CLIP(1)                     General Commands Manual                    CLIP(1)

       clip - command line image processing for mrc files.

       clip process  [options]  input_files...  [output_file]

       The processes that clip can do are listed below. One and only one
       process must be selected on the command line.  Only the first three or
       four letters of the process name have to be entered.

       add    Add several images together.

       average (avg)
              Average several images together.
              Brighten image by scaling intensities.
       color  Add false color to image.
              Adjust contrast by scaling intensities.
              Do a auto/cross correlation.
              Do 2d anisotropic diffusion.
       divide Divide one image volume by another or by a single image.
              Fill in dark edges in drift-corrected images.
              Calculate a gradient as in 3dmod image processing.
       graham Apply Graham filter as in 3dmod image processing.
       info   Print header information to stdout.
       fft    Calculate a FFT or inverse FFT transform.
       filter Calculate a bandpass filter.
              Flip an image by x y or z.
              Print histogram of values or analyze for bimodal distribution.
              Join images from 3 byte files into one RGB file.
              Apply Laplacian filter as in 3dmod image processing.
              Take the logarithm of the image intensities.
       median Apply median filter.
              Multiply one image volume by another or by a single image.
              Truncate extreme values, apply gain reference, scale by factor
              Apply Prewitt filter as in 3dmod image processing.
              Correct disparities between quadrants in images from 4-port
              readout camera.
       resize Box out image to a new size.
       rotx   Rotate a volume by -90 degrees about X axis.
       shadow Adjust darkness of image by scaling intensities.
              Sharpen image as in 3dmod image processing.
       smooth Smooth image as in 3dmod image processing.
       sqroot Take the square root of the image intensities.
       sobel  Apply Sobel filter as in 3dmod image processing.
              Compute a square, scaled and/or reduced power spectrum.
              Split an RGB file into 3 byte files.
       stats  Print min, max, mean, standard deviation, and location of min
              and max.
              Compute the standard deviation of a set of images.
              Subtract one image volume from another.
              Make binary (black/white) image by applying a threshold.
              Limit pixel values at low or high end, or both.
       unpack Unpack 4-bit values, with optional scaling by reference (same as
       unwrap Undo wraparound of values in integer data.
              Compute the variance of a set of images.

       These options are available to most processes.

       -v     View output data file using 3dmod.

       -2d    Use 2d instead of 3d (default) processes if a 2d process exists.
              Each input file is considered a stack of 2D images to be pro-
              cessed.  For most processes, this will change only the way that
              the -iz option is interpreted.

       -3d    Use 3d process. Each input file is considered a volume to be

       -a     Append data to output file.  Append and overwrite are not avail-
              able for processing modes that do not take standard input and
              output size and centering options.

       -ov section
              Overwrite output starting at section number section.  Range is
              from 0 (first section) to z size - 1 (last section) unless the
              -1 option is entered to number sections from 1.

       -p value
              Image coordinates with no image data are padded with the given
              value.  The default is the mean value of the input image.

       -c[xyz] value
              Adjust the center of input image. Default is center of first
              input file.  The -cx option will center the x coordinate on the
              given value, the -cy option will center the y coordinate on the
              given value and the -cz option will center the z coordinate on
              the given value.

       -ix value
       -iy value
       -iz value
              Sets the size of input image.  The default is the size of the
              first input file.  The -ix option sets the x input size, the -iy
              option sets the y input size.  The -iz option sets the z input
              size, or specifies a list of Z values if the -2d option is
              included.  In the latter case, the value is interpreted as a
              comma-separated list of ranges. Commas indicate individual sec-
              tion numbers and dashes (or minus symbol) indicate a range of

       -x value,value
       -y value,value
              These options are an alternative way of specifying the size and
              center of the input image.  The two values are the starting and
              ending coordinates, numbered from 0 (i.e., the first pixel in an
              image is (0, 0)).  The -x option sets the X coordinates, and
              neither -cx nor -ix may be entered with it.  The -y option sets
              the Y coordinates, and neither -cy nor -iy may be entered with
              it.  These coordinates are not constrained to lie within the
              volume; regions outside the volume will be filled with the pad-
              ding value.

       -ox value
       -oy value
       -oz value
              Size of output file.  Default is same as input size, options -a
              and -ov override these setting.  The -ox option sets the x out-
              put size, the -oy options sets the y output size and the -oz
              option sets the z output size.

