Program Descriptions and Man Pages for IMOD Version 4.11

Programs with misleading names

• binvol : Will do antialiased reduction instead of binning in all dimensions, as long as the reduction is the same in X and Y; can also do expansion by padding the 3-D FFT.
• boxstartend : Can extract volumes or 2-D images of selected size at specified model points.
• assemblevol : Can be used easily to paste together 2-D images side-by-side.
• dm2mrc : Converts all versions of Digital Micrograph files to MRC files, not just version 2.
• edpiecepoint : Can make a list of piece coordinates from scratch to fit almost any set of montaged images.
• extracttilts : Can extract any information, not just tilt angles, from extra header area of image file or from associated ".mdoc" file.
• imodmop : Can output arbitary values such as to use for a mask as well as cut out image data inside of model features.
• mrc2tif : Can convert any kind of file that 3dmod can read, not just MRC, and can make PNG and JPEG files as well as TIFF.
• mtffilter : The main filtering program to use for high or low pass filtering as well as for specialized filtering like dose-weighting and compensation for camera MTF.
• tiltxcorr : The main program for correlation of 2-D images, regardless of whether they are tilted; can also track multiple patches of image both for tilt series alignment and serial slice alignment with warping.

• Graphical user interface programs
  • 3dmod : Model editing and image display program. 3dmod can display three-dimensional graphic data sets in many views simultaneously, can model these data sets, and can display models and graphic data in 3-D. The views include a slice through the 3D volume, a projection of a sub-volume and orthogonal views with contour overlays.
  • 3dmodv : View a 3dmod model in 3D. Includes the ability to view smooth skins over contour data, adjust lighting and color, control clipping planes, and adjust viewing orientation.
  • midas : Allows manual alignment of serial section or other image data by translation, rotation and stretching, using mouse movements, controls or hotkeys. Two sections being aligned can be viewed alternately in quick succession, or in a two-color overlay mode. Midas also allows one to adjust the contrast and brightness of each section independently.
  • etomo : Interface for building single- and dual-axis tomograms with IMOD, processing multiple tilt series in batch mode, joining tomograms from serial sections, filtering with nonlinear anisotropic diffusion, or aligning and averaging subvolumes from tomograms with our PEET package.
  • ctfplotter : Estimate defocus values, and optionally astigmatism and phase shift, for CTF correction of tilt series images, combining data from multiple images in the tilt series where necessary.

• Model utility programs.
  • clonemodel : Make a model with many copies of an input model at different locations and orientations.
  • imodauto : Generate a contour based model from a 3D image using a threshold based algorithm.
  • imodchopconts : Chop up contours in IMOD model based on length or color
  • imod-dist : Measure and report distances between model points and a reference location.
  • imodinfo : Print information about an IMOD model, or print model in ascii format.
  • imodmesh : Generate a triangle mesh surface from contour data.
  • imodfillin : Fill in missing contours using information in a mesh.
  • imodmop : Cut out image data inside of model closed contours, circles, spheres or along lines; optionally reproject a tilt series of the image data.
  • imodsetvalues : Store general values for contours or points in a model.
  • imodtrans : Transform an IMOD model.
  • imodjoin : Join two IMOD models, selecting objects from each.
  • imodextract : Extract a subset of objects into a new IMOD model.
  • imodexplode : Make an "exploded" model by shifting objects by various amounts.
  • imodsortsurf : Sort contours not connected by a mesh into different surfaces or objects.
  • patch2imod : Make an IMOD model of displacement vectors from a patch displacement file.
  • point2model : Convert point listing to IMOD model file.
  • imodcurvature : Analyze radius of curvature of contours or surfaces and encode in model.
  • imod2patch : Make a patch displacement file from an IMOD model.
  • model2point : Convert model file to point file.
  • rec2imod : Convert an HVEM3D rec model file from a PC to an IMOD file.
  • slashmasksort : Sort or split contours into new objects based on whether they fall inside a mask object
  • wmod2imod : Convert a WIMP model file to an IMOD file.
  • imod2rib, imod2vrml, imod2vrml2, imod2obj, and imod2meta : Convert IMOD models to other model formats.

