alignframes(1)              General Commands Manual             alignframes(1)

       alignframes - Aligns and sums camera movie frames and stacks sums

       alignframes options

       Alignframes aligns frames from direct electron detectors and other cam-
       eras that can output a set of frames from an acquisition.  It can take
       input from multiple frame files and produce a single stack that is
       ready to use for tilt series processing.  It implements two basic
       alternatives for an initial alignment that can optionally be refined:
       aligning each frame to a reference accumulated from previously aligned
       frames; or solving for the shifts of individual images by fitting to
       shifts measured between many pairs of frames.  The latter approach has
       several advantages and can be applied in various ways.  The advantages
         1) It involves multiple measurements for every image and thus can
       average over more information for aligning the first few frames than
       the cumulative method can.
         2) Robust regression is used for the fitting, so a small proportion
       of bad alignments can be tolerated and should not degrade the result.
       Thus, this method should be more resistant to occasional failed corre-
       lations due to fixed pattern noise.
         3) The fitting yields an estimate of the residual error for each mea-
       surement, from which it is possible to derive an error measure that
       reflects the overall quality of the alignment and that can be used to
       compare results with different parameters.

       The fitting to shifts between pairs of frames is done for successive
       sets of frames, 7 by default.  With that setting, each frame is aligned
       to all preceding frames for the first 7 frames, then the first fit is
       done and a best shift determined for the first frame.  The 8th frame is
       then aligned to frames 2 through 7, and the next fit yields a shift for
       the second frame.  It is possible to align every frame to every other
       one and do one fit to find all of the shifts at once, but this approach
       does not seem to give any advantage in the typical case, and the number
       of correlations can become quite large because it is proportional to
       the square of the number of frames.  When pairwise fits with sets of
       more than 7 frames are indicated, another alternative strategy is to do
       pairwise fits with sets of half the frames (see below).

       The program allows one to test the quality of the fits with different
       high frequency filter cutoffs, and even with different binnings.  Mul-
       tiple filters can be tested quickly in one run through the data, but
       testing multiple binnings require multiple runs through the data.  As
       of IMOD 4.12.19, every fit to the pairwise shifts includes a cross-val-
       idation step: the fit is done multiple times with one or a few pairwise
       shifts omitted each time, and the solved frame shifts are used to pre-
       dict the pairwise shifts that were left out.  The result is a mean
       "leave-out" error, which is a much more reliable indicator than the
       mean residual error of whether one set of fitting parameters is better
       than another.  The mean residual can be misleadingly low when the ratio
       of measurements to values being solved for is too low to average out
       the random error in the values being fit.

       After the initial alignment, it is possible to realign each frame to a
       reference consisting of all other aligned frames.  (For high-noise
       data, it is essential to leave the frame being aligned out of the ref-
       erence, or it would dominate the alignment.)  This refinement can help
       after alignment to a cumulative reference, but has seemed superfluous
       in most tests with initial alignments from pairwise shifts.

       All frame data are maintained as Fourier transforms, so each additional
       alignment only involves one inverse FFT.  Frames are shifted into
       alignment in Fourier space to avoid losses from interpolation, and they
       are reduced in size for the final sum (if at all) by cropping in
       Fourier space to avoid aliasing.

       If you want to compute a Fourier ring correlation, enter either the
       -lines option with a value of 3 or the -frc option with a filename.
       Fourier transforms of even and odd frames are summed separately and a
       Fourier ring correlation is computed.  The program reports the frequen-
       cies at which the FRC crosses 0.5 and 0.25 in cycles/pixel of the
       summed images, and also reports the mean value around a frequency of
       0.25/pixel (half-Nyquist).  The FRC is the only tool for comparing
       results with the cumulative alignment to those with pairwise alignment
       or for assessing the change from refining a pairwise alignment at the
       end. The FRC can also be used for validating the choice of filter or
       binning suggested by trying multiple values.  However, changes in the
       FRC may generally be quite small, so it will usually be helpful to
       assess a change a parameters with a number of frame stacks.  The pro-
       gram Subtractcurves can help in this assessment as described below.

       Quite strong high-frequency filtering is needed for typical frame
       alignments.  The filter cutoff is entered in frequency units of the
       unbinned data so that a particular value has about the same effect at
       different binnings.  The default filter (0.06/pixel) is close to what
       is typically needed, but smaller values (down to 0.05) or possibly
       larger values (up to ~0.1) may give better results.  Binning (actually
       antialiased reduction in size) accomplishes most of the removal of
       high-frequency noise prior to the application of the frequency filter,
       so these two operations are partly redundant.  Most of the motivation
       for binning is to speed up the alignment; however, after a certain
       point, additional binning will somewhat reduce the accuracy with which
       the correlation peak position can be measured.  Thus, the program
       facilitates testing with different binnings, although such testing is
       probably only needed when getting started with a particular class of
       data, whereas testing with multiple filters is likely to be used more

   Alignment Strategies
       The big challenges in aligning frames are the low signal-to-noise ratio
       and interference from fixed pattern noise.  There are some significant
       distinctions between tilt series and single particle data when consid-
       ering what methods to apply.  First, tilt series may have a lower dose
       per frame, but they are likely to have more features in the image than
       some single-particle images, and thus more signal to align with.  Sec-
       ond, there can be beam damage such as doming of the ice within a series
       of single-particle frames, which would not be apparent for a set a tilt
       series frames with a low dose per tilt image.

       One can think of a series of possible strategies for dealing with
       increasingly difficult data:
          1) When there is strong signal and no appreciable fixed pattern
       noise, the simple method of aligning to a cumulative reference of
       already aligned frames may be adequate.  Here, refinement at the end
       may help if it improves the shifts for the first few frames, which were
       subject to the noisiest correlations.  2) Images with reasonable SNR
       and little fixed pattern noise should work with the default method of
       aligning all pairs among successive sets of 7 frames.  3) If the noise
       is higher or signal lower, or if there is serious fixed pattern noise,
       then pairwise alignment among much larger sets of frames will be
          3A) For tilt series data, using all pairs of frames would generally
       be appropriate.
          3B) For single particle data, it is better to do pairwise alignment
       among half the total number of frames, to avoid correlating across
       large changes in the specimen.  However, if fixed pattern noise is a
       problem, it may be necessary to use all pairs instead, so that some
       correlations with large shifts will be available for all frames.
       (Fixed pattern noise makes the correlations unreliable or inaccurate
       for small shifts; even when the filtered peak at the origin is smaller
       than the true correlation peak, it can displace the peak position if
       the two peaks overlap.)
          3C) Refinement at the end is risky if there is serious fixed pattern
          4) If the noise is just too high for alignments between single
       frames to work, then grouping can be used.  A group size of 3 can help
       considerably.  Refinements can be done at the end by correlating either
       single frames or, if necessary, just the grouped frames with sums of
       other frames.

   Text Output with Single Parameter Settings
       In cases where there is one set of frames per file, output for a file
       starts with a line like
         File 1  (Feb21_10.12.15.mrc): 11 frames
       When multiple sets of frames are contained in a single input file, the
       output for each set starts with a line with "Set", such as for a fast-
       incremental single-exposure tilt series:
         Set 3 (pilY13_005.tif): 10 frames from 803 to 812   (-54.0 deg)
       When there is only one filter and binning being used, the following two
       lines present summary statistics for the results of the doing robust
       fitting to the shifts for each set of pairwise alignments.  All of the
       values and distances are in unbinned pixels.  The first line has these
         Weighted residual mean (abrreviated as Wgt resid mean):
         The mean residual error value, averaged over all of the fits.  This
         is a weighted error, so aberrant shifts that are completely
         down-weighted are not reflected here.
         mean max: The mean value of the maximum weighted residual, averaged
       over all the fits
         max max: The maximum weighted residual seen in any of the fits
         leave-out error (abbreviated as l-o err): The mean
         leave-out error from the cross-validation fits
       The second line has these items:
         Max unweighted resid mean: The average of the maximum unweighted
       residual values seen in the fits
         max: The maximum unweighted residual seen in any fit
         Dist: Raw sum of distances from one frame position to the next
         smoothed: Sum of smoothed distances.  If spline smoothing is used,
       this is the distance for the smoothed shifts that are used to sum the
       images.  Otherwise, this is based on a local polynomial smoothing that
       is not very good.
       When the -lines option is entered with a 3, there is also a summary of
       the output from Fourier ring correlation.  This line reports the fre-
       quencies (in cycles/pixel) at which the curve crosses below 0.5, 0.25,
       and 0.125.  The last number on the line is the mean value of the curve
       around 0.25/pixel (half-Nyquist).  If the sum is reduced in size, these
       frequencies are in terms of the binned pixels.

