raw2mrc(1) General Commands Manual raw2mrc(1) NAME raw2mrc - Create an MRC image stack from raw image data. SYNOPSIS raw2mrc [options] raw_image_files... MRC_output_file DESCRIPTION raw2mrc can be used to create MRC image files from many types of raw binary image data. Command line options are used to adjust the image size and to skip the input image header. Several raw images can be combined into one file by listing all of their filenames before the name of the output file. OPTIONS -x width Set the width of the image, the default value is 640 pixels. -y height Set the height of the input image, the default is 480 pixels. -z sections Set the number of sections in each input image file, the default is 1. -t type Set the type of input data, the default byte data. The allowed types are byte, short, ushort, long, ulong, float, double, and rgb. Where byte is 8-bit integer values, short is 16-bit signed values, ushort is 16-bit unsigned values, long is 32-bit signed values, ulong is 32-bit unsigned values, float and double are 32-bit and 64-bit floating point values and rgb is three byte values--one for each color. -s Swap input bytes. Does not work for doubles. -o offset Set the offset value used at the beginning of the file, the default is 0. -oz offset Set the offset value used at the end of each section, the default offset is 0. -f Flip the images around the X axis. -i Produce an inverted output stack by both inverting the order in which files are processed and inverting the order of reading Z slices from each file. -iz Invert the order of reading Z slices from each individual file. -d Divide unsigned 16-bit values by 2, or divide any 32-bit inte- gers or 64-bit doubles being converted to 16 bits by 2. The default for unsigned short values is to subtract 32767, which allows all unsigned short values to be stored as signed short integers in the MRC file of mode 1. Use this option if you do not want negative numbers and do not care about the loss of pre- cision. If the values in the input files are all less than 32768, then specify that the input data are short rather than ushort. -u Store unsigned 16-bit values without modification in an MRC file of mode 6; or store doubles in mode 6 if the -c option is given also. -c Convert 32-bit integers or 64-bit doubles to 16-bit integers instead of to 32-bit floating-point numbers. If the type is long, you can use this option alone if values are between -32768 and 32767; or you can use the option with -d to divide by 2 if values are between -65536 and 65535. If you specify the type as ulong, then by default 32767 will be subtracted from the input values, so that values from 0 to 65534 can be stored as -32767 to 32767. Again, -d can be used to divide by 2 instead, so that values from 0 to 65534 can be stored as 0 to 32767. Also, -u can be used to store the numbers as unsigned integers in a file of mode 6. Thus, doubles with a range of 0 to 131070 can be stored as unsigned 16-bit values using all of -c, -d, and -u. If values in the input files are all less than 32768, then spec- ify the type as long instead of ulong. -p pixel Set the pixel spacing of the MRC file header to the given value, which should generally be a pixel size in Angstroms. -pz pixel Set the Z pixel spacing of the MRC file header to the given value if it is different from the one given with the -p option. FILES If the output file already exists, it will be made a backup file by adding ~ to its name. AUTHORS Jim Kremer, David Mastronarde SEE ALSO tif2mrc BUGS Email bug reports to mast at colorado dot edu. IMOD 4.11.0 raw2mrc(1)