       -1     Z values are numbered from 1 instead of 0, the default.  This
              option affects the interpretation of lists of Z values entered
              with -iz when the -2d option is given, and the interpretation of
              the Z value entered with the -oz and -cz options.  When running
              "clip stat", slices will be referred to as views instead and
              numbered from 1 with this option.

Selected options
       The following options are valid for selected processes:

       -s     Switch, use depends on process.

       -m mode
              Output modes: "byte", "ubyte", "sbyte", "short", "float", "com-
              plex", "ushort", "rgb", "4-bit", or 0-4, 6, 16, or 101.  0 =
              byte, 1 = short, 2 = float, 3 = complex short, 4 = complex
              float, 6 = unsigned short, 16 = rgb, 101 = 4-bit data.  "byte"
              will produce byte output that is signed or unsigned depending on
              the default for this version of IMOD and the value of the envi-
              ronment variable WRITE_MODE0_SIGNED.  Use "ubyte" or "sbyte" to
              force unsigned or signed byte output regardless of other set-
              tings.  Unsigned output is needed to work with versions of IMOD
              before IMOD 4.2.23; signed output is now the MRC standard and
              the default.  Regardless of the representation in the file,
              bytes are read into IMOD programs as unsigned with a range of 0
              to 255.

       -h level
              Has many uses: 1) Level for high pass filter. Range is (0.0 -
              0.71 / pixel).  The default value is 0. 2) High level for image
              truncation; the default is no truncation.  3) Width of area ana-
              lyzed in quadrant correction.  4) Upper limit for histogram out-
              put.  5) Value assigned to pixels above threshold when thresh-
              olding.  6) Threshold above which values will be truncated with
              4-bit unpacking or normalizing.  7) Relative diameter of ring
              for setting high scaling limit of power spectrum.

       -k value
              K threshold value for anisotropic diffusion; the default is 2.0.

       -l level
              Has multiple uses: 1) Level for low pass filter. Range is (0.0 -
              0.71 / pixel).  The default value is 1.0.  2) Sigma of Gaussian
              kernel for smoothing; the default is to use the standard kernel
              shown below.  3) With diffusion, this specifies the lambda value
              or step size; the default is 0.2. 4) With statistics, sets the
              number of slices over which to determine outliers in the min and
              max values. 5) When using "add" or taking an average, standard
              deviation, or variance, sets a factor for scaling the output
              values. 5) With image truncation, sets the low level for trunca-
              tion (default is no truncation). 6) With quadrant correction,
              sets a base to be added to values for scaling.  7) Lower limit
              for histogram output.  8) When truncating values from 4-bit
              unpacking or normalizing, sets the value to assign to a pixel
              above the truncation threshold.  9) When thresholding, sets the
              value assigned to pixels below threshold.  10) Background gray
              level for power spectrum output.

       -cc value
              Specifies type of edge stopping function for diffusion: 1 for
              exponential function, 2 for rational function, 3 for Tukey
              biweight.  The default is 2.

       -n value
              Input number. Use depends on process: threshold for averaging;
              scaling factor for brightness/contrast/shadow; base value to add
              when taking logarithm or square root; padding for correlations;
              iterations for smoothing or anisotropic diffusion; size for
              median filter, criterion for determining outliers in statistics;
              value to add when undoing wraparound; number of images to ana-
              lyze together for quadrant correction; bin size for histogram
              output; scaling for multiply, divide, and unpacking 4-bit values
              or normalizing and applying a gain reference.

       -r value
              Red value;   Range is (0.0 - 1.0) Default is 1.0.

       -g value
              Green value; Range is (0.0 - 1.0) Default is 1.0.

       -b value
              Blue value;  Range is (0.0 - 1.0) Default is 1.0.

       -t value
              Threshold value for thresholding; or used for a histogram to
              report the threshold at which the given fraction of values occur
              in the cumulative distribution.