       The most important values on the first line are the weighted residual
       mean and the leave-out error.  After each fit, the shift between each
       pair of images is computed from the solved shifts of the individual
       images, and the residual for that shift is the difference between the
       computed and measured values, multiplied by the weighting factor
       applied to the measurement.  The leave-out errors were explained above,
       except for the fact that the error for each predicted pairwise shift is
       multiplied by the same weighting factor that was obtained for that
       shift in the solution with all data included.  The means of both of
       these errors give some indication of how accurate the shifts should be,
       on average, but the leave-out error is a more reliable indicator.  Good
       values for the mean residual are in the range of 0.05 to ~0.3, but some
       sets may give values in the range of 1-3.  The latter cases are a sign
       that one should try analyzing a higher number of pairwise shifts or
       even try grouping.  Using more pairwise shifts will generally increase
       the mean residual but will allow greater averaging over these random
       errors and thus reduce the leave-out error; grouping should improve the
       residuals and leave-out errors.

       The maximum residual values on the first line should not be many times
       larger than the mean; these values indicate that there may be a shift
       in error by that amount.

       The Max unweighted resid mean on the second line reflects how often
       there are bad shifts measured between pairs of images.  With no bad
       shifts, it should be not very much bigger than the maximum weighted
       residual; values above a few pixels may indicate that there are bad
       correlations in most fits.  Reducing the filter cutoff, reducing the
       maximum allowed shift, and grouping may improve this value; increasing
       the number of pairs being fit will increase the ability of the program
       to reject the bad shifts as outliers.  (As long as the weighted maximum
       residuals are not high, the program is already able to reject the bad

       The distance values on the second line reflect the total specimen move-
       ment, and comparison between raw and smoothed distances gives some
       indication of how jittery the solved shifts are.  They become more
       important when trying different filter settings, as explained below.

   Text Output with Tests of Binning and/or Filters
       If you specify either multiple filters with the -vary option or multi-
       ple binnings with the -test option, there will be output similar to
       what was just described for each condition being tested.  An initial
       line for each condition shows the binning, the filter cutoff value, and
       the sigma for the filter falloff.  The latter is varied in proportion
       to the cutoff value.

       When there are multiple filters, the program will compose a "hybrid"
       solution that is based on the filter that gives the lowest leave-out
       error after each fit to a set of pairwise shifts.  The set of results
       from this hybrid solution appear after the ones for the various fil-
       ters, with an initial line showing Hybrid results, bin =.  This solu-
       tion is not used by default, only if the -hybrid option is given.

       After all of the results, there will be a line indicating which condi-
       tion is considered best, such as:
       File 1: Best at bin = 8  rad2 = 0.060  sig 0.009  mean res = 0.121  l-o = 0.180

       However, the selection of a best solution must be treated with caution.
       If fixed pattern noise is significant, the fit may appear to improve
       dramatically with high filter cutoffs.  One sign that fixed pattern
       noise could be taking over is a substantial decline in the distance
       travelled with higher filter settings; the program will not consider
       these filters to be better if the decline is too great.

       If the program is run on more than one file, then at the end there will
       be a report of the number of times each combination of binning and fil-
       ter cutoff gave the best solution.  For example:
       Number of times each condition is best  (rad2 in parentheses):
       bin = 6      3 (0.050)    1 (0.060)    0 (0.080)
       bin = 8      3 (0.050)    1 (0.060)    1 (0.080)
       This indicates that a cutoff of 0.05 is generally better than 0.06, and
       that there is not much difference between binnings 6 and 8.

       Not all combinations of binning and filter cutoff are meaningful.  Fil-
       ter cutoffs that are at or above the Nyquist frequency for a particular
       binning will have little or no effect.  Here are the Nyquist frequen-
       cies for common binnings:

          Binning   Nyquist frequency
             2           0.25
             3           0.167
             4           0.125
             6           0.083
             8           0.062

   Support for Frame Files with Extended Header Data
       If the frame files have an extended header (as files saved by UCSFtomo
       do), the program will look for several features:
         1) If the header is large enough to contain a gain reference, then
       these data will be extracted and used to gain-normalize the frames,
       unless a different gain reference is supplied with the -gain option.
       The reference will be assumed to be in the correct orientation to apply
       to the frames; but if it is not, the -rotation option can be used to
       reorient it.
         2) If the header appears to contain valid tilt angles, the program
       will use these values to break the frames into separate sets for align-
       ing and summing, unless the -break option is given.  It will recognize
       one place where there are two sets at the same angle and make two sums
       there, provided that there are at least 5 sets of frames of the same
       size prior to that place.  This, if you use -frame to try aligning a
       subset of tilt angles right around the starting point of a tilt series,
       you may have to use -break to prevent these two images from being com-
       bined.  The tilt angles will be placed into the extended header of the
       output file unless provided by another source (the -tilt or -stack
         3) If the extended header contains valid entries for pixel size and
       tilt axis rotation angle, the pixel size will be placed into the stan-
       dard header location and a title will be added with the rotation angle.

       Note that although multiple files can still be entered when there is an
       extended header, the program will insist that their properties match.

   Dose Weight Filtering
       The program can do dose weight-filtering of frames before summing for
       sets of frames from either tilt series or single-particle acquisition.
       The filter is as described in Grant and Grigorieff, 2015
       (DOI:10.7554/eLife.06980) and the implementation follows that in their
       "unblur" program.  At any frequency, the filter follows an exponential
       decay with dose, where the exponential is of the dose divided by 2
       times a "critical dose" for that frequency.  This critical dose was
       empirically found to be approximated by a * k^b + c, where k is fre-
       quency; the values of a, b, c in that paper are used by default but can
       be modified with the -critical option.  This filter function is applied
       for all frequencies (complete attenuation above the "optimal dose" is
       no longer considered appropriate).  For each set of frames, the program
       will apply a weighting that changes through the set of frames as dose
       accumlates.  If just an overall dose for the image is specified, this
       dose is divided equally among the frames.  However, if frames are not
       of equal duration, it is possible to specify the different doses of the
       frames.  For a tilt series, the weighting also changes through the
       frame sets according to the amount of dose prior to each set of frames.

       A variety of options are described below for providing dose information
       to the program.  The ".mdoc" file from SerialEM can be a convenient
       source of such information, particularly if frames are not of equal
       duration.  If an .mdoc is supplied for single particle data with the
       -dfile option, it can contain entries for many images; the program will
       pick out the dose information that applies to the frame sets being
       aligned.  For tilt series, the .mdoc provides cumulative dose informa-
       tion directly if created by SerialEM in 2017 or later; if that informa-
       tion is missing, it can be derived from the date-time stamps of the
       frames.  When the -adjust option is used to write a new .mdoc file, the
       program makes several changes to make the new file usable or more
       robust for dose weighting.  If there are dose entries but no cumulative
       (prior) dose entries, prior dose entries will be added.  If some tilt
       images are subsequently removed with Excludeviews, the .mdoc file
       made in that process will still be valid for dose weighting, whereas
       prior dose values derived from date-time stamps instead would then be
       incorrect.  If you enter a fixed total dose per frame stack with -dto-
       tal, either because there is no dose information in the .mdoc or
       because you wish to override the dose value in the file, the program
       will add or replace both the dose per tilt image and the prior dose
       entries so that they are correct for the new value.  Again, this allows
       Excludeviews to be used.

   Computer and GPU Memory Usage
       The amount of computer memory required for this processing depends
       mostly on the size of the images and whether all of the frames will be
       held in memory until all alignments are completed.  Each frame held in
       memory requires 4 times as many bytes as pixels.  Frames will be held
       in memory if only one binning is used and any of the following options
       are used: multiple filters (unless the -hybrid option is used to allow
       the final setting of one shift after each pairwise fit), pairwise
       alignment among all frames, refinement after initial alignment, or
       smoothing of shifts (which occurs by default with 15 or more frames).
       Otherwise, the number of frames held until the end will equal the num-
       ber of frames used for pairwise fits (plus the group size minus one, if
       grouping).  However, when more than one binning is tested, the program
       will not hold any frames but instead read them in again on a second

       The amount of memory needed for the binned images being aligned can
       also become large if the binning is small.  These images are all held
       until the end if there is refinement of the initial alignment; other-
       wise the number retained will be the number used for pairwise fits.

