imodinfo(1) 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 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.
The program computes surface area and volume in two different ways,
depending upon whether an object is meshed or not:
1) Volume is computed without mesh information 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) 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 referred to as the mesh volume because it uses mesh
information, even though it is not the volume inside the mesh. It han-
dles the problem of skipped sections and also gives a slightly more
accurate volume measurement for the capped regions because it inte-
grates with a trapezoidal approximation.
3) Surface area is computed without mesh information 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.
4) 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 , -l , -o , -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.
-c Print volume, surface area, and center of gravity for each
object in column output.
-l Print lengths of open contours in column output.
-s Print volumes and surface areas for each separate surface in an
object.
-p Print point size information, including a summary of mean
radius, and the implied total surface area and volume of scat-
tered points.
-r Print ratio of length to area for closed contours.
-o <list>
Print full report on 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
underestimated by 22%. Use mesh surface areas whenever possible.
Email bug reports to mast at colorado dot edu.
BL3DEMC 3.11.2 imodinfo(1)