• Image processing programs for MRC image files, written in C.
  • clonevolume : Embed multiple copies of a subvolume in a volume at different locations and orientations.
  • mrc2tif : Create a series of TIFF, PNG, or JPEG image files from an MRC or other type of image file.
  • tif2mrc : Converts TIFF files to the MRC file format.
  • raw2mrc : Converts raw image data to the MRC file format.
  • dm2mrc : Converts Digital Micrograph image data to an MRC image stack.
  • mrcbyte : Converts an MRC file to byte type data, with scaling and subvolume options.
  • mrctaper : Tapers edges of transformed images to avoid sharp transitions.
  • mrcx : Converts MRC image files for different machines by byte swapping.
  • clip : Command line image processing tool for 2D or 3D image data. Includes the following processing abilities.
    • FFT,
    • Correlation and filters.
    • Averaging, summing, multiplying, dividing.
    • Brightness and contrast adjustments.
    • Gain normalization, defect correction and other specialized operations.
  • nad_eed_3d : Nonlinear anisotropic diffusion with edge enhancing diffusion in 3D, by A. Frangakis and R. Hegerl.
  • ctfphaseflip : Corrects tilt series for microscope CTF by phase flipping.
  • imodfindbeads : Finds gold particles in 2D images.
  • imodholefinder : Finds regularly spaced holes in support film.
  • slashfindspheres : Finds spheres in a volume given example points

• General Image Processing Programs.
  • alterheader : Change MRC image file attributes.
  • addtostack : Add sections to end of existing image stack.
  • avganova : Compare images using nested analysis of variance.
  • avgstack : Average stack of images into single image.
  • avgstatplot : Plot the output of imavgstat
  • blendmont : Blend montaged images together.
  • boxavg : Average images at specified points.
  • binvol : Bin a volume down in 3D, with potentially different binning in X, Y and Z, and potentially with antialiased reduction instead of binning.
  • boxstartend : Clip out portions of an image around specified model points.
  • ccderaser : Automatically remove X-rays, erase spot and line flaws in image from CCD camera, and erase fiducials.
  • colornewst : Run newstack operations on RGB color files.
  • edgeeraser : Erase bad parts of image near edge. See ccderaser.
  • edmont : Move images into, out of, or between montages.
  • edpiecepoint : Edit a list of piece coordinates or make one from scratch.
  • enhance : 2D gaussian bandpass filter. See mtffilter.
  • eraser : Erase small flaws in image. See ccderaser.
  • excise : Extracts images from specified areas in an image file. See boxstartend.
  • excludeviews : Reversibly remove undesired views from a tilt series stack.
  • extractmagrad : Extract magnification gradients for each image from extra header of image file.
  • extractpieces : Extract piece coordinates from header of montaged image file or from associated ".mdoc" file.
  • extracttilts : Extract tilt angles and other information from extra header area of image file or from associated ".mdoc" file.
  • extstack : Extracts images from objects with rotational symmetry.
  • extposition : Get list of position numbers for axoneme doublets.
  • filterplot : Plot the filter curve created by the 4 parameters sigma1, sigma2, radius1, radius2.
  • findbeads3d : Find gold particles in 3D volumes.
  • fixmont : Substitute sections from one montage into another
  • fftrans : Calculate a 2-D FFT from an MRC file.
  • header : Print MRC header information.
  • imavgstat : Compute mean and SD images and mean intensity in subareas.
  • justblend : Run blendmont on multiple 2-D montages.
  • makepyramid : Make a set of image files from a very large volume to allow rapid viewing in 3dmod.
  • matchvol : Transform a volume to match another with a general linear transformation.
  • montagesize : Report actual X, Y, and Z dimensions of a montaged image file.
  • mtffilter : Apply high or low pass and/or inverse MTF filter or dose-weighting to 2D images or 3D FFTs.
  • edgemtf : Measure MTF curve for camera from image of an edge.
  • newstack : Create a MRC image stack(s) from existing MRC file(s), with numerous options for image transformation, resizing, and scaling.
  • numericdiff : Compare numeric entries between two text files.
  • recombine : Recombine an MRC file split apart with splitmrc.
  • reducefiltvol : Manages antialiased size reduction with binvol and/or filtering with mtffilter.
  • reducemont : Recuts montaged images and reduces them by pixel binning.
  • rotatevol : Rotate 3-dimensional data to arbitrary angles.
  • rotmont : Rotates sections from a montage by 90 degrees.
  • setupcoms : Creates command files for averaging images from cross-sections of axonemes.
  • setuplong : Creates command file for averaging of a longitudinal section of an axoneme.
  • splitmrc : Splits an MRC file into chunks for burning to CDs.
  • subimage : Subtracts one image from another.
  • subimanova : Subtracts image averages with analysis of variance.
  • subimstat : Subtracts one average image from another with a t-test.
  • sumdensity : Adds densities for pixels above a threshold within contours.
  • trimvol : Trim a volume and scale it to bytes.
  • warpvol : Warp a volume to match another with a set of linear transformations.
  • xcorrstack : Cross-correlate a single image with a whole image stack.
  • xyzproj : Project 3-dimensional data at a series of tilts around the X, Y, or Z axis.