       When using a GPU, the size of unbinned images dominates the usage, but
       space is needed for only 3 or 4 image-sized arrays.  This can approach
       1 GB for ~8K images.  The frames are actually held in computer memory
       until their shifts are finalized.  Binned images for alignment will
       also consume significant amounts of the GPU memory; these images stay
       on the GPU instead of in computer memory, and the requirements there
       are the same as they would be in computer memory.  If binning is only
       to ~2Kx2K and there are 60 frames, with refinement at the end, then 1
       GB would be needed; fewer frames or more binning (both typical) would
       result in half this requirement for the aligned frames.  Thus, 2GB of
       memory should suffice for typical usage, but 4 GB would handle almost
       any anticipated need.

       Alignframes uses the PIP package for input (see the manual page for
       pip).  Options can be specified either as command line arguments
       (with the -) or one per line in a command file (without the -).
       Options can be abbreviated to unique letters; the currently valid
       abbreviations for short names are shown in parentheses.

         These options specify the input to the program or are related to
       input options

       -input (-in) OR -InputFile     File name
              Input file with images to correlate.  Non-option arguments will
              also be used for input files, with those entries used after any
              names entered with this option.  If -foutput is entered, all
              non-option arguments will be used for input files; otherwise all
              but the last will be.  Input files need not be entered if an
              .mdoc file is entered with the names of the frame files.  (Suc-
              cessive entries accumulate)

       -output (-ou) OR -OutputImageFile   File name
              If this option is not entered, the last non-option argument will
              be used for this output file.  An output file is required unless
              -nosum is entered.

       -list (-lis) OR -ListOfInputFiles   File name
              Name of file with list of input files, one per line.  Filenames
              entered this way are equivalent to ones entered with -input or
              as non-option arguments; the latter two entries cannot be used
              along with a file list.

       -break (-br) OR -BreakFramesIntoSets     Integer
              If the input consists of a series of single-frame files, this
              option must be used to combine them into one or more sets of
              frames to be aligned and summed.  Additionally, the option can
              be used to break a file with many frames into multiple sets of
              frames, each of which will be aligned and summed.  The input
              frames (either the whole collection of single-frame files, or
              the frames in one multi-frame input file) will be divided into
              groups of the given size, with any extra frames distributed
              among the initial groups.  For  example, for 50 single-image
              files or one file with 50 frames, and an entry of 8, there will
              be 6 summed images, with 9 frames in the first two and 8 frames
              in the rest.  There must be at least as many single-image files,
              or as many frames in each input file, as the number given.  For
              single-image files, this option cannot be entered with the
              -frame or -assess options.  For multi-frame files, the option
              cannot be entered with -assess and will work with -frame.  In
              either case, the option should work with -stack or -mdoc unless
              frame filenames are being taken from the mdoc file.  Frame files
              with tilt angles in the extended header will automatically be
              broken into sets by tilt angle, so this option is not needed in
              that case.

       -saved (-sa) OR -SavedFrameListFile      File name
              Name of file with list of frames saved from a fast-incremental
              single exposure tilt series where blanked frames were not saved.
              There must be only a single frame input file and it must have
              the same number of frames as lines in this list file.  Every set
              of contiguous values is assumed to be from one tilt angle.
              There are several changes in IMOD 4.10.36: 1) A negative entry
              means that the frame should be skipped; this should occur only
              at the start or end of a frame set.  2) The frame numbers need
              not increase within a frame set, so the list could use the same
              number for all frames in a set.  3) The frames numbers need not
              be sequential within a frame set; there can be gaps as large as
              the value entered with the -gap option, and the program will not
              start a new frame set at such a gap.  4) The program will auto-
              matically eliminate the first or last frame if there is a large
              enough gap between it and the adjacent frame and the average
              size of frame sets is at least 4, and if there are no negative
              values in the file.  SerialEM has to write these frames, and as
              of 3.8beta7 it will mark them with negative frame numbers, but
              this automatic detection should work with older frame lists.  If
              data are lost from entire tilt angles because they fell below
              the threshold for saving, Alignframes can also use relative
              starting and ending frame numbers from a tilt angle file or an
              .mdoc file to sort out which angles were lost (this information
              is output by SerialEM as of 12/16/19).  This entry cannot be
              used with -frame, -assess, or -break.

       -gap OR -MaxGapWithinFrameSet       Integer
              Maximum size of a gap in sequential frame numbers allowed before
              starting a new frame set, when using a saved frame list.  The
              value is thus the number of frames that might have been lost
              within a frame set because the threshold was set too high during
              acquisition.  The default is 0.

       -skip (-sk) OR -SkipFileChecks
              Skip initial check that all input files have the same size and
              data mode; this check can take significant time with many non-
              MRC single-frame files.  This option is allowed only with sin-
              gle-frame input files.

       -stack (-sta) OR -CorrespondingStack     File name
              Name of image stack of sums corresponding to the input files,
              such as a tilt series where each image is a sum of unaligned
              frames.  This file will be used for the basic header information
              of the output file, thus preserving titles and extended header

       -mdoc (-md) OR -MetadataFile   File name
              Name of a metadata autodoc (mdoc) file with a section for each
              input file to be aligned and stacked.  This file is an alterna-
              tive way to get basic header information for the output file, as
              well as tilt angles into the extended header.  In addition, if
              there are no input filenames entered as arguments, input file-
              names will be obtained from all of the sections in the .mdoc
              file with "SubFramePath" entries.  However, the paths in those
              entries are ignored; the frame files must all be in the current
              directory unless the -path option is entered with an alternative
              path.  This capability is useful for bidirectional tilt series
              or if a Record image was acquired more than once at a tilt
              angle, since only the frame file for the last Record image will
              be used.  If input filenames are entered as arguments, there
              must be at least as many sections in the .mdoc file as input
              files if tilt angles are to be obtained from the .mdoc file
              (i.e., if -tilt is not entered).  The exception to this is when
              a saved frame list file is entered with the single input frame
              stack from a tilt series.  In this case, the .mdoc file from
              SerialEM is a frame stack mdoc file with a "FrameSet" section
              followed by a brief section for each tilt, with the angle,
              expected relative starting and ending frames, and dose informa-

       -path (-pat) OR -PathToFramesInMdoc      Text string
              Current path to the frame files listed in an .mdoc file, when
              these are being used as the input filenames.  If this option is
              not entered, the program must be run in the directory where the
              frames are located to access files listed in an .mdoc file.

       -ignore (-ig) OR -IgnoreZvaluesInMdoc
              Take sections in order from the .mdoc file instead of by Z
              value.  With this option, .mdoc file sections can be removed or
              rearranged to control which frame files are stacked.  Otherwise,
              sections must exist for all Z values being accessed, starting at

       -adjust (-ad) OR -AdjustAndWriteMdoc
              Correct entries in the input .mdoc file for changes in image
              size, binning, pixel size, data mode, or dose, and write a new
              file with the name of the output file plus .mdoc.  This option
              has no effect unless an .mdoc is entered.  If tilt series data
              are processed in order by tilt angle, the new file will be writ-
              ten in the new order and it can be used later for dose-weighting
              in Mtffilter.  If the dose entries in the .mdoc file are
              superseded by a fixed total dose entry with -dtotal, the Expo-
              sureDose lines will be modified or added to contain the new dose
              value, and PriorRecordDose lines will be modified or added as

       -reorder (-reo) OR -ReorderByTiltAngle   Integer
              Process sets of frames in order by increasing or decreasing tilt
              angle.  Enter 0 for no reordering, 1 to reorder from negative to
              positive unless the angles already decrease monotonically, 2 to
              reorder always from negative to positive, -1 to reorder from
              positive to negative unless angles already increase monotoni-
              cally, or -2 to reorder always from positive to negative.  The
              default is 1 unless -ignore is entered, in which case it is 0
              and this option cannot be entered.

       -pixel (-pi) OR -PixelSize     Floating point
              Pixel size in nanometers.  A pixel size is needed for dose
              weighting.  This entry is needed only if the pixel size in the
              image file header or files entered with -stack or -mdoc is
              incorrect; it overrides any other source of pixel size.

