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 and 3.x. Note that almost all IMOD programs can
read DM 3 and DM 4 files directly if they have a supported data type
(i.e., not 32-bit integers or 64-bit floating point). Thus, if you do
not need any of the conversion options here, and the multiple files are
all similar, you can just use Newstack to stack the files.
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 5.0.2 dm2mrc(1)