• General alignment programs.
  • alignframes : Align and sum frames from direct detectors and other CMOS cameras.
  • checkxforms : Find maximum displacement & rotation in a set of transforms.
  • joinwarp2model : Make starting model for refining tomogram join from initial warping.
  • xf2rotmagstr : Convert transforms to rotations, magnifications, and stretches along an axis.
  • xfalign : Automated alignment of an image stack.
  • xfinterstack : Transform a model to match model built on other stack
  • xfinverse : Forms inverse of a list of transformations.
  • xfjointomo : Finds transforms for refining alignment of serial section tomograms.
  • xfmodel : Aligns image using model points; transforms model.
  • xfproduct : Forms product of two lists of transformations.
  • xfsimplex : Searches for best transformation between two images.
  • xftoxg : Converts transforms between sections into alignment transforms.

• General model programs. These programs store information internally in the WIMP model format and do not have access to all of the information in the IMOD format. In general, when a program reads a model, manipulates it in some way, and writes out a new model, the model header information and the properties of the objects should be preserved. If problems arise or information is lost, use one of the C-language programs above if possible.
  • clipmodel : Clip out portions of a model based on location or object number.
  • contourmod : Generate contour maps of an image as a model file.
  • convertmod : Convert an IMOD model file to a WIMP model file
  • endmodel : Make a model file with starting and ending points of objects.
  • fenestra : Calculate projected area of holes (fenestrae) in a 3D model.
  • joinmodel : Join two models together.
  • mtk : Analyze distances between model objects in 3D.
  • nda : Do neighbor density analysis of point positions in plane.
  • realscalemod : Scale a model to microns, adjusting for tilts
  • reducecont : Reduces the number of points in model contours.
  • remapmodel : Remap Z values and shift coordinates of a model.
  • resamplemod : Turn a model perpendicular to Z axis and resection.
  • scalemodel : Rescale a model for changes in image origin, delta or tilt
  • sda : Do surface density analysis of point positions on a surface.
  • smoothsurf : Smooth a surface defined by model contours.