       -D file
              Name of defect list file produced by SerialEM, for correction of
              column, row, and point defects in images that have not had this
              correction applied.  Specifically, frames containing electron
              counts from a K2 camera that have not been software gain-normal-
              ized cannot be corrected validly until they have been gain nor-
              malized and scaled up or converted to float to represent frac-
              tional counts properly.  This option is thus available with the
              "unpack", "normalize", and "multiply" commands that are used to
              apply such gain normalization; it is also available with
              "divide", "resize", "brightness", "contrast", "shadow", "thresh-
              old", "truncate", and "unwrap".  The defect list file has
              entries to indicate the camera size upon which the coordinates
              are based, and whether it has been scaled up by a factor of 2 to
              correspond to pixels in a super-resolution mode image.  Given
              these entries and the size of the input image, or of the gain
              reference image if one is being applied, the program decides
              whether to scale the coordinates up by a factor of 2 if the
              image is larger than the camera size.  It also deduces the
              effective binning of the images relative to the coordinates used
              in the file by assuming that images are not subareas of half or
              less.  These decisions on scaling and binning are usually
              reported by the program and can be overridden in rare cases by
              the options described next.  If an acquired image is a subarea
              of the camera area, then it is assumed to be centered, and cor-
              rection will not work properly if it is not.  The -ix, -iy, -cx,
              -cy, -ox, and -oy can still be used to process subareas of the
              acquired images, and these subareas need not be centered.

       -B value
              Set the assumed binning to the given value; if the defect coor-
              dinates have been scaled up by 2, then entries can range down to
              0.5 for unbinned super-resolution mode.  This could be needed if
              the image is a subarea of half or less.

       -S     Scale the defect list coordinates up by a factor of 2 if the
              file does not indicate that it was already scaled up.  This
              could be needed at some time in the future if the defect list
              was not already scaled up and if the image is a subarea of half
              or less in super-resolution mode.

       -R value
              Apply a rotation and flip specified by the given value to the
              gain reference when normalizing with the "normalize/unpack" com-
              mand.  A rotation/flip value is the number of 90-degree rota-
              tions counterclockwise (i.e., 1, 2, or 3 for 90, 180, or -90
              degree rotations), plus 4 if the image is flipped around the Y
              axis BEFORE the rotation.  An entry of -1 means that the rota-
              tion/flip value is to be read from a title in the image file
              header after the text "r/f".

       -P file
              Name of piece list file, in order to have coordinates in statis-
              tics converted to position in a montage displayed with adjusted
              overlap.  The overlap in the display is assumed to be zero,
              unless overlap is specified with the -O option.

       -O value,value
              Overlap values in X and Y to be used when printing coordinates
              corresponding to positions in a displayed montage.  Negative
              values correspond to spaces between the displayed pieces.

       -E fraction,direction
              Used with histogram to find the point at which the given frac-
              tion of extra values on one side of the histogram peak is found.

       -F fraction,direction
              Used with histogram to find the point at which the histogram
              falls off most rapidly past a certain point defined by the given
              fraction value.  If direction is positive, the fastest falling
              point above the given fraction of values is found; if it is neg-
              ative, the fastest falling point below the fraction is found.

       -M size,direction
              Used with threshold to mark points as above (or below) threshold
              only if they are part of a set of adjacent points at least as
              big as the given size, for direction positive (or negative).

       A brief description of each process is given below.

       add    Add image volumes together.  All of the input files (there must
              be at least two) are added together slice by slice.  All input
              images must be the same size.  Standard input and output options
              are available.  The output values can be scaled with -l and the
              output mode can be changed.

              (avg) Average images together.  If more than one input file is
              given, it adds all of the input files together slice by slice
              and then divides the sum by the number of input files.  All
              input images must be the same size.  Standard input and output
              options are available.  With one input file, it averages the 2D
              slices to produce one output slice.  In this case, use the -n
              option to set a threshold such that pixels below threshold are
              not included in the average.  Standard input options are avail-
              able but output cannot be resized.  In either case, the output
              values can be scaled with -l and the output mode can be changed.
              As of IMOD 4.2.15, the distinction between 2D and 3D averaging
              is controlled by the number of input files and not by the -2d
              versus -3d options.

       shadow Increase or decrease image brightness, contrast, or darkness.
              These options scale the image intensity by the value entered
              with the -n option, with intensity fixed at one point.  With
              brightness, intensity is fixed at the minimum so scaling up
              increasing brightness.  With contrast, intensity is fixed at the
              mean; with shadow, intensity is fixed at the maximum so dark
              parts are scaled more.  Scaling values less then 1 will decrease
              the chosen property, values greater then 1 increase it.  With
              the -2d option, the min, max, or mean are taken from the indi-
              vidual sections.

       color  Colorize a black and white image.  Color 3d version: reads in a
              whole mrc file as byte data and then scales the image to a color
              ramp that starts at black and goes to the -r, -g, and -b values
              given on the command line.  The default color values are 1.0.
              Standard options for input and output size are not implemented.
              Color 2d version: reads in data slice by slice without scaling
              it to bytes, the scales the image to a color ramp using the -r,
              -g, and -b values.  The size of these values may need to be
              adjusted to get output data within the desired range (0-255).
              Standard options are available.

