deg)
4 float pixel_size Pixel size of image (m)
4 float magnification Magnification used
4 float remainder Not used (filling up to 128 bytes)

How to use:

A file with the default extension .mrc can be loaded by just double clicking on the file in the open file dialog box. Files with another extension which are in an mrc format can be loaded by right clicking on the file in the dialog box and choosing Format from the popup menu. In the file format chooser select "MRC Format" and press OK. Press the Open Button in the open file dialog box. For files with the extension .rec make sure that they are in MRC Format otherwise the built in MRC reader will be used and the data cannot be processed.
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