dm2mrc(1)                   General Commands Manual                  dm2mrc(1)



NAME
       dm2mrc - Create an MRC image stack from Digital Micrograph files.

SYNOPSIS
       dm2mrc  [options]  DM_files...  MRC_image_file

DESCRIPTION
       dm2mrc will convert Digital Micrograph (DM) image files to an MRC
       stack, using raw2mrc.  The program should be able to convert version
       DM 2.5 files produced by DM 2.5 running on a Macintosh, DM 2.5 files
       exported by DM 3 running on a Windows PC, DM 3 files, and DM 4 files
       produced by GMS 2.x.

       The program will convert signed 16-bit integers, unsigned 16-bit inte-
       gers (by subtracting 32767), signed bytes (by adding 127), unsigned
       bytes, and 32-bit floating point numbers by saving values of the data
       size, and 64-bit floating point numbers (double) or 32-bit integers by
       producing 32-bit floating point output.  This default behavior can be
       modified by the options listed below, which is highly desirable with
       data from 16-bit cameras that have been stored as 32-bit or 64-bit num-
       bers.

       The program will first scan through all of the files to determine the
       version of DM file, the data type, the image dimensions, and the header
       offset to the beginning of the data in the file.  If all of these
       attributes are the same, it will convert them in one call to
       raw2mrc.  Otherwise, it will convert each one independently into a
       temporary file, then make a stack from the temporary files with new-
       stack(1).  DM files that contain stacks of identically sized images
       will be handled; all of the images from each file will be included in
       the output file.

       The program will use the pixel size in the input files to set the pixel
       spacing in the header of the output file, if one can be determined.  If
       there is a separate Z pixel size, this will be used to set the Z pixel
       spacing also.  It uses the value from the first input file having a
       pixel size.

OPTIONS
       -s     Treat unsigned data as signed.  Use this option for unsigned
              16-bit data if the values are all less than 32768, or for
              unsigned 32-bit data being converted to 16-bit values with the
              -c option.  -c.

       -r     Reduce (divide) unsigned data by 2 instead of subtracting 32767.
              Use this option for data that are to be written as 16-bit values
              if the values range above 32767 and you prefer to lose one bit
              of precision to having negative numbers.  The option can also be
              used when converting doubles to 16-bit integers with the -c
              option, in which case an input range of -65535 to 65535 can be
              stored as integers.

       -u     Store unsigned data in a 16-bit unsigned MRC file (mode 6)
              instead of subtracting 32768.  If given with -c, this option
              will also store doubles as mode 6 instead of mode 1, allowing an
              input range of 0 to 65535 to be stored as integers, or a range
              of 0 to 131070 to be stored with the -r option as well.

       -c     Convert 32-bit integers to 16-bit (short) integers instead of to
              floating point numbers.  If the data are signed integers, you
              can use this option alone if values are between -32768 and
              32767; or you can use the option with -r to divide by 2 if val-
              ues are between -65536 and 65535.  If the data are unsigned,
              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, -r can be used to divide by 2 instead, so that values
              from 0 to 65534 can be stored as 0 to 32767.  If values in the
              input files are all less than 32768, then use the -s option to
              avoid subtracting 32767.

       -i     Invert the order of images in the output stack.  Input files
              will be processed in inverted order, and slices inside of stack
              files will also be read in inverted order.  This option will
              preserve handedness if the images being stacked are serial
              images as a block face was cut and are in the same orientation
              as views looking down on the block.

       -t dir Use the given directory for temporary files.  By default, tempo-
              rary files are written to the directory where the output file is
              being placed.

AUTHOR
       David Mastronarde

SEE ALSO
       raw2mrc(2), newstack(2)

BUGS
       The program has been written by inpecting examples of a variety of Dig-
       ital Micrograph files, so it might fail with files outside the range of
       this experience.  Email reports of problems to mast at colorado dot
       edu.



IMOD                                4.10.10                          dm2mrc(1)