              Calculate auto or cross correlation functions.  3d correlation
              takes 1 or 2 volumes and does an auto or cross correlation
              respectively.  If the volumes are fourier transforms, the output
              file will be a fourier transform.  2d correlation takes 1 or 2
              slices for input and does an auto or cross correlation respec-
              tively.  Select the slices with the -iz option.  Input files in
              this case may not be fourier transforms.  All other input types
              are automatically padded, FFT transformed, correlated and
              inverse FFT transformed.  One or two input files can be given
              and one output file needs to be given.  Input is automatically
              padded with the mean value unless the -p option is given to
              change the pad value. The -n option selects the type of padding:
              "-n 0" selects no padding; "-n 1" selects padding with mean
              value. (default) Float is the only output mode supported.  Input
              sizes must have dimensions that fit the requirements for an FFT:
              the size in X must be a multiple of two.

              Apply 2D anisotropic diffusion to individual slices, using the
              simple Perona and Malik diffusion technique.  The gradients in
              this method are simply pixel-to-pixel differences.  The ratio
              between these pixel-to-pixel differences and the threshold K
              determines how much diffusion is allowed between pixels.  The
              number of iterations is specified with the -n option (default
              5).  The edge stopping function is selected with the -cc option
              and can be 1 for the exponential function, 2 for the rational
              function, or 3 for the Tukey biweight function (default 2).  The
              K value for controlling the edge stopping function is entered
              with the -k option.  For byte data, start with values on the
              order of 1; the rational edge function may require lower values
              and the Tukey biweight may require larger values.  The effect of
              the value scales proportional to the range of the data.  The
              step size, lambda, is specified with the -l option; the default
              is 0.2, which should be small enough to give stable results.
              These computations correspond to those done in the image pro-
              cessing window in 3dmod, but better results will generally by
              obtained with nad_eed_3d.

              Find and fill in the dark edges left by summing shifted images
              where empty areas were not filled in, as occurs for drift cor-
              rection with a OneView camera.  Pixel values will be analyzed
              over the central 1024 pixels along each edge, or nx/4 if the
              image is larger than 4096; a different length can be set with
              the -l option.  The width of pixels analyzed will be 60 or 30
              depending on whether nx is more or less than 3000; a different
              width can be set with the -n option.  The mean and SD are mea-
              sured for the difference between pixels in successive lines and
              the median and MADN are computed for the ratio of the mean to
              the SD of this difference.  Progressing towards the edge, the
              start of the lines that need correcting is taken as the point
              where the number of MADNs above the median for a difference
              exceeds a criterion of 9, which can be modified with the -h

       fft    Calculate a Fast Fourier Transform.  fft does either a forward
              or inverse FFT, depending on the input data type.  The output
              for a forward transformation is complex float.  For a forward
              transform, the input size in X must be a multiple of two.  Both
              2D and 3D output match the format of the FFT output by
              fftrans, in which no data is duplicated and the center is
              shifted to x = 0, y = ny/2.  Older FFT files produced by clip
              before IMOD 3.5, in which the data were replicated to the left
              of the Y axis, are no longer accepted as input as of IMOD
              4.6.25.  Input size and centering options can be used for the
              forward transform, and output size and mode can be set for the
              inverse transform.

       filter High and/or low pass filtering in frequency space (2D only).
              Filters an FFT or an image using the -l and -h options.  An FFT
              and inverse FFT is automatically done if needed.  The units for
              -l and -h are cycles/pixel so they range from 0 to 0.5.  Every-
              thing higher than -l and lower then -h is filtered.  The attenu-
              ation will be 0.5 at the given frequency; the filter factor is
              the product of 1/(1+(r/l)**3) if -l is entered and
              1/(1+(h/r)**3) if -h is entered, where r is the radius in
              cycles/pixel.  The input size in X must be a multiple of two.