• Special programs used for tomography. These programs are of use mainly for calculating tomographic reconstructions from a tilt series obtained from an electron microscope, or for post-processing of such volumes.
  • alignlog : Extract useful parts from the output of tiltalign.
  • alttomosetup : Facilitates processing of an alternative raw stack with same alignment parameters as main stack.
  • assemblevol : Assemble an image file from an array of subvolumes or 2-D images
  • autofidseed : Automatically make a seed model for tilt series fiducial tracking
  • autopatchfit : Run 3D patch correlation and fitting iteratively to achieve target error.
  • batchruntomo : Make a tomographic reconstruction automatically.
  • beadtrack : Track fiducial gold particles through a tilt series.
  • combinefft : Combine FFTs of tomograms from a double-axis tilt series.
  • copytomocoms : Generate command files needed for processing a tilt series.
  • corrsearch3d : Search for displacements between two volumes at an array of positions.
  • cryoposition : Find angles and Z positioning for a cryo-tomogram.
  • ctf3dsetup : Generate command files for computing a tomogram with CTF corrected in 3-D
  • densmatch : Scale densities in one volume to match those in another volume or to have a given mean/SD.
  • densnorm : Normalize densities in an image file to represent projected mass density.
  • dualvolmatch : Find initial matching between dual-axis tomograms with image correlations.
  • edgepatches : Do initial steps in stitching together adjacent overlapping tomograms.
  • filltomo : Replace pixels in combined tomogram with values from one.
  • findbeads3d : Automatically locate spherical beads in a tomographic volume.
  • findsection : Locate section boundaries in tomogram slices.
  • findwarp : Find a series of transformations to warp one volume into another.
  • finishjoin : Do final steps in joining tomograms from serial sections.
  • fitpatches : Manage and fit to patch vector files in stitching together adjacent overlapping tomograms.
  • flattenwarp : Compute warping transformations for flattening a volume from a model of lines or points on surfaces.
  • goodframe : Only used as a call from scripts.
  • makecomfile : Make a command file for an optional step in tilt series processing.
  • makejoincom : Generate command file for initial steps in joining tomograms from serial sections.
  • matchorwarp : Find final transformation(s) between two volumes and make matching volume.
  • matchshifts : Find X, Y, and Z shifts between two volumes by cross-correlation (obsolete).
  • multifiltsetup : Generate command files for running Tilt with a series of filter values.
  • onepatchcorr : Cross-correlate patches between two volumes at a single position.
  • patchcorr3d : Cross-correlate patches between two volumes at an array of positions (obsolete).
  • patchcrawl3d : Search for displacements between two volumes at an array of positions. using corrsearch3d (obsolete).
  • pickbestseed : Used by autofidseed to select an optimal seed model for fiducial tracking.
  • preNAD : 2D anisotropic diffusion filter for tilt projections.
  • preNID : 2D non-linear isotropic diffusion filter for tilt projections.
  • RAPTOR : Automatically find fiducials in tilt series images.
  • rawtiltcoords : Get positions and angles of tomogram points in raw tilt series.
  • refinematch : Solve for a refined match between two tomograms.
  • repackseed : Eliminate empty contours from seed model produced by transferfid.
  • restrictalign : Restrict tilt alignment parameters for low number of fiducials.
  • setupcombine
  • serieswatcher : Watch for completed tilt series and make reconstructions through batchruntomo.
  • setupstitch : Set up for stitching together adjacent overlapping tomograms.
  • sirtsetup : Set up multiple command files for simultaneous iterative reconstruction (SIRT).
  • solvematch : Solve for transformation matching one tomogram to another.
  • sortbeadsurfs : Sort a model of gold bead positions into two surfaces and/or modify it to match a particular volume.
  • sorttiltframes : Sort filenames by tilt angle in their names.
  • squeezevol : Reduce a volume in all dimensions by interpolation using matchvol.
  • stitchalign : Find tranformations for aligning adjacent tomograms to be stitched together.
  • subtomosetup : Sets up command files for reconstructing multiple subvolumes.
  • swaptomostacks : Exchange tilt series files in order to process a companion stack with the same parameters and alignment.
  • taperoutvol : Excise a subset of a volume, with padding and tapered edges outside the actual image.
  • tapervoledge : Excise a subset of a volume, with padding and tapering of the actual image inside the edges.
  • tilt : Calculate 3-D tomographic reconstruction from a tilt series.
  • tiltalign : Align a tilt series using fiducial points.
  • tiltxcorr : Find preliminary alignment of tilt series by cross-correlation; also used for patch tracking in tilt series and serial slice alignment including warping.
  • tomocleanup : Remove or list intermediate files after processing a tilt series.
  • tomodataplots : Make an X/Y plot of some output from tilt series processing
  • tomopieces : Determine how to chop a tomogram into pieces.
  • tomopitch : Find angles of tomogram from models of section surface in samples.
  • tomostitch : Transform adjacent tomograms into alignment and stitch them together.
  • transferfid : Make a seed model for second axis from the fiducial model on first axis.

