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 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 tetraheda 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. 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 , -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. 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. -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. 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. -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 underesti- mated by 22%. Use mesh surface areas whenever possible. Email bug reports to mast at colorado dot edu. BL3DEMC 4.3.7 imodinfo(1)