       flip   The flip command is just the root of several types of image
              transformations.  The flipx and flipy commands will each create
              a new file where each slice is the mirror image of the input
              slice around the x or y axis.  The flipz command will invert the
              order of slices (mirror around the x/y plane).  The flipxy,
              flipyz, or flipzx commands will exchange x and y coordinates, y
              and z, or z and x coordinates, respectively, and also change the
              size of the output file to match (e.g., with flipyz, the sizes
              in y and z are exchanged).  No input size or centering, or out-
              put size options will be applied.  An output mode can be speci-
              fied except for flipyz and rotx.  All of these options invert
              the handedness of the structures in the image file.  Use the
              rotx command instead of flipyz to reorient a volume without
              changing handedness.

       sobel  These options apply simple 2D filters to the input image, using
              the same method as for the respective entry in the 3dmod image
              processing dialog.  The prewitt and sobel filters seem to be the
              most useful.

       info   Print information about an image.  All header information in the
              mrc file is printed to standard output.  If the file is not an
              mrc file the information is still printed with a warning that
              the file is not an mrc file.

              Print a histogram of pixel values from the selected region of
              selected slices, or analyze for a bimodal distribution of values
              (with the -s option).  The basic histogram function operates
              differently depending on the type of data. For byte, integer, or
              RGB data, a full histogram is built of all values.  For byte or
              RGB data, counts are then printed for all values between the min
              and the max values encountered.  For integer data, counts are
              combined into bins, if necessary, to give around 256 bins.  For
              floating point or complex data, values are counted directly in
              256 bins between the min and max in the image file header, then
              bins are output between the min and max values actually encoun-
              tered.  This behavior can be changed by entering a bin size with
              the -n option (the entry is rounded to the nearest integer for
              data with integer values).  You can also enter -l and -h with
              the lower and upper limits of the histogram to build (for float-
              ing point or complex values) or the limits of the range to out-
              put (for integer-valued data).  Only values within the given
              limits are counted in the histogram; values outside the range
              are ignored.  With integer-valued data, the last bin may have
              fewer counts because it represents a smaller range of values
              than the rest.
                 With the -t option, the program will compute a cumulative
              distribution and report the point by which the given fraction of
              values has occurred.
                 Two specialized analyses of the histogram can be done with
              the -F and -E options.  Both of these options take a fractional
              value representing a percentile point in a distribution, plus a
              direction value to indicate the direction of the analysis.  With
              -F, the program finds the fastest falling point in the histogram
              past the indicated fraction of values, which would typically be
              a large fraction.  With a positive direction, the cumulative
              distribution is computed from low to high and the fastest
              falloff is sought when going to higher values.  With a negative
              direction, the cumulative distribution is computed in the oppo-
              site order and the falloff is found going to lower values.
                 With the -E option, the program identifies extra counts on
              one side of the histogram and finds the point by which the given
              fraction of these counts has occurred.  Specifically, it finds
              the interpolated position of the peak of the histogram, then
              subtracts from each bin above the peak (for a positive direc-
              tion) the interpolated value of the histogram an equal distance
              below the peak.  If a positive peak appears in this difference,
              a cumulative distribution is computed out to the point past this
              peak where the difference goes negative, and the point by which
              the given fraction of extra counts have occurred is reported.
              Again, a negative direction inverts the direction of analysis.
                 With the -s option, the program will instead analyze kernel
              (smoothed) histograms of a sample of the image data (up to
              1,000,000 pixels), looking for two peaks in such a histogram.
              If successful, it will report the intensity of the two peak val-
              ues and of the lowest point (dip) between them, as well as the
              fraction of pixels below the value of the dip.  The -l, -h, and
              -n have no effect and will cause an error if used.  With the -2d
              option, the program will analyze each input slice separately;
              otherwise it will analyze the full range of the input volume in
              one histogram.

              Combine 3 input files containing red, green, and blue informa-
              tion into one RGB file.  The 3 input files must all be byte mode
              and their names must be entered in the order red, green, and
              blue, followed by the output file name.  The -r, -g, and -b
              options can be used to scale the components (default scaling is
              1).  The -a option can be used to append to an existing color
              file of the same size in X and Y.  No other options except -v
              will work with this process.