       -eer (-ee) OR -EERSuperResZSumPadding    Three integers
              Amount of super-resolution to retain (0 for none, 1 for 2x, or 2
              for 4x), an entry controlling the summing of frames into succes-
              sive groups, and the amount of "padding" for row/column defects
              when reading from an EER file.  The super-resolution reduction
              and the Z summing both occur in the TIFF reading module and
              these two entries determine what size the EER file appears to be
              to Alignframes, both the size in X and Y and the number of
              frames.  A positive Z summing value specifies the number of
              frames to sum into each group, where the groups become the
              frames that Alignframes reads.  A negative value directly speci-
              fies the number of grouped frames for the reading module to pro-
              duce.  All pixel-related entries and outputs from Alignframes
              are in terms of the pixels returned to the program from that
              module, not the original 4X super-resolution pixels.  When the
              summing value does not evenly divide the total number of frames,
              the specified frame summing is the maximum summing that will
              occur, and the frames will be distributed as evenly as possible,
              with the summing lower by 1 at the beginning of the stack.  The
              default for super-resolution is 1, or a value set with the envi-
              ronment variable IMOD_DFLT_EER_SUPER_RES.  The default for sum-
              ming is 10, or a value set with the environment variable
                 When a gain reference is provided with a defect list
              included, the third entry controls the kind and extent of pad-
              ding around row and column defects; -1 can be entered to use the
              default padding.  A number less than 10 specifies the additional
              physical pixels to be corrected for extreme super-resolution
              bias by averaging over the super-resolution pixels in a physical
              pixel in the direction perpendicular to the defect.  When not
              reading with antialiasing, a value of 1 appears to be sufficient
              and is used when the entry is -1.  A value over 10 specifies 10
              times the number of pixels to widen the defect by on each side.
              When reading with antialiasing, a value if 20 (widening by 2
              pixels on each side) is necessary and is used when the entry is
              -1.  If you need to adjust the defect list more than that, you
              will have to run Clip with the -ed option to output the
              defect list in SerialEM format, modify that, and enter it here
              with the -defect option.

       -aaeer (-aa) OR -ReadEERWithAntialiasing      Integer
              Type of antialias filter to use when reading an EER file.  This
              filtering is done by adding a packet of 100 counts to the image
              for each electron event.  The packet is centered on the super-
              resolution location of the event and distributed among 16 pixels
              of the image being composed according to the filter function.
              Enter 0 to disable this filtering, 1 for a Lanczos 2 filter, or
              2 for a Mitchell filter (which should not be as good).  The
              default is 1.

       -super (-su) OR -SuperGainFactorFile     File name
              File with factors for adjusting the gain reference for an EER
              file to correct for bias among the super-resolution pixels
              within each physical pixel.  These factors can be calculated
              from all the pixels in one or more EER files using the "clip
              supergain" command, which produces the file to be input here.
              The adjustment is quite minor when reading with 2x2 super-reso-
              lution, where the factors range up to ~1.7%, but may be more
              significant with 4x4 super-resolution, where the factors range
              up to ~7%.  See the FILES section of the Clip man page for
              the format of this file.

         These options specify the output of the program or are related to
       output options

       -binning (-bin) OR -AlignAndSumBinning   Two integers
              Image reductions to apply when aligning and when summing.  The
              default for summing is 1, and the default for aligning is chosen
              by seeing which binning out of 2, 3, 4, 6, or 8 brings the size
              being correlated closest to 1250, or to 1560 for frames in a
              size range that could come from a K3 camera.  Enter a negative
              number for the alignment binning to use the default instead of
              having to specify it.  If -test is entered with one or more bin-
              nings, an entry for alignment binning is ignored.

       -target (-tar) OR -TargetAlignSize       Integer
              Use a reduction factor that brings images for alignment close to
              the given size.  The default is 1250 pixels, or 1560 pixels for
              frames recognized as from a K3 camera.

       -frames (-fra) OR -StartingEndingFrames       Two integers
              First and last frame in each file to align and sum, numbered
              from 1.  The default is to do all the frames.  The starting
              frame number must be no bigger than the smallest number of
              frames in any file.

       -partial (-par) OR -PartialFrameThresholds    Two floats
              Relative thresholds for skipping one frame at the start and the
              end of a frame set, when using a saved frame list.  The values
              must be less than 1 and greater than 0.  The mean of the middle
              frame of the set is taken as a reference; the first frame is
              skipped if its mean is less than the first threshold times the
              reference; the last frame is skipped if its mean is less than
              the second threshold times the reference.  A higher threshold
              might be appropriate for the first frame if there tends to be
              excessive drift then.  The only reason to skip a partial frame
              at the end of a set is to avoid including a frame with insuffi-
              cient signal-to-noise ratio.  There is no test for statistical
              significance, so do not set the threshold so high (e.g., 0.99)
              that you risk dropping frames just due to random variations in
              the means.

       -drift (-dr) OR -DriftLimitDistAndNumber      Two floats
              Maximum shift between frames above which to drop initial frames
              of the set, and either the maximum fraction or the maximum num-
              ber of frames to drop.  The shift is in unbinned pixels.  If a
              maximum fraction is entered, it must be between 0 and 0.5.  With
              this option, the program will do the alignment, then if initial
              shifts are above threshold, it will redo the alignment with
              those frames dropped.

       -sets (-se) OR -RangeOfSetsToDo     Two integers
              First and last frame set or file to process, numbered from 1.
              The default is to process all input data.  The file or set num-
              bers correspond to the numbers shown in the text output and
              apply after reordering by tilt angle, if any.  This option is
              here for convenience in testing and assessment, and it may not
              work in all cases.  The correct tilt angles should be placed in
              the the file header, but an adjusted .mdoc file will not be cor-

       -mode (-mo) OR -ModeToOutput   Integer
              Mode for output image file: 0 for bytes, 1 or 6 for signed or
              unsigned integers, or 2 or 12 for 32-bit or 16-bit floating
              point.  The default is to use the mode of the input file unless
              is it 0, in which case the default is to use mode 1; however,
              the default mode of floating point output for MRC files is gov-
              erned by the value of environment variable

       -scale (-sc) OR -ScalingOfSum       Floating point
              Amount to scale summed values before output.  The default is no
              scaling; however, note that reduction of the output size will
              scale the data up by the square of the reduction factor.  Such
              scaling mimics the summing of counts by binning during data

       -total (-to) OR -TotalScalingOfData      Floating point
              Search the titles of the first input file for a scaling factor,
              and apply an additional scaling to the summed values to bring
              the total scaling to the amount entered.  If no scaling is found
              in a title, it is assumed to be 1 and the full scaling specified
              here will be applied.  A default total scaling of 30 or 32 will
              be applied if the input data consists of bytes or 4-bit values,
              gain normalization is being applied, and the output mode is not
              set to 2.  A default of 32 is used if the gain reference is
              clearly from a K3 camera.

       -meansd (-mea) OR -MeanAndSDtoScaleTo    Two floats
              Scale each summed image to the given mean and standard deviation
              if the given SD is greater than 0, or just scale to the given
              mean if SD is 0 or less.

       -rfsum (-rf) OR -SumRotationAndFlip      Integer
              Rotation and flip operation to apply to sum before output.
              Enter a number from 0 to 7, chosen by taking the rotation angle
              counterclockwise divided by 90, plus 4 for a flip around the Y
              axis before the rotation.  (This corresponds to the RotationAnd-
              Flip property used in SerialEM for several kinds of cameras.)
              Enter -1 to have this value taken from a "need" entry in a title
              of the first input file from SerialEM, or from the orientation
              tag in an EER file.  If there is no "need" entry for a SerialEM
              file, this option with -1 is ignored, but if there no orienta-
              tion entry for an EER file, it is an error.

       -tilt (-til) OR -TiltAngleFile      File name
              File with tilt angles to insert into the header of the output
              file.  The file should have one tilt angle per line, and must
              have at least as many angles as frame files or sets being
              stacked.  Tilt angles will be placed into the extended header in
              the UCSF/FEI format, one floating point value per section.  With
              this entry, tilt angles will not be used from a corresponding
              stack or mdoc file.  If this entry is used with a list of saved
              frames and a single input frame stack, each line of the file can
              also have the expected relative starting and ending frame num-
              bers for that tilt following the tilt angle.

       -axis (-ax) OR -AxisRotationAngle   Floating point
              Rotation angle from the Y axis to the tilt axis, counterclock-
              wise positive.  This angle will be placed into a title in the
              output file readable by Etomo.  It will override an angle from
              an mdoc file or from a corresponding tilt series.

       -xfext (-x) OR -TransformExtension       Text string
              Extension for output file(s) with image transformations having
              shifts in columns 5 and 6.  One file will be produced for each
              input file, with the input file extension replaced by the given
              extension.  These files have the absolute shifts being applied
              to each frame, in unbinned pixels, not relative shifts between
              successive frames.

       -frc OR -FRCOutputFile    File name
              Output file for Fourier ring correlations between sums of even
              and odd frames, which are computed when a sum is produced.  The
              file will have a series of lines, each with the file number, the
              frequency at the center of ring, and the correlation coeffi-
              cient.  When a GPU is used, the program may not compute the FRC
              if there is only enough memory to sum into one buffer on the GPU
              instead of two.

