mrc2tif(1)                                                          mrc2tif(1)



NAME
       mrc2tif - Create TIFF, JPEG, or PNG files from an MRC image file.

SYNOPSIS
       mrc2tif  [options]  mrc_input_file  tiff_file_root_name

DESCRIPTION
       mrc2tif usually creates a series of TIFF files with the prefix
       tiff_file_root_name and with the suffix .nnn.tif, where nnn is the z
       number.  Byte, signed and unsigned 16-bit integer, float, and RGB color
       files (modes 0, 1, 6, 2, 16) can be converted.  There are options to
       create JPEG or PNG files instead of TIFF.  The data will be written to
       a TIFF file in the same mode as in the input file by default, but there
       are options that allow the integer and float modes to be scaled to
       bytes; the same options allow scaling of byte and RGB values.  If the
       input file has only one section, then the output file will simply be
       the tiff_file_root_name with no suffix added.

       When the output mode is integer or float, the TIFF file will contain
       the minimum and maximum value for the data in the file.  When a TIFF
       stack is created, each image will have the same overall minimum and
       maximum, rather than values specific to that image.  This way, 3dmod
       will be able to read in the data with proper scaling.  However, Photo-
       shop pays no attention to these values when displaying integer data, so
       when the integer data have a relatively small range, the image will
       initially appear black or very dark.  The simplest solution for this
       problem is to apply the scaling options described next.

       When either the -S or the -C option is entered, integer and floating
       point data will be scaled to bytes and any values outside the range of
       0 to 255 will be truncated.  If the input data is already in bytes
       (either byte data or RGB data), these options will cause the data to be
       scaled, and values outside the range truncated.  To have the range of
       the input data mapped into the full range of byte data, just enter "-C
       0,255".  To have a subset of the input range mapped to 0 to 255, either
       enter the limits of the subset of the range directly with the -S
       option, or adjust the contrast in 3dmod to give the desired expan-
       sion of the dynamic range for that subset of the image data, and enter
       the contrast settings withs the -C option.

       -j or the -p option.  There are some restrictions in these cases.  An
       output stack cannot be created, only a series of single-image files.
       The type of compression cannot be specified, but the quality or degree
       of compression can.  Tiling cannot be specified.  Only byte and RGB
       output is available.  Integer and floating point files are converted to
       byte based either on the minimum and maximum densities in the input
       file or on the values entered with -S or -C.  In addition to the fact
       that JPEG images cannot be bigger than 65535 pixels in X or Y, problems
       may be encountered with images much bigger than 1 gigapixel.

       Since IMOD is distributed with version 4 of the TIFF library, this pro-
       gram will write files bigger than 4 GB in the BigTIFF format, and con-
       tinue to write smaller files in classical TIFF format.

OPTIONS
       -s     Create a single output file, a TIFF stack with all of the sec-
              tions in the input file.

       -j     Produce JPEG files instead of TIFF files.  See above for the
              restrictions with this kind of output.

       -p     Produce PNG files instead of TIFF files.  See above for the
              restrictions.

       -c value
              Compress the data in TIFF files with the type of compression
              indicated.  The most useful compression types are LZW (value 5),
              Zip or Deflate (value 8), and JPEG (value 7).  For these types,
              the value can be given as a text string: "lzw", "zip", or
              "jpeg".  These are available on all operating systems when run-
              ning with the TIFF libraries distributed with IMOD.  On Linux,
              see /usr/include/tiff.h for other numeric values that can be
              tried; some of these will work, depending on the data type.
              Also note that JPEG compression is not available with 16-bit
              data.

       -q value
              Set the quality for JPEG or ZIP compression (ZIP compression is
              used in PNG output).  For JPEG, the quality ranges from 0 to 100
              with a default of 75; higher numbers preserve more information
              but with less compression.  For ZIP/PNG, which is a lossless
              compression, the quality factor ranges from 1 to 9 with a
              default of 6 and specifies a tradeoff between speed and amount
              of compression.  Higher numbers giving somewhat more compression
              for more computational time.  Lower numbers give somewhat less
              compression with potentially much less computational time.

       -S min,min
              Specify an initial intensity scaling that will scale "min" to 0
              and "max" to 255, just as is achieved with the -s options to
              3dmod and mrcbyte.

       -C black,white
              Specify intensity scaling to match the scaling achieved with the
              given black and white contrast settings in 3dmod, with the -c
              option to mrcbyte, or the "-contrast" option to newstack.  If
              both -S and -C are entered, the final scaling will be the prod-
              uct of these two scalings.  If -S is entered alone, the
              black/white values are 0/255 (no scaling for contrast).  If -C
              is entered alone, the initial scaling will be from the minimum
              in the input file to 0, and from the maximum in the file to 255.
              If you have integer data and you want to convert it to bytes,
              you will generally want to apply some scaling with black/white
              values to preserve the dynamic range of the data of interest.

       -z min,max
               Starting and ending Z slices in file to output, numbered from
              0.  -i value Initial file number.  The default is the number of
              the first Z slice output, where Z is numbered from 0.  -r value
              Set the resolution setting of the output file in dots per inch
              to the given value.  -P Use the pixel spacing in the MRC file
              header to set the resolution in the output file.  The resolution
              will be set in dots per inch and will typically be a very large
              number, but this value allows the pixel spacing to be recovered
              if the file is converted back with Tif2mrc.

       -T xsize,ysize or size
              Organize output data in tiles instead of strips, which can allow
              faster access to subareas of very large images.  Enter one num-
              ber for the tile size in both dimensions, or two numbers to
              specify a different size in X and Y.  The TIFF library requires
              that all tiles be the same size, which means that the image file
              will be padded so that tiles on the bottom and right sides have
              the same sizes as the rest.  The program will pick an actual
              tile size near the entered number that is a multiple of 16 and
              that minimizes the amount of padding required.

       -t value
              Set the criterion for processing each image in strips to the
              given value in megabytes (fractional values are allowed).  Whole
              images will be read in, processed, and saved as a unit if they
              are less than this criterion (default 100 MB).  Above the crite-
              rion, images will be read, processed, and saved in strips, with
              much lower memory requirements.

       -o     Use old IMOD code instead of libtiff for writing the files (for
              testing purposes).

AUTHORS
       Jim Kremer, David Mastronarde

SEE ALSO
       clip, newstack

BUGS
       Complex and long integer data modes are not supported.

       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                          mrc2tif(1)