              Take the logarithm of the image intensities after adding an
              optional base value entered with -n.  The program avoids taking
              the log of negative or very small values by using a minimum
              value of 1.e-5 times the data range of the input file (from the
              minimum and maximum densities in the header).  The output mode
              is set to float unless a different output mode is entered.

       median Apply a median filter by replacing each pixel with the median of
              the values in a block of neighboring pixels.  The size of the
              block is given by the -n option; its default is 3.  The default
              is to do a 3D filter (thus taking the median in cubes of data),
              but the -2d option can be used to apply a 2D filter that consid-
              ers only the pixels in one section.  Note that an even size will
              offset the data by half a pixel.

       divide Multiply or divide the first input file by the second input
              file.  Use "multiply" to apply a mask to a volume, such as one
              produced by Imodmop.  The files must be the same size in X
              and Y, and they must either be the same size in Z or the second
              file must be a single image.  Standard input and output options
              can be used.  The first input file may be any mode.  The second
              input file must have a single "data channel" (i.e., byte, inte-
              ger, or float) unless either a) the first input file is complex,
              in which case the second file can be either a single-channel or
              a complex file, or b) the output mode is float, in which case
              the second input file is converted to a single channel of float
              data.  The -n option can be used to set a factor for scaling the
              output, and the mode can be changed to preserve resulting values
              outside the range of the input mode.


       unpack Processes movie frames acquired from a direct detector camera
              (primarily ones from the Gatan K2), optionally converting from
              4-bit data, scaling, gain-normalizing, and truncating extreme
              values.  The command was originally called "unpack" and used
              exclusively to unpack 4-bit data that were packed into a byte
              mode file with half the actual size in X.  As of IMOD 4.8.41,
              files like this saved by the SerialEMCCD plugin from a K2 cam-
              era, and 4-bit files with the non-standard MRC mode 101, are
              recognized by the file-reading system and converted from 4 bits
              to bytes automatically.  Clip no longer does this data conver-
              sion, and it will thus work with byte and integer mode files as
              well.  The same command thus works with the more general name,
              "normalize".  If only one input file is given, the data are not
              scaled and will have their original values.  If two input files
              are given, the second is assumed to be a file to multiply by
              (i.e., a gain reference file).  It must be mode 2 (floating
              point).  The -R option can be used to specify a rotation and
              flip to be applied to the reference, or to indicate that the
              rotation/flip value is to be obtained from the header of the
              first input file.  The gain reference size must match that of
              the first input file (after the rotation and flip, if any).
              When normalizing, data are scaled by 16, by default.  The -n
              option can be used to set a different scaling factor.  Values
              can be truncated at a level entered with the -h option.  Values
              above that level will be set to the mean of up to 40 surrounding
              pixels, excluding the 8 adjacent ones, or to a different value
              entered with the -l option.  If normalization is being done, the
              truncation will be applied after the normalized and before the
              additional scaling, if any.  (The mean of surrounding values and
              truncation after normalization started being used in IMOD
              4.8.46.)  The -m option can be used to set a different output
              mode, and all input and output size and centering options can be
              If you have a byte file with packed 4-bit data that IMOD fails
              to recognize automatically, the unpack command will no longer
              work on it.  You can use the command
                   alterheader -4bit 1 filename
              to change the file to mode 101, and then it should work cor-
              rectly in Clip and elsewhere.  In such a file, the low-order 4
              bits are assumed to be the first of the two pixel values, going
              from left to right.

              Analyze and correct for differences between quadrants in images
              from 4-port-readout cameras.  The boundary between quadrants
              must be in the exact image center in X and Y.  By default, the
              program analyzes and corrects each section separately by finding
              the mean in areas adjacent to the boundary that are 20 pixels
              wide and extend parallel to the boundary from the center out to
              within 5% of the image edge.  Scaling factors are computed that
              do the best job of equalizing these means across the boundaries.
              There are four options that affect this behavior:
              1) The -iz option can specify a list of sections to correct; all
              other sections are simply copied to the output file.  This
              option allows you to run the correction on subsets of the data
              with different parameter settings if necessary.
              2) The -n option sets the number of images to analyze together.
              The sections are considered in successive groups of this size.
              An overall mean is obtained from the average of the boundary
              areas, and a single scaling is computed and applied to all the
              sections in the group.  Enter any number larger than the number
              of sections in the file to have all images analyzed together.
              3) The -l option sets a base amount to add to the data.  By
              default, the program will add a base if necessary to avoid ana-
              lyzing negative mean values from boundary areas, but this may
              not work well.  If you have data from FEI software that have had
              32768 subtracted, you must enter "-l 32768" to have the correc-
              tion work correctly.
              4) The -h option sets the width of the boundary areas.
              The output file will have the same dimensions as the input file;
              options for selecting subareas are ignored.  Extra header data
              are copied over to the output file.  The -m option can be used
              to change the mode of the output.