       -ring (-ri) OR -RingSpacingForFRC   Floating point
              Spacing between the rings of the Fourier ring correlation, in
              cycles/pixel of the summed images.  The default is 0.005, which
              is needed for resolving closely spaced CTF oscillations.
              Smaller values like 0.02 - 0.05 will provide more averaging for
              situations with more widely spaced oscillations.  See the sec-
              tion below, Evaluating and Visualizing Differences with FRC

       -evenodd (-ev) OR -EvenAndOddSumOutput   Integer
              Output two additional files, with sums of even and odd frames,
              where frames are numbered from 0.  Thus, if there is an odd num-
              ber of frames, the "even" sum will have one more frame than the
              "odd" sum.  If the output file name does not have an extension
              of 4 or fewer characters, names will be the output filename with
              "_even" and "_odd" appended.  Otherwise, with an entry of 1, an
              output name of "rootname.ext" will give names "root-
              name_even.ext" and "rootname_odd.ext".  With an entry greater
              that 1, the program will use names appropriate for a dual-axis
              tilt series if the root of the output filename ends in "a" or
              "b".  For example, an output file name of "setnamea.ext" will
              give names of "setname_evena.ext" and "setname_odda.ext".

       -lines (-lin) OR -LinesOfAlignSummary    Integer
              Number of lines summarizing the fitting and FRC results.  Set to
              3 for full output, 2 to eliminate the FRC line, or 1 for a con-
              densed output with the weighted mean residual, maximum of maxi-
              mum weigted residual, and the raw and smoothed distances. When
              using the -saved option to enter a saved frame list file, the
              output will also include the shifts of the first four frames;
              enter a negative value to suppress this output.

       -plottable (-pl) OR -PlottableShiftFile       File name
              Filename for output file with raw and smoothed shifts in
              unbinned pixels.  The smoothed shifts will be from spline
              smoothing if it was done, otherwise from local polynomial
              smoothing.  The shifts will be put into the file one per line,
              starting with a type number of 10 times the file number for the
              raw shifts or that value plus 1 for the smoothed shifts (e.g.,
              10 and 11 for the first file).

       -nosum (-nos) OR -NoSumsOutput
              Do alignments without making a summed image; no output filename
              should be entered.

         These options provide for initial processing of the data before

       -titles (-tit) OR -RefAndDefectFromTitles
              Normalize the data using a gain reference and possible defect
              file listed in the header titles of the first frame file from
              SerialEM, or use a gain reference listed in the metadata of an
              EER file.  For a SerialEM file, the title with the reference
              name must contain "ref" or "Ref" and end in ".mrc", ".dm4", or
              ".tif".   The title with the defect name must contain "defect"
              and end in ".txt".  Each file must exist in the directory with
              the frame file.  This entry also causes the rotation and flip
              operation found in a title to be applied, so -rotation -1 need
              not be entered.  An entry with the -gain, -defect, or -rotation
              option overrides the respective information found in a title.
              For an EER file it will be an error if the metadata is not found
              or does not contain a gain reference name.  Use "header -t 65001
              filename" to see the metadata in an EER file.

       -gain (-gai) OR -GainReferenceFile       File name
              Gain reference for normalizing unprocessed or dark-subtracted
              frames.  The gain reference should be a floating point file with
              a mean of 1.  If this option is entered, it supercedes a gain
              reference found in the extended header of the frame files.  If
              the gain reference is a TIFF file or the frame input is an EER
              file, then the gain is allowed to be exactly 2 or 4 times
              smaller than the frames.  In that case, the gain reference is
              expanded by replicating the value for a pixel to all the super-
              resolution pixels within it.

       -rotation (-ro) OR -RotationAndFlip      Integer
              Rotation and flip operation that needs to be applied to the gain
              reference to match the orientation of the frames being cor-
              rected.  Enter a number from 0 to 7 by taking the rotation angle
              counterclockwise divided by 90, plus 4 for a flip around the Y
              axis before the rotation.  (This corresponds to the RotationAnd-
              Flip property used in SerialEM for a K2 camera, but it is also
              possible to save such frames without the rotation and flip.)
              Enter -1 or -2 to have this number taken from an "r/f" entry in
              the title of the first input file, in which case it is an error
              for the "r/f" entry to be absent.  Entering -2 is equivalent to
              entering -1 for the -rfsum option and makes it take the rotation
              and flip for output from a "need" entry in that title unless the
              -rfsum option was entered.

       -dark (-da) OR -DarkReferenceFile   File name
              Dark reference to be subtracted before multiplying by a gain
              reference when the frames are saved as unprocessed data.

       -defect (-def) OR -CameraDefectFile      File name
              File of camera defects to correct.  The defect file is put out
              by SerialEM for versions of DigitalMicrograph from GMS 2.3.1 and
              higher when frames are not gain-normalized.  The program will
              determine the binning of the image relative to these defect
              coordinates by assuming that the images are more than half the
              camera size.  It will decide to scale the coordinates in the
              defect list up by 2 if necessary for super-resolution frames.
              These decisions will be reported and can be overridden with the
              next two options.  If this option is entered, it supercedes the
              defect list found in a TIFF gain reference file.

       -double (-do) OR -DoubleDefectCoords
              Scale camera defect coordinates by 2 if they are not already
              scaled.  This option should not be needed.

       -imagebinned (-im) OR -ImagesAreBinned   Floating point
              Binning of images, which could be needed for defect correction
              if frames are not bigger than half the camera size.

       -truncate (-tru) OR -TruncateAbove       Floating point
              Replace values above a limit with the mean of surrounding val-
              ues.  The mean is taken from pixels in a 7x7 area, excluding the
              center 9.  Enter a positive number to specify an absolute limit
              in counts that applies to all frames being processed.  Enter a
              negative number to specify the number of standard deviations
              above the mean at which to truncate (e.g., -8 for 8 SD's above
              the mean).  This limit will be determined separately for each
              frame file or set of frames, using the first frame of the set.
              When the saved option is entered with a saved frame list file,
              the limit is determined separately again for the second frame
              and that limit is used for the rest of the frames in the set, in
              case the first frame is a partial exposure.

         These options control the strategy and main parameters of the align-

       -pair (-pai) OR -PairwiseFrames     Integer
              Number of frames or groups to use in successive pairwise align-
              ments, or 0 to use alignment to a cumulative reference of
              already-aligned frames.  The default is 7.  With an entry of -1
              or a value equal to or bigger than the number of frames, the
              program will align all pairs of frames or groups and do a single
              fit.  With an entry of -2, -3, or -4, it will do pairwise align-
              ments among sets of one-half, one-third, or one-fourth of the
              frames or groups, but with a minimum of 7 included.

       -reverse (-rev) OR -ReverseOrder
              Reverse order of processing and start with the last image.  This
              should make very little different when using pairwise align-
              ments, but is a potentially useful option when using alignment
              to a cumulative reference, unless there is substantial fixed
              pattern noise.

       -shift (-shi) OR -ShiftLimit   Integer
              Limit on distance to search for correlation peak, in unbinned
              pixels.  If the previous frame was aligned to the same reference
              being aligned to, the center of the region searched corresponds
              to the peak position for the previous frame.  The default is 20.

       -group (-gr) OR -GroupSize     Integer
              Number of frames to sum for correlations between groups of
              frames; such groups are needed when correlations between single
              frames are too noisy to give reliable results.  Since correla-
              tions are done only between non-overlapping groups, grouping
              reduces the number of measured shifts from which each frames's
              shift can be determined.  Frames will be grouped in one of two
              ways: in non-overlapping blocks, or in successive overlapping
              groups, referred to as "slide grouping".  The latter is used
              only when the total number of frames is large enough to allow a
              linear equation to be fit to the shifts; for example, this
              requires 8 frames for a group size of 3.  With slide grouping,
              each frame will have a different shift.  If the program has to
              drop back to block grouping, all frames in a block will have the
              same shift.

       -radius2 OR -FilterRadius2     Floating point
              High spatial frequencies in the cross-correlationd will be
              attenuated by a Gaussian curve that is 1 at this cutoff radius
              and falls off above this radius with a standard deviation speci-
              fied by FilterSigma2.  Unlike in other applications, this value
              is entered in frequency units (1/pixel) of the input frames, not
              of the reduced images being correlated.  It is scaled by the
              reduction before being applied to the reduced image, which means
              that a particular value will give about the same amount of fil-
              tering regardless of the binning. The default is 0.06.

