imodinfo(1)                 General Commands Manual                imodinfo(1)



NAME
       imodinfo - Prints information about IMOD files.

SYNOPSIS
       imodinfo  [options]  IMOD_filename

DESCRIPTION
       Prints information about an IMOD model to standard output.  The types
       of information output vary, depending upon the options.  Typical uses
       include printing out lists of objects, contours and point data in an
       IMOD file; printing out areas, lengths and centroids of contours; and
       printing out surface areas and volumes of objects or surfaces.  The
       measurements of lengths, areas, and volumes are generally expressed in
       terms of the units of the pixel size defined in the model header (e.g.,
       nm or microns), if one is defined.  A Z-scale in the model header is
       also applied as appropriate.  However, reported positions are always in
       pixels.

       The program computes surface area and volume in several different ways,
       depending upon whether an object is meshed or not:
            1) If there is no mesh information, volume is computed by taking
       the area of each contour times the thickness of the sections (defined
       by pixel size and Z-scale), summed over all of the contours.  This is
       referred to as cylinder volume.  It will be inaccurate if you skipped
       sections in modeling, especially if you skipped sections routinely.
       Other than this, it will be very close to correct.
            2) If there is no mesh information, surface area is computed by
       taking the length of each contour times the section thickness, summed
       over all contours.  This is referred to as cylinder surface area and it
       is grossly inaccurate.
            3) With mesh information, the program determines which contours
       are connected to other contours or to cap points by a mesh, and sums
       the area of contours times the distance to the connected contours in Z.
       This measure is now referred to as the contour volume.  (It used to be
       referred to as mesh volume because it uses mesh information, even
       though it is not the volume inside the mesh.)  It handles the problem
       of skipped sections and also gives a slightly more accurate volume mea-
       surement for the capped regions because it integrates with a trape-
       zoidal approximation.  This computation is valid only for closed con-
       tour, planar objects.
            4) With a mesh, the program also computes a volume from the mesh
       by summing the volumes of tetrahedra formed between each mesh triangle
       and a single point at the center of the mesh.  This is referred to as
       the volume inside the mesh.  It will be slightly more accurate than the
       contour volume if the mesh completely encloses the volume, but it can
       be quite inaccurate if the mesh is not capped.  This computation is
       valid for any fully meshed volume, including tubular meshes around an
       open contour, as well as saved isosurface objects.  Such a volume can
       be computed for each surface if the option to use surface information
       was used when meshing.
            5) With a mesh, surface area is computed by adding the areas of
       all the triangles in the mesh.  This is referred to as mesh surface
       area and it is an exact measure of the area of the mesh.  However, to
       the extent that the mesh is not smooth, it can overestimate the true
       surface area of the object.
       If any of your model objects has complex topology, with contours inside
       of other contours, the computed volumes will not be correct unless the
       program analyzes for inside contours, which it does not do by default.
       Use -i option to have the program do this analysis.  However, if you
       use -x or -y to specify a subset range in X or Y, or use -t to restrict
       the analysis with clipping planes, the inside-contour analysis is done
       automatically and you do not need to specify -i separately.  With these
       other options, the program will give the same outputs as with the -i
       option.

       The options -a , -c , -e , -l , -L , -F , -p , -r and -s are mutually
       exclusive.

OPTIONS
       -a     Print ascii readable IMOD output. Not all of the types of data
              stored in a binary model are printed in an ascii model file, but
              all contour and mesh data are printed.  Also, slicer angles,
              clipping planes, and general values assigned to contours and
              points will be printed.

       -c     Print volume, surface area, and center of gravity for each
              object in column output.  For closed contour objects, the cen-
              troid is computed from the area enclosed inside each contour.
              For open contour objects, the centroid is computed from the line
              segments themselves.

       -l     Print lengths of open contours in column output.

       -L     Print lengths of contours broken out by fine-grained color, if
              any, and excluding gaps.  For each object, a table is printed
              for each color used.  This table shows the contour number and
              the length of the portion assigned that color, for each contour
              that uses the color.  If the -h option is given, only summary
              information on total and mean lengths os printed.  Unlike in
              other length reports, this one excludes gaps from the total
              length, so this option is useful for getting correct lengths of
              what is drawn when there are gaps, even if there are no fine-
              grained colors.