       resize Cut out or pad an image to a new size without doing any other
              operations.  Resize 3d cuts out an image of size ix, iy, iz,
              centered around cx, cy, and cz.  The output size of the file is
              ox, oy, and oz.  The default input size is the size of the input
              file, the default center is the center of the input file and the
              default output size is the same as the input size.  The default
              padding is the average value of the input file; the padding can
              be changed with the -p option.  Resize 2d cuts out a list of
              slices specified by the -iz option.

       rotx   Rotate an image volume by -90 degrees about the X axis.  This
              rotation is preferable to flipyz because it preserves the hand-
              edness of structures.  The origin and tilt angles in the header
              will be modified to retain the coordinate system of the original
              volume, as is done by Rotatevol.

              These options will filter images by convolving with a simple 3x3
              or larger kernel, using the same method as for the respective
              entry in the 3dmod image processing dialog.  The smoothing fil-
              ter is the most useful; by default, its kernel is
                  1 2 1
                  2 4 2
                  1 2 1
              However, a Gaussian kernel can be used for smoothing instead if
              a standard deviation (sigma) is entered with the -l option.  The
              kernel will be 3x3 for sigma up to 1.0, 5x5 for sigma up to 2.0,
              and 7x7 for higher sigma values.

              Compute power spectra from images.  The spectra will be square
              and optionally reduced in size and/or scaled to bytes.  The
              default is to produce spectra that are reduced to 1024x1024 if
              the larger image dimension (after padding) is greater than 1044,
              and scaled to bytes after taking the logarithm.  The output size
              can be set with -ox or -oy, which must be equal if both are
              entered.  The scaling is controlled by two parameters: 1) a
              background gray level, the mean value at the edge of the spec-
              trum after scaling to bytes; 2) the diameter of an annulus of
              pixels whose mean value would scale to 255, relative to the size
              of the spectrum.  The default gray level is 48 and it can be set
              with the -l option.  The default diameter is 0.02 and it can be
              set with the -h option; bigger numbers saturate more of the cen-
              ter of the spectrum.  The scaling to bytes can be disabled by
              entering "-l 0", in which case there will just be an initial
              scaling to integers ranging from 0 to 32000 and default output
              in mode 1.  Input options can be used to take the spectrum of a
              subarea or a subset of images.  The output mode can be set with
              -m, but this does not affect the scaling into bytes or short
              integers before output.  The pixel size will be changed by the
              amount of image reduction.

              Output the 3 color channels of an RGB file into three separate
              files, so that other operations can be performed on them (such
              as transformations).  With this process, the output file name
              will be used as a root for three filenames ending in .r, .g, and
              .b.  A subset in Z may be extracted from the file, where the -iz
              entry is interpreted as usual depending on whether -2d is speci-
              fied.  No other options except -v will work with this process.

       sqroot Take the square of the image intensities after adding an
              optional base value entered with -n.  Negative values after
              adding the base will be replaced by 0.

              Compute standard deviation or variance of a set of volumes or a
              set of images in a stack.  These operations work the same as the
              "average" option, so if the same options are given, the results
              should be usable together for statistical tests, such as with
              Subimstat.  If more than one input file is given, it computes
              the statistics for each pixel from all of the input files and
              outputs a volume.  All input images must be the same size and
              mode. Standard input and output options are available in this
              case.  With one input file, it computes the statistics for each
              pixel in X/Y across the slices and produces one output slice.
              Just as with averaging, use the -n option to set a threshold
              such that pixels below threshold are not included in the statis-
              tic.  Standard input options are available but output cannot be
              resized in this case.  For both cases, if a scaling factor is
              entered with the -l option, then standard deviations will be
              scaled by this factor but variances will be scaled by the square
              of the factor.  to prevent saturation with byte input data, you
              will generally need either to scale the output appropriately or
              to change the output mode to floating point.