       -vary (-va) OR -VaryFilter     Multiple floats
              Set of radius2 filter values to test.  This option can be
              entered separately for each binning, but that should not be nec-
              essary, for two reasons.  First, because these values are in
              unbinned frequency units, each one would have about the same
              effect for the different binnings.  Second, there is little cost
              to applying extra filters, because different filters are applied
              to a small subarea of an unfiltered correlation.  Sigma2 will
              automatically be set for each filter so that it is in the same
              ratio to the particular radius2 value as the basic sigma2 is to
              the basic radius2 value.  Thus, to provide a different set of
              sigma2 values for these filters, you need to enter -radius2 or
              -sigma2.  (Successive entries accumulate)

       -hybrid (-hy) OR -UseHybridShifts
              Derive a set of shifts while alignments are being done by using
              the results from the best filter after each individual fit.  By
              default, when given multiple filters to test, the program will
              decide on the best overall filter after all fits are done and
              use the shifts from that filter.  This option will reduce memory
              requirements, unless the alignment is being refined at the end.

       -refine (-ref) OR -RefineAlignment       Integer
              Refine an initial alignment based on pairwise correlations by
              correlating each frame with an aligned sum of all but that
              frame. The entry gives the maximum number of iterations that
              will be run, but iterations will stop if the biggest change in
              shift falls below a threshold.

       -rgroup (-rg) OR -RefineWithGroupSums
              When using group sums for the initial alignment, refine the
              alignment with group sums as well, instead of single frames.
              This may be needed if the signal-to-noise ratio is too low even
              for the correlation between a single frame and the sum of other
              frames.  The shifts converge more slowly in this case, so more
              iterations may be needed.

       -stop (-sto) OR -StopIterationsAtShift   Floating point
              Maximum change in shift at which to stop iterating the refine-
              ment of initial shifts by correlating with the sum of frames.
              The default is 0.1.

       -rrad2 (-rr) OR -RefineRadius2      Floating point
              High frequency filter cutoff (radius 2) for refining the align-
              ment.  The default is to use the same filter that was used to
              obtain the alignment, or the filter that gave the best overall
              error value when a hybrid alignment was used.

       -smooth (-sm) OR -MinForSplineSmoothing       Integer
              Smooth the shifts with a spline curve whose smoothing parameter
              is found with generalized cross-validation, but only if the num-
              ber of frames is at least as big as the entered value.  This
              method requires a fairly large number of frames to be reliable;
              the documentation for the cross-validation code being used sug-
              gests 20 frames may be needed.  Smoothing should not be used
              with less than 10 frames. For numbers between 10 and ~20, a
              minority of images may come out slightly worse with smoothing,
              so it would be advisable to evaluate results with and without
              smoothing, such as with an FRC.  The default is currently 20;
              enter 0 to disable smoothing.

       -gpu (-gp) OR -UseGPU     Integer
              Use the GPU (graphical processing unit) for computations if pos-
              sible; enter 0 to use the best GPU on the system, or the number
              of a specific GPU (numbered from 1).  If GPU memory is a limita-
              tion, the program will prioritize forming the sum on the GPU
              over doing the alignment there, and will compute odd and even
              sums as the lowest priority.  If alignment becomes possible on
              the GPU only by deferring the summing, and if CPU memory is suf-
              ficient for that, then it will keep the entire stack of frames
              in memory and sum them after aligning.

       -memory (-mem) OR -MemoryLimitGB    Multiple floats
              Limit on CPU memory usage, and optionally a limit on GPU memory
              usage, in gigabytes or as a negative fraction of total memory.
              Enter a value > 0.05 to specify that number of GB, or a value
              between -0.05 and -0.95 to specify between 0.05 and 0.95 for
              total memory.  The default for the CPU limit is 3/4 of system
              memory for system memory less than 16 GB, half of system memory
              for system memory more than 24 GB, and 12 GB between those lim-
              its or when system memory cannot be determined.  When the memory
              usage would exceed the limit for a set of input frames, the pro-
              gram will run through the data in two passes, one to get the
              alignment and one to make the sum.  This may not be possible if
              the -assess option is used.  The default GPU limit is 0.85 times
              the GPU memory.

         These options control "dose weighting", which filters out high fre-
       quencies as a function of the dose already applied to a cryo-specimen.

       -dtype (-dty) OR -TypeOfDoseFile    Integer
              This option both enables dose weighting and indicates what kind
              of file is being provided with the dose information.  Type 4
              indicates key-value information in the autodoc format, such as
              an .mdoc file produced by SerialEM.  If an .mdoc file has been
              entered with the -mdoc option, this is the file that will be
              used, and no filename can be entered with the -dfile option.
              The other four types are simple text files with a line for each
              output image (i.e. each set of frames being aligned).  These
              types are:
                1: A single value per line, just the dose for each image;
                2: Two values, the prior accumulated dose followed by the
              image dose;
                3: The prior dose followed by the cumulative dose at the end
              of that image;
                5: One or more pairs of entries indicating the dose per frame
              and the number of frames with that dose.  For example, "0.5 15
              0.75 10 1.0 15" specifies a dose of 0.5 for 15 frames, 0.75 for
              15 frames, and 1.0 for 15 frames.  The total number of frames on
              such a line must match the number of frames in the set.
              For these four types of text files, if the files or frame sets
              are being processed in order by tilt angle, the lines should be
              in the same order as the processing would occur without this
              reordering, i.e., the original order of the data, or of the Z
              values in an mdoc file.

       -dfile (-dfi) OR -DoseWeightingFile      File name
              Name of file with dose information for dose weighting.  This
              entry is required if -dtype is entered, unless a 4 is entered
              there and a file was entered with the -mdoc option.

       -dtotal (-dto) OR -FixedTotalDose   Floating point
              Total dose for each set of frames, in electrons/square Angstrom.
              This option independently enables dose weighting and cannot be
              entered with -dtype or -dframe.

       -dframe (-dfr) OR -FixedFrameDoses       Floating point
              List of frame doses and numbers that applies to all sets of
              frames.  The list is a set of paired numbers: a dose in elec-
              trons/square Angstrom and the number of frames taken at that
              dose (e.g., enter "2,10,4,5" for 10 frames of 2 e/A^2 and 5
              frames of 4 e/A^2).  This option independently enables dose
              weighting and cannot be entered with -dtype or -dtotal.

       -dprior (-dp) OR -InitialPriorDose       Floating point
              Dose applied before any of the images in each frame set were
              taken; this value will be added to all the prior dose values (if
              any), however they were obtained.

       -bidir (-bid) OR -BidirectionalNumViews       Integer
              Number of views in the first part of a bidirectional tilt
              series, where the order of images in the input file is inverted
              from their order of acquisition.  This entry is essential for a
              bidirectional series if a fixed dose is entered with -dfixed or
              if a dose file of type 1 or 5 is entered.  It is ignored for
              types 2 and 3.  It is not needed for type 4 and an .mdoc file
              entered with the -mdoc option, where the correct doses are
              available either from PriorRecordDose entries or from analysis
              of DateTime entries.  However, it would be needed for an .mdoc
              file entered with -dfile unless the -accum option is entered
              with a 2 to use prior dose information from the .mdoc file.

       -accum (-ac) OR -DoseAccumulates    Integer
              This option can be used to override the program's assumptions
              about whether images are from a tilt series where dose should be
              accumulated between successive images.  By default, dose accumu-
              lates whenever -stack, -tilt, or -saved is entered, or when
              -mdoc is entered with an .mdoc file having tilt angles that vary
              more than 1 degree; otherwise it does not.  When there is such
              an .mdoc file, the cumulative dose information is taken from
              either the prior Record dose (if present) or the sum of doses of
              earlier images, even when only a subset of frame sets (images)
              are being used.  However, if an .mdoc file is entered as a dose
              file, the dose will not accumulate.  For this option, enter 0 to
              prevent accumulating dose or 1 or 2 to accumulate dose.  The
              latter will have the same effect except when a subset of images
              is being aligned and an .mdoc file is entered with -dose instead
              of -mdoc. In that case 1 will make it accumulate dose by summing
              the doses over the images being aligned, while 2 will make it
              use cumulative dose information from the whole set of images in
              the .mdoc file.

       -normalize (-nor) OR -NormalizeDoseWeighting
              Normalize the dose weight filters so that they add up to to 1.0
              within each set of frames.  This option is designed for tilt
              series where the true dose weighting of the tilt images is to be
              done later (e.g., with Mtffilter).  It compensates for the
              difference in dose effect among the frames of an individual
              image, which can be significant for some early images if the
              dose is high enough.  However, it results in no net filtering of
              the summed tilt image, leaving this dose weighting for a later
              stage.  If this option is applied to a single-particle frame
              stack, the high frequencies will be boosted in early frames to
              compensate for their being attenuated in later frames.