• Scripts for (parallel) processing of large volumes.
  • chunksetup : Set up command files for processing a volume in chunks.
  • processchunks : Run command files in parallel on multiple processors.
  • queuechunk : Script for processchunks to run jobs on cluster queue.
  • splitbatch : Produce command files for running batchruntomo in parallel.
  • splitblend : Produce command files for running blendmont in parallel.
  • splittilt : Produce multiple command files for running Tilt in parallel.
  • splitcombine : Produce command files for running volcombine in parallel.
  • splitcorrection : Produce command files for running ctfphaseflip in parallel.

• Programs used for working with distortions and other microscope properties.
  • finddistort : Solves for image distortion field from overlapping images.
  • findgradient : Finds magnification gradient that minimizes montage blending error.
  • findhotpixels : find pixels to exclude from X-ray analysis in SerialEM.
  • idfprocess : do operations on and get statistics from distortion fields.
  • makegradtable : Make a magnification gradient table.
  • matchrotpairs : find transform between best matching pair of rotated, slightly tilted views.

• Special programs used for microtubule (MT) studies.
  • checkmtmod : Check various features of a MT model.
  • howflared : Measure microtubule end flaring and curvature.
  • fiberpitch : Measure pitch of fibers and position relative to an axis.
  • mtdetect : Detect circularly symmetric features.
  • mtlengths : Compute lengths of MTs in a model.
  • mtmodel : Build a MT model out of individual points.
  • mtoverlap : Display and analyze overlap of spindle MTs.
  • mtpairing : Analyze pairing between MTs.
  • mtrotlong : Extract MTs rotated into longitudinal orientation.
  • mtsmooth : Smooth a model of MTs.
  • mtteach : Develop criteria for feature recognition.
  • reducemtmod : Reduce the number of points in a MT model.
  • selfalign : Refine alignment of a MT model based on MT trajectories.

• General utilities and plotting programs
  • subm/submfg : Run one or more IMOD command files in the background.
  • vmstocsh : Convert IMOD command file to C-shell script.
  • vmstopy : Convert IMOD command file to Python script.
  • expandargs : Expand wildcards in command-line arguments and run a program.
  • imodkillgroup : Kill a process or process group for one or more process IDs.
  • framewatcher : Watch for command files or stacks to run with alignframes.
  • genhstplt : Plot histograms and 2-D plots on screen or to Postscript files.
  • gpuallocator : Assigns a set of GPUs to processes upon request.
  • manageshrmem : Manages running a sequence of programs that pass data from one to the next through shared memory files.
  • modifymdoc : Reorders an ".mdoc" file by tilt angle and changes dose or size information to make it valid for use in alignframes or with a tilt series.
  • onegenplot : Script for getting one plot in genhstplt with a simple command.
  • stackframemdocs : Concatenates frame stack ".mdoc" files to make a valid image stack ".mdoc" file for use in alignframes or mtffilter
  • subtractcurves : Subtract curves between two files.
  • gputilttest : Test whether a GPU is reliable for computing reconstructions with the tilt program.
  • adocxmlconv : Convert autodoc to XML or conforming parts of XML file to autodoc.