       stats  Calculate stats on a file. A table is printed with the minimum,
              maximum, mean and standard deviation.  The locations of the max
              and min are also printed.  The locations are calculated by doing
              a quadratic fit around the extreme value.  If the -s option is
              given, the location of the max is adjusted by half the image
              size, which may be appropriate for a cross-correlation.  Other-
              wise, if statistics are done on a subarea, the location is
              adjusted to give the coordinates in the full image. If either
              the -l or the -n option is given, min and max values will be
              analyzed for outliers by comparing the min or max value for a
              slice with the respective values for nearby slices or for all
              slices.  The comparison is by the ratio of the distance of a
              value from the median, to the median of such distances.  The
              criterion for this ratio is set with the -n option and has a
              default of 2.24; use higher values to have fewer slices marked
              as outliers.  The number of nearby slices used for comparison is
              set with the -l option; otherwise the comparison is with the
              values for all slices.  Each outlier is marked with a star, and
              at the end the slices with outlier values are listed.

              Subtract the second input file from the first one.  Both files
              must be the same size and mode, but standard input and output
              options are available.  There is no provision for scaling, but
              the mode of the output can be changed, .e.g., to preserve nega-
              tive values.

              Make binary image by setting pixels above a threshold entered
              with -t to a high value, otherwise to a low value.  The thresh-
              old must correspond to a value in the file, which is usually not
              the same as a threshold value visualized in 3dmod.  The
              Threshold panel in the image processing dialog in 3dmod
              (opened with Edit-Image-Process) will show the value in the file
              corresponding to a particular threshold setting there.  The
              default low and high values are 0 and 255.  If the -s option is
              given, the low and high values will be set to the minimum and
              maximum of the input image file.  The low value can also be set
              with -l and the high value with -h.  Standard input and output
              options can be used.
                 If the -M option is given with a minimum size and a direc-
              tion, the thresholding will be done by a separate routine that
              enforces a minimum size for adjacent sets of points on one side
              of the threshold (above or below the threshold for a positive or
              negative direction, respectively).  Points are considered adja-
              cent if they are next to each other in X, Y, or Z, but not if
              they are diagonal to each other.  The routine operates most
              efficiently if the regions on the selected side of threshold are
              relatively sparse and compact, and may consume much more time
              and/or memory if this is not the case.  The image size in X and
              Y is limited to between 2 and 4 gigapixels.  With the -2d
              option, sets of points are not connected between slices and the
              minimum size applies to the sets of adjacent points on one

              Truncate pixel values at a lower or upper limit, or both.  Enter
              the lower limit with -l and the upper limit with -h.  If the -s
              option is given, values beyond the limit will be replaced by the
              image mean.  Standard input and output options can be used.

       unwrap Add the value specified by the -n option (32768 by default for
              signed integer data) and adjust any values that are now out of
              range for the input data mode by adding or subtracting 65536.
              This process can be used to recover data that wrapped around
              when they were saved as integers.  Two examples of wraparound
              are: 1) Unsigned data that went higher that 32767 but were saved
              as signed integers, in which the values above 32767 now appear
              as large negative numbers.  2) Data with negative values that
              had 32768 subtracted before saving, in which the negative values
              became large positive ones (this has been seen with FEI acquisi-
              tion software).  In case 1, the default value to add (32768) is
              appropriate but the data then need to be saved as unsigned (mode
              6) or as floating point.  In case 2, the default value is appro-
              priate as long as the original data did not range higher than
              32767; if they did, then you need to determine a different value
              to add, such as a small number just sufficient to bring the
              originally negative numbers above 0.  This process will also
              work with unsigned input data but a -n entry is required.  Stan-
              dard input and output options can be used.  Extra header data
              are copied from the input file to the output file if neither the
              -iz nor the -oz option is entered.

       Originally most processes loaded all data into memory unless the -2d
       option was given, and the -2d option did not provide for any output
       padding.  Work in Jan 2005 fixed this so that only 3D correlation and
       FFTs and 3D color load the whole volume; everything else does slice-by-
       slice processing, with proper handling of output padding and appending
       regardless of whether -2d or -3d is selected.  Rotation, translation,
       and zoom were not well-implemented and were abandoned.

       Jim Kremer
       David Mastronarde
       The anisotropic diffusion is based on a program by Alejandro Cantarero

       3dmod, newstack, rotatevol, matchvol, fftrans, subim-
       stat(1), imodmop

       There are not checks for the validity of all input values, and some
       nonsensical mode conversions are allowed.  The extended header is not
       copied over to the output file, except by the quadrant and unwrap pro-

       Email bug reports to mast at colorado dot edu.

IMOD                                4.9.10                             CLIP(1)