       -volt (-vo) OR -Voltage   Integer
              Microscope voltage in kV; this value must be either 200 or 300.
              The default is 300; if 200 is entered, the computed critical and
              optimal doses are multiplied by 0.8.

       -optimal (-op) OR -OptimalDoseScaling    Floating point
              Factor by which to scale the computed optimal and critical doses
              that determine how much to attenuate a spatial frequency for a
              particular dose.  Enter a factor greater than or less than 1 to
              indicate that the specimen is more or less resistant to damage
              than the equations indicate.  Another use for this entry would
              be to adjust the critical dose for a voltage other than 200 and
              300 kV.

       -critical (-c) OR -CriticalDoseFactors   Three floats
              Replacement factors a, b, and c in the equation
                 critical_dose = a * k**b + c
               where k is frequency in reciprocal Angstroms.  The default fac-
              tors are directly from Grant and Grigorieff and the unblur pro-
              gram.  Enter 0 for any of the factors to use the default for
              that factor.

       -unweight (-un) OR -UnweightedOutputFile      File name
              File name for output of summed images that have not been dose
              weighted in addition to the dose-weighted images placed in the
              main output file.

         This section includes options that are useful for assessing alignment
       parameters (mainly binning and filters) and advanced options that
       should not need adjustment.

       -test (-te) OR -TestBinnings   Multiple integers
              Set of binnings at which to test pairwise alignments.  Each bin-
              ning involves a separate pass through the frames of an input
              file, plus another pass to make a sum at the end with the best

       -assess (-as) OR -AssessWithFrames       Two integers
              Starting and ending frame to use during testing of parameters
              with multiple binnings or filters, numbered from 1.  The default
              is to use all frames.

       -good (-go) OR -GoodEnoughError     Floating point
              Combined error measure that is sufficient to stop testing bin-
              nings.  This error is a weighted sum of two measures: the mean
              of the weighted mean residual errors from the set of fits, and
              the maximum weighted residual seen in any fit.  The latter is
              weighted by the value entered by -weight option.

       -weight (-w) OR -MaxResidualWeight       Floating point
              Weighting applied to maximum weighted residual from all fits
              when combining with the mean weighted residual to obtain a sin-
              gle error measure.  The default is 0.1.

       -trim (-tri) OR -TrimFraction       Floating point
              Fraction of image size to trim off each edge for correlations.
              The default is 0.02, which is the same amount as the padding.

       -taper (-tap) OR -TaperFraction     Floating point
              Fraction of image size to taper on each edge for correlations.
              The image is tapered down to the mean at its edge.  This taper-
              ing is usually an important component for reliable correlations.
              The default is 0.1. If this fraction is set to 0 and there is no
              trimming, the program obtains the FFT for cross-correlation by
              extracting it from the FFT of the full image instead of by
              reducing, padding and tapering the image and taking an FFT of
              that.  The padding/tapering extent of the full image is
              increased from 2% on each edge to 5% in this case.

       -antialias (-an) OR -AntialiasFilter     Integer
              Type of filter for image reduction when trimming or tapering.
              The standard values of 1 to 6 are available as in Newstack,
              with 1 corresponding to binning.  The default is 4 for a
              Mitchell filter, which seems to be optimal on average for this

       -radius1 OR -FilterRadius1     Floating point
              Low spatial frequencies in the cross-correlations will be atten-
              uated by a Gaussian curve that is 1 at this cutoff radius and
              falls off below this radius with a standard deviation specified
              by FilterSigma2.  Spatial frequency units range from 0 to 0.5.
              This option is here for the sake of completeness; use Filter-
              Sigma1 instead of this entry for more predictable attenuation of
              low frequencies.

       -sigma1 OR -FilterSigma1       Floating point
              Sigma value to filter low frequencies in the correlations with a
              curve that is an inverted Gaussian.  This filter is 0 at 0 fre-
              quency and decays up to 1 with the given sigma value.  However,
              if a negative value of radius1 is entered, this filter will be
              zero from 0 to |radius1| then decay up to 1.  The default is
              0.03, expressed in frequency units (1/pixel) of the reduced
              images being correlated.

       -sigma2 OR -FilterSigma2       Floating point
              Sigma value for the Gaussian rolloff below and above the cutoff
              frequencies specified by FilterRadius1 and FilterRadius2.  Like
              radius 2, this value is entered in unbinned frequency units and
              will be scaled by the reduction being applied for alignment.
              The default is 0.0086.

       -kfactor (-k) OR -KFactorForFits    Floating point
              K factor for robust fitting to pairwise alignments.  The default
              is 4.5; a smaller value will down-weight more outliers in the

       -debug (-deb) OR -DebugOutput       Integer
              This entry is a sum of flags for particular kinds of output: the
              last digit controls the printed output from the program (1 for
              basic output, 2 for more verbose output from each fit and dose
              weighting filters); 10 will give timing output, 100 will give
              output of cross-correlations during initial alignment; 1000 will
              give output of refining correlations; 10000 will give output of
              the sums of odd and even frames.  Images are output with names
              "faimg-n.mrc" where n is increased sequentially.

       -flags (-fl) OR -FlagsForGPU   Integer
              Flags to control which kinds of initial processing occur on the
              GPU.  These flags are for testing and supersede the decisions
              that the program would make based on the memory available.
              Enter a sum of
                 1 to do noise-taper-padding of full images on the GPU
                 10 to do reduction and taper-padding of alignment images on
              the GPU
                 100 to stack full-sized, unpadded frames on the GPU, provided
              that both the noise padding and reduction padding are to be done
                 1000 to do gain normalization, defect correction, and trunca-
              tion on the GPU, provided that noise padding or reduction pad-
              ding are to be done there

                 10000 times the maximum number of frames to stack on the GPU

       -shrmem (-shr) OR -ShrMemTest
              Use shrmemframe to do align frames (special Windows build only)

       -help (-he) OR -usage
              Print help output

              Read parameter entries from standard input

       The example commands below would all be entered in one line, or as mul-
       tiple lines with a backslash at the end of every line except the last,
       as they are shown here due to line length limits. Most options could be
       abbreviated more than they are.

   Frames from Tilt Series
       An image from a tilt series with ~4Kx~4K images might align well with a
       command as simple as

         alignframes Feb21_10.43.50.mrc Feb21_10.43.50_ali.mrc

       where you can add "-gpu 0" to use a GPU on this or any of the following
       commands.  This will use a default binning of 3 and filter cutoff of
       0.06/pixel.  If you already know that you want a different binning
       (say, 4) or filter (say, 0.05), then the easiest way to enter this is

         alignframes -bin 4,1 -vary 0.05 Feb21_10.43.50.mrc \

       where using -vary will scale the sigma for the filter rolloff automati-

       If the frame files for your tilt series list in order from one high
       tilt to the other and the tilt series file is available (say,

          alignframes -bin 4,1 -vary 0.05 -stack cell4.mrc Feb21_*.mrc \

       will process the entire tilt series and move information from the
       header of the tilt series file into the new file.  However, if the tilt
       series was taken bidirectionally and the frames files do not list in
       order, or if the there were any duplicate images taken, then you want
       to supply the .mdoc file instead of the stack and input files:

          alignframes -bin 4,1 -vary 0.05 -mdoc cell4.mrc.mdoc cell4_ali.mrc

       which will process the frames in the right order and place essential
       information in the output file header.

       To explore filter settings, it is best to run on a collection of files,
       perhaps about 20.  Suppose "Feb21_10.4*.mrc" lists the desired number
       of files, you could explore a range of filters at binning 3 with

          alignframes -vary 0.05,.06,.08,.1 -nosum Feb21_10.4*.mrc

       The summary at the end will tell which filter gave the lowest mean
       residual.  Be sure to scan through the results and look at whether
       either the mean residual or the distance moved declines a lot with
       increased filtering, which may be a sign that fixed pattern noise is a
       problem.  Also note whether the maximum unweighted residual is high.
       If it goes over 5-10 pixels, you can problem reduce the occurrence of
       bad fits by restricting the allowed shift with "-shift 10" or even
       "-shift 5".  Obviously, you do not want to set this limit lower than
       the maximum possible shift from one frame to the next.

   Evaluating and Visualizing Differences with FRC Curves
       Suppose you want to use FRCs to evaluate the difference between two
       conditions, such as filter 0.05 versus 0.06, or with and without
       refinement.  You need to make output sums to get an FRC.

          alignframes -vary 0.05 -frc sample.frc Feb21_10.4*.mrc sample.mrc

          alignframes -vary 0.05 -ref 5 -frc sample-refine.frc \
             Feb21_10.4*.mrc sample.mrc

       The ".frc" files have all of the FRC curves for a run, each with a
       "type" number equal to its file number in the alignframes text output.
       You can plot one curve (say, the fourth one) with

          onegenplot -ty 4 -sym 0 sample.frc

       To compare FRC's, run

         subtractcurves -ave 10 -rad 2 sample-refine.frc sample.frc \

       which will subtract each pair of corresponding curves and average over
       10 points to reduce the noise in the differences.  You could have
       avoided the averaging here with the option "-ring .05" to alignframes,
       which will make the FRC curve much less noisy in Onegenplot.  (The
       default FRC output is good for seeing the CTF oscillations in single-
       particle data, but a larger ring size will often be more appropriate
       for tilt series.)  You could examine each difference in a separate
       graph with

          onegenplot -ty 1 -sym 0 refine-diff.dat &
          onegenplot -ty 2 -sym 0 refine-diff.dat &

       But to assess the overall benefit of the difference in conditions, it
       is more efficient to look at a lot of points at once:

          onegenplot -ty 1,2,3,4,5,6,7,8,9,10 refine-diff.dat &
          onegenplot -ty 11,12,13,14,15,16,17,18,19,20 refine-diff.dat &

       When looking at these curves, treat any improvements below about 1.3
       times the cutoff frequency with caution because they could arise from
       overfitting.  Improvements past this point would not reflect overfit-
       ting, although if the fit is locking in on fixed pattern noise, it
       would boost high frequency correlations.

   Frames for Single-Particle Reconstruction
       For single-particle data, the best initial approach is to fit to pair-
       wise shifts among about half of the frames.  So for a set of 34 frames,
       if you wanted to do an initial assessment with two filters and look at
       the FRC,

          alignframes -vary 0.05,.06 -pair 17 -frc test.frc \
             Feb15_10.13.15.mrc test.mrc

       which will use a default binning of 6 for ~8K frames.  A more flexible
       command for fitting to shifts among half the frames, regardless of the
       exact frame count, is

          alignframes -vary 0.05,.06 -pair -2 -frc test.frc \
             Feb15_10.13.15.mrc test.mrc

       If you had some indication that fixed pattern noise was a problem, or
       if the data seemed particularly noisy, giving mean residuals above 1,
       you could use pairwise shifts among all frames with

          alignframes -vary 0.05 -pair -1 -frc test.frc Feb15_10.13.15.mrc \

       For even noisier situations, you can use grouping to reduce the mean
       residual and improve the fits:

          alignframes -vary 0.05 -pair -1 -group 3 -refine 5 -frc test.frc \
             Feb15_10.13.15.mrc test.mrc

       where the refinement at the end may or may not be beneficial, depending
       on just how noisy the single frames are.  The option specifies up to 5
       iterations of refinement, which is almost always sufficient unless
       refining the data as groups with the -rgroup option.

   Processing of Raw Frames
       If you have collected dark-subtracted data from a K2 camera into MRC or
       compressed TIFF files, you can process them with

          alignframes -gain SuperRef_Feb20_20.26.21.dm4 -scale 39.3 -rot -1 \
             -defect defects_Feb20_20.26.21.txt -pair 17 Feb21_10.32.56.tif \

       using the gain reference copied into the data directory and the defect
       file written there by SerialEM.  The option "-rot -1" specifies that
       the gain reference needs to be rotated by the value for rotation and
       flip indicated by "r/f" in a label in the file header.  MRC files
       started having this label in SerialEM 3.4, TIFF files in SerialEM 3.5,
       so check either kind of file by running "header" on the file.  If the
       label does not show "r/f", the number to use in the "-rot" entry would
       be the RotationAndFlip value in the SerialEM properties file.  If
       frames were saved without rotation, do not include this option.

       Either the "-scale" option as shown here, or the "-total" option with a
       total scaling, or the option "-mode 2", should be entered to preserve
       the precision of the data when they are written. The program will use a
       default total scaling of 30 when normalizing if the input data are byte
       values and data are not being written as floating point with "-mode 2".
       However, it is probably better not to rely on the default and instead
       scale the electron counts by the same factor that is applied in Seri-
       alEM (39.3 in this example, a typical value when not dividing by 2).

       You could add an option such as "-trunc 7" to replace values above 7
       with the local mean.  Use the command

          clip hist Feb21_10.32.56.tif

       to see the distribution of pixel values.  There will be a point at
       which the values stop falling rapidly and then have a long tail;
       removal of values above there is indicated.

   Assessing Fixed Pattern Noise
       This procedure is not convenient, but does work.  The first step when
       fixed pattern noise is suspected to affect the correlations is to out-
       put the individual shifts with the option "-deb 2".  Use only a single
       filter for simpler output.  You will see a series of lines like

       1 to 0  -1.95  -0.17   near 0.00  0.00
       2 to 0  -1.57  0.02   near -1.95  -0.17
       2 to 1  -0.60  -0.77   near 0.00  0.00
       3 to 0  -1.79  0.44   near -1.90  -0.30
       3 to 1  0.44  -1.32   near -0.28  -0.45
       3 to 2  0.36  0.02   near 0.00  0.00

       Each line shows a shift between a pair of frames (numbered from 0),
       then the shift that it was assumed to be "near" when comparing with the
       maximum allowed shift.  If you see many shifts close to 0 (but not
       exactly 0), then they could be due to fixed pattern noise.  (shifts of
       exactly 0 might indicated thatthe maximum shift was too low.

       Try with some higher filter values and see if the incidence of near-
       zero values increases.  Set a binning lower than the default (e.g., 4
       instead of 6, 2 instead of 3) if necessary to make a filter value be
       below Nyquist.  In the above example, a higher filter gave:

       1 to 0  -0.80  -0.22   near 0.00  0.00
       2 to 0  -0.71  0.07   near -0.80  -0.22
       2 to 1  -0.08  -0.38   near 0.00  0.00
       3 to 0  -0.92  0.42   near -0.77  -0.15
       3 to 1  0.17  -0.81   near -0.02  -0.15
       3 to 2  0.30  -0.29   near 0.00  0.00

       To visualize the correlation peak from fixed pattern noise, you need to
       run the program with options that will make it save unbinned correla-
       tions with no high-frequency filtering.  This is available only when
       not using a GPU and when specifying more than one filter.

          alignframes -bin 1,1 -vary 0.05,0.06 -deb 102 -frame 1,5 -nosum \

       There will be series of lines indicating the names of saved images and
       the measured shift between a pair of frames.  Pick one with more than a
       few pixels of shift, which may end up being the one between frames 0
       and 4.  For example:

       Saved lf correlation image frame 4 in ./faimg-18.mrc    mean -0.00
       Saved correlation image frame 4 in ./faimg-19.mrc    mean -0.03
       4 to 0  -0.59  -2.70   near -1.90  0.14

       The last line shows the shift between frames 4 and 0, then the shift
       that it was assumed to be "near" when comparing with the maximum
       allowed shift.  You want to examine the "lf correlation image" in
       "faimg-18.mrc" ("faimg-19.mrc" is a small subarea with high-frequency
       filtering, centered on the expected shift, so is not suitable).  You
       can open this file directly in 3dmod, but it will easier to load a cen-
       tered subarea.  Run "header faimg-18.mrc" to see its size, NX and NY.
       Determine these values:
           xst = NX / 2 - 200
           xnd = NX / 2 + 199
           yst = NY / 2 - 200
           ynd = NY / 2 + 199
       and open the file with

          3dmod -x xst,xnd -y yst,ynd  faimg-18.mrc

       Open a slicer window and close it; this will place the current point
       marker on the middle pixel.  Zoom the Zap window up to about 6 and turn
       off the high-quality display (the checkerboard) to see individual pix-
       els.  Adjust black and white levels to 0 and 255.  The degree to which
       this central pixel stands out indicates the amount of fixed pattern
       noise.  Increase the black level to see just how much it stands out.
       If you can see 4 brighter pixels around the central one, the situation
       is particularly bad.

       You may wonder where the real correlation peak went!  It is very dif-
       fuse and the high-frequency filtering is essential.  Use Edit-Image-
       Process to open the processing dialog and select the Fourier filtering
       panel.  Set the high frequency cutoff to your filter value and the
       falloff to one-seventh of that and press "Apply" to filter.  The real
       peak will now be prominent.  If it is close to the origin, you might
       see its position change with different filters as it merges with the
       fixed pattern peak.

       David Mastronarde

       Email bug reports to mast at colorado dot edu.

IMOD                                4.12.60                     alignframes(1)