       -s     Print volumes and surface areas for each separate surface in an
              object, as defined by contour surface numbers and possibly by
              mesh surface numbers.  The maximum extent, or biggest distance
              between any two points in the surface contours, is also
              reported.  If a mesh is available, the cylinder surface area is
              omitted from the report.  If any meshes have a surface number
              greater than 0, the volume inside the mesh (mesh volume) will be
              reported for each surface.  If such information seems to be
              available for all surfaces, the cylinder volume will be omitted.
              To get mesh volumes, be sure to cap and to select the option to
              use surface information when meshing.

       -p     Print point size information, including a summary of mean
              radius, and the implied total surface area and volume of scat-
              tered points.  There will be a size output for every point in
              any contour that has points with non-zero size.  If there is a
              default point size for the object, that size will be listed when
              there is no size defined for an individual point.  These sizes
              will be in the model units.  Note that the ascii model output
              will also show point sizes in pixels for each point that has one
              defined.

       -r     Print ratio of length to area for closed contours.

       -e     Print properties of equivalent ellipses for closed contours.
              The equivalent ellipse is the one with the same second moments
              as the area enclosed by a contour.  If limits are entered with
              -x, -y, or -z, only contours with center coordinates within the
              limits are in reported.  Only the X and Y coordinates of the
              points are considered when computing these ellipses.  For each
              contour, the values reported are the X and Y center coordinates
              of the ellipse (i.e, the centroid of the contour area), the
              average Z coordinate of the contour points, all in pixels, the
              semi-major and semi-minor axes in scaled units, the eccentricity
              (a value between 0 for a circle and 1 for a maximally elongated
              ellipse), and the angle of the semi-major axis (a value between
              0 and 180 except as described next).  If the range of angles is
              less than 80 degrees, then numbers will be reported that are
              suitable for simple averaging.  This is accomplished based on
              the angle of the first contour for an object: if it is less than
              44, then all subsequent angles greater than 136 will have 180
              subtracted to give negative angles; if it is greater than 136,
              180 is then added to angles less than 45.  Means and and stan-
              dard deviations are also reported for these four measures; the
              mean of the angles will be adjusted to be between 0 and 180.
              BEWARE: if the range of angles is greater than 88 degrees, the
              mean will be meaningless unless the distribution of angles does
              not wrap around at 0 or 180, so you need to examine the individ-
              ual angles before using the mean.

       -F     Print full report on the objects, a collection of summary infor-
              mation.

       -o list
              Print data only from the objects given in the list, a comma-sep-
              arated list of ranges.

       -i     Analyze for inside contours and adjust computed volume by sub-
              tracting rather than adding the areas of contours that represent
              inside-out surfaces.  This option works only for closed con-
              tours.  It is invoked automatically if you analyze a subset in X
              or Y, or use clipping planes.  Individual contour data will not
              be printed for closed contour objects.

       -x min,max

       -y min,max

       -z min,max
              Compute areas and volumes within the subvolume specified by the
              minimum and maximum values.  One or two of these three options
              may be entered if desired.  Subvolume analysis works only with
              closed contour and scattered point objects.  It works for
              options that print surface areas and volumes and with the -p
              option.  In the standard output, the number of scattered points
              within the subvolume will be reported for each object.

       -t 1/-1
              Truncate objects by their respective clipping planes; enter -t 1
              or -t -1 to use region shown or not shown by the clipping
              planes, respectively.  All currently active object clipping
              planes will be applied, as well as any active global clipping
              planes for objects that do not have the setting to skip the
              global planes.  Like the subvolume analysis, this option works
              only with closed contour and scattered point objects, and for
              options that print surface areas and volumes and with the -p
              option.  Clipping plane truncation can be used together with
              subvolume analysis.

       -v[v]  Print more verbose output. The -vv option will increase the
              level of output information even further.  These options over-
              ride the -h option.

       -h     Suppress the information about each contour in the standard
              model output.  Use this option to extract summary information
              more easily from large models.

       -f filename
              Write output to given filename instead of to standard output.

AUTHORS
       Jim Kremer
       David Mastronarde

SEE ALSO
       3dmod

BUGS
       Cylinder surface areas are erroneous because they do not account for
       the obliquity of the surface; for a sphere the area will be underesti-
       mated by 22%.  Use mesh surface areas whenever possible.

       Email bug reports to mast at colorado dot edu.



IMOD                                4.10.10                        imodinfo(1)