mrc2tif(1)                  General Commands Manual                 mrc2tif(1)

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

       mrc2tif  [options]  mrc_input_file  tiff_file_root_name

       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.  The input file need not
       be an MRC file; it can be any kind of file readable by other IMOD pro-
       grams, plus the image file types readable by 3dmod using Qt libraries,
       of which the most useful are PNG, JPEG, and BMP.  There are options to
       create JPEG or PNG output 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, the -C, or the -a 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
       expansion of the dynamic range for that subset of the image data, and
       enter the contrast settings withs the -C option.

       Output to JPEG or PNG files is selected by entering the -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 compres-
       sion 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, -C, or -a.  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.

       When images are written to TIFF files with ZIP or LZW compression, the
       program will use compress the data in parallel threads, with the number
       of threads depending on the image size.  However, if the image is
       larger than a certain threshold, it is processed in chunks instead of
       read  in all at once, and the parallel compression routine cannot be
       used.  The default threshold is 400 MB.  To ensure parallel compres-
       sion, you can either raise this threshold with the -t option or over-
       ride the default behavior with "-O 1".  Note that with parallel com-
       pression, memory usage will be about 2.2 times the size of the image.

       -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

       -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".  The other allowed values are 32773 for Packbits and
              32946 for a possibly different Deflate.  These are available on
              all operating systems when running with the TIFF libraries dis-
              tributed with IMOD.  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.

       -a mean,SD
              Scale data for conversion to bytes so that it has the given mean
              and standard deviation.  Enter 0 for either value to use the
              default for auto-contrasting in 3dmod, which is a mean of 150
              and an SD of 40.  This option cannot be entered with -S or -C,
              since it supercedes the scaling specified by them.

       -z min,max
               Starting and ending Z slices in file to output, numbered from

       -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 resolu-
              tion 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 con-
              verted 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 400 MB).  Above the crite-
              rion, images will be read, processed, and saved in strips
              (unless "-O 1" is entered), with much lower memory requirements.

       -O value
              Override the default behavior on whether to compress data in
              parallel.  Specifically, a value of 0 will force data not to be
              compressed in parallel if it ordinarily would be.  A value of 1
              will force large images to be compressed in parallel if they
              would ordinarily be read in chunks instead.

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

       Jim Kremer, David Mastronarde

       clip, newstack

       Complex and long integer data modes are not supported.

       Email bug reports to mast at colorado dot edu.

IMOD                                4.11.0                          